Scientific Output
Over 10.000 scientific papers have been published by members of the Materials Chain since the foundation of the University Alliance Ruhr in 2010. This tremendous output is proof of the excellent environment the Ruhr Area provides for research in the field of materials science and technology.
Below, you can either scroll through the complete list of our annually published material, or search for a specific author or term via the free text search to get to know our research strengths. You can also review the publication record of every Materials Chain member via his or her personal member’s page.
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2024 • 319 In Nanoconfined Environments, Larger Ions in the Electrolyte Influence the Local Proton Availability for the Oxygen Reduction Reaction
Sims, Matthew and Wang, Minzhi and Wordsworth, Johanna and Alinezhad, Ali and Tilley, Richard D. and Schuhmann, Wolfgang and Ho, Junming and Benedetti, Tania M. and Gooding, J. Justin
Journal of Physical Chemistry C 128 157 – 165 (2024)The impact of the electrolyte ion size on electrocatalytic reactions that occur within nanoconfined volumes is currently unknown. Herein, the effect of the size of solvated alkali metal ions on the oxygen reduction reaction (ORR) in acidic electrolytes was explored by using nanoparticles that contain isolated Pt nanochannels of 1-2 nm in diameter. The exterior surface of the nanoparticles was passivated to ensure that the ORR occurred only in the nanoconfined volume defined by the nanochannels. A number of alkali metal ions, with different hydrated sizes, were added into the acidic electrolyte, and different electrolyte ionic strengths were used to establish different levels of nanoconfinement. The results show that the ORR activity at comparatively positive applied potentials is not affected by the presence and nature of the alkali metal ions in the electrolyte. At less positive potentials, however, the activity is influenced by the presence of alkali metal ions in the electrolyte, and this is dependent on both the identity of the alkali metal ions and the electrolyte ionic strength. The differences in activities at less positive potentials are attributed to differences in the alkali metal ions’ accessibility to the nanoconfined space with Li+ being accessible and decreasing the electrocatalytic activity relative to inaccessible K+ ions that cannot enter the nanoconfined channels. This was corroborated by molecular dynamics modeling suggesting that the energy penalty for the alkali metal ions to enter the nanochannels is different for the different alkali metal ions and is affected by the surface charge of the nanochannel walls. © 2023 American Chemical Societyview abstract doi: 10.1021/acs.jpcc.3c07344 2024 • 318 Microscopic insights on field induced switching and domain wall motion in orthorhombic ferroelectrics
Khachaturyan, Ruben and Yang, Yijing and Teng, Sheng-Han and Udofia, Benjamin and Stricker, Markus and Grünebohm, Anna
Physical Review Materials 8 (2024)Surprisingly little is known about the microscopic processes that govern ferroelectric switching in orthorhombic ferroelectrics. To study these processes, we combine ab initio-based molecular dynamics simulations and data science on the prototypical material BaTiO3. We reveal two different field regimes: For moderate field strengths, the switching is dominated by domain wall motion, while a fast bulklike switching can be induced for large fields. Switching in both field regimes follows a multistep process via polarization directions perpendicular to the applied field. In the former case, the moving wall is of Bloch character and hosts dipole vortices due to nucleation, growth, and crossing of two-dimensional 90° domains. In the second case, the local polarization shows a continuous correlated rotation via an intermediate tetragonal multidomain state. © 2024 American Physical Society.view abstract doi: 10.1103/PhysRevMaterials.8.024403 2023 • 317 A Dynamic Water Channel Affects O2 Stability in [FeFe]-Hydrogenases
Brocks, Claudia and Das, Chandan K. and Duan, Jifu and Yadav, Shanika and Apfel, Ulf-Peter and Ghosh, Subhasri and Hofmann, Eckhard and Winkler, Martin and Engelbrecht, Vera and Schäfer, Lars V. and Happe, Thomas
ChemSusChem (2023)[FeFe]-hydrogenases are capable of reducing protons at a high rate. However, molecular oxygen (O2) induces the degradation of their catalytic cofactor, the H-cluster, which consists of a cubane [4Fe4S] subcluster (4FeH) and a unique diiron moiety (2FeH). Previous attempts to prevent O2-induced damage have focused on enhancing the protein's sieving effect for O2 by blocking the hydrophobic gas channels that connect the protein surface and the 2FeH. In this study, we aimed to block an O2 diffusion pathway and shield 4FeH instead. Molecular dynamics (MD) simulations identified a novel water channel (WH) surrounding the H-cluster. As this hydrophilic path may be accessible for O2 molecules we applied site-directed mutagenesis targeting amino acids along WH in proximity to 4FeH to block O2 diffusion. Protein film electrochemistry experiments demonstrate increased O2 stabilities for variants G302S and S357T, and MD simulations based on high-resolution crystal structures confirmed an enhanced local sieving effect for O2 in the environment of the 4FeH in both cases. The results strongly suggest that, in wild type proteins, O2 diffuses from the 4FeH to the 2FeH. These results reveal new strategies for improving the O2 stability of [FeFe]-hydrogenases by focusing on the O2 diffusion network near the active site. © 2023 The Authors. ChemSusChem published by Wiley-VCH GmbH.view abstract doi: 10.1002/cssc.202301365 2023 • 316 Ab Initio-Based Study on Atomic Ordering in (Ba, Sr) TiO3
Dimou, Aris and Biswas, Ankita and Grünebohm, Anna
Physica Status Solidi - Rapid Research Letters (2023)Solid solutions and nanostructures based on (Formula presented.) – (Formula presented.) are of high technological importance. However, there are gaps in knowledge on the impact of atomic ordering on local polarization, phase stability, and field-induced switching. Herein, density functional theory and molecular dynamics simulations are combined to investigate the impact of Sr concentration and atomic ordering on the structural and ferroelectric properties of (Ba, Sr) (Formula presented.). On one hand, the macroscopic structural properties are rather insensitive to atomic ordering. On the other hand, the Curie temperature and polarization differ by 9% and 17% for different Sr distribution, respectively. Local ordering of Sr furthermore induces preferential polarization directions and influences the relative stability of the three ferroelectric phases. © 2023 The Authors. physica status solidi (RRL) Rapid Research Letters published by Wiley-VCH GmbH.view abstract doi: 10.1002/pssr.202300380 2023 • 315 Active learning strategies for atomic cluster expansion models
Lysogorskiy, Yury and Bochkarev, Anton and Mrovec, Matous and Drautz, Ralf
Physical Review Materials 7 (2023)The atomic cluster expansion (ACE) was proposed recently as a new class of data-driven interatomic potentials with a formally complete basis set. Since the development of any interatomic potential requires a careful selection of training data and thorough validation, an automation of the construction of the training dataset as well as an indication of a model's uncertainty are highly desirable. In this work, we compare the performance of two approaches for uncertainty indication of ACE models based on the D-optimality criterion and ensemble learning. While both approaches show comparable predictions, the extrapolation grade based on the D-optimality (MaxVol algorithm) is more computationally efficient. In addition, the extrapolation grade indicator enables an active exploration of new structures, opening the way to the automated discovery of rare-event configurations. We demonstrate that active learning is also applicable to explore local atomic environments from large-scale molecular-dynamics simulations. © 2023 American Physical Society.view abstract doi: 10.1103/PhysRevMaterials.7.043801 2023 • 314 Descriptor for slip-induced crack blunting in refractory ceramics
Sangiovanni, Davide G. and Kraych, Antoine and Mrovec, Matous and Salamania, Janella and Odén, Magnus and Tasnádi, Ferenc and Abrikosov, Igor A.
Physical Review Materials 7 (2023)Understanding the competition between brittleness and plasticity in refractory ceramics is of importance for aiding design of hard materials with enhanced fracture resistance. Inspired by experimental observations of crack shielding due to dislocation activity in TiN ceramics [Kumar, Int. J. Plast. 27, 739 (2011)10.1016/j.ijplas.2010.09.003], we carry out comprehensive atomistic investigations to identify mechanisms responsible for brittleness and slip-induced plasticity in Ti-N systems. First, we validate a semiempirical interatomic potential against density-functional theory results of Griffith and Rice stress intensities for cleavage (KIc) and dislocation emission (KIe) as well as ab initio molecular dynamics mechanical-testing simulations of pristine and defective TiN lattices at temperatures between 300 and 1200 K. The calculated KIc and KIe values indicate intrinsic brittleness, as KIc≪KIe. However, KI-controlled molecular statics simulations - which reliably forecast macroscale mechanical properties through nanoscale modeling - reveal that slip plasticity can be promoted by a reduced sharpness of the crack and/or the presence of anion vacancies. Classical molecular dynamics simulations of notched Ti-N supercell models subject to tension provide a qualitative understanding of the competition between brittleness and plasticity at finite temperatures. Although crack growth occurs in most cases, a sufficiently rapid accumulation of shear stress at the notch tip may postpone or prevent fracture via nucleation and emission of dislocations. Furthermore, we show that the probability to observe slip-induced plasticity leading to crack blunting in flawed Ti-N lattices correlates with the ideal tensile/shear strength ratio (Iplasticityslip) of pristine Ti-N crystals. We propose that the Iplasticityslip descriptor should be considered for ranking the ability of ceramics to blunt cracks via dislocation-mediated plasticity at finite temperatures. © 2023 authors. Published by the American Physical Society. Published by the American Physical Society under the terms of the "https://creativecommons.org/licenses/by/4.0/"Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI. Funded by "https://www.kb.se/samverkan-och-utveckling/oppen-tillgang-och-bibsamkonsortiet/bibsamkonsortiet.html"Bibsam.view abstract doi: 10.1103/PhysRevMaterials.7.103601 2023 • 313 Hydrogen atom scattering at the Al2O3(0001) surface: a combined experimental and theoretical study
Liebetrau, Martin and Dorenkamp, Yvonne and Bünermann, Oliver and Behler, Jörg
Physical Chemistry Chemical Physics 26 1696 – 1708 (2023)Investigating atom-surface interactions is the key to an in-depth understanding of chemical processes at interfaces, which are of central importance in many fields - from heterogeneous catalysis to corrosion. In this work, we present a joint experimental and theoretical effort to gain insights into the atomistic details of hydrogen atom scattering at the α-Al2O3(0001) surface. Surprisingly, this system has been hardly studied to date, although hydrogen atoms as well as α-Al2O3 are omnipresent in catalysis as reactive species and support oxide, respectively. We address this system by performing hydrogen atom beam scattering experiments and molecular dynamics (MD) simulations based on a high-dimensional machine learning potential trained to density functional theory data. Using this combination of methods we are able to probe the properties of the multidimensional potential energy surface governing the scattering process. Specifically, we compare the angular distribution and the kinetic energy loss of the scattered atoms obtained in experiment with a large number of MD trajectories, which, moreover, allow to identify the underlying impact sites at the surface. © 2024 The Royal Society of Chemistry.view abstract doi: 10.1039/d3cp04729f 2023 • 312 Influence of domain walls and defects on the electrocaloric effect
Grünebohm, Anna and Teng, Sheng-Han and Marathe, Madhura
JPhys Energy 5 (2023)The electrocaloric (EC) effect is the adiabatic temperature change of a material in a varying external electric field, which is promising for novel cooling devices. While the fundamental understanding of the caloric response of defect-free materials is well developed, there are important gaps in the knowledge about the reversibility and time-stability of the response. In particular, it is not settled how the time-dependent elements of microstructure that are always present in real materials act on the field-induced temperature changes. Ab initio based molecular dynamics simulations allow us to isolate and understand the effects arising from domain walls (DWs) and defect dipoles and to study their interplay. We show that DWs in cycling fields do not improve the response in either the ferroelectric (FE) phase or at the FE phase transition, but may result in irreversible heat losses. The presence of defect dipoles may be beneficial for the EC response for proper field protocols, and interestingly this benefit is not too sensitive to the defect configuration. © The 2023 Author(s). Published by IOP Publishing Ltd.view abstract doi: 10.1088/2515-7655/acd86f 2023 • 311 Investigating the microplastic behavior of hierarchical polycrystalline γ-TiAl microstructures
Motahari, Soroush and Chauniyal, Ashish and Janisch, Rebecca
Computational Materials Science 226 (2023)Hierarchical, nano-twinned microstructures are a promising route to optimize the strength and deformability of metals and alloys. The present paper investigates the role of grain and twin boundaries and the effect of twin spacing on the evolution of plasticity in a twinned, polycrystalline γ-TiAl microstructure. Via atomistic simulations of uniaxial compression tests it is possible to disentangle these influencing factors, and the results show that the onset of plasticity is governed by the sub-grain structure of the samples, while the Schmid factor does not play a prominent role. At high strains in uniform or only slightly twinned models, grain boundary sliding is one of the major deformation mechanisms, whereas twin-boundary-mediated plastic deformation dominates the highly twinned structures. Moreover, based on analyzing the degree of localization parameter, it is inferred that upon decreasing the lamellae size, higher uniformity of shear strain in the samples can be achieved. These results can be used to inform mesoscale numerical modeling of hierarchical TiAl microstructures. © 2023 Elsevier B.V.view abstract doi: 10.1016/j.commatsci.2023.112197 2023 • 310 Mechanical properties and thermal stability of ZrCuAlx thin film metallic glasses: Experiments and first-principle calculations
Poltronieri, C. and Brognara, A. and Bignoli, F. and Evertz, S. and Djemia, P. and Faurie, D. and Challali, F. and Li, C.H. and Belliard, L. and Dehm, G. and Best, J.P. and Ghidelli, M.
Acta Materialia 258 (2023)In this work, we provide a holistic picture about the relationship between atomic structure, mechanical properties, and thermal stability of ZrCuAlx thin film metallic glasses (TFMGs) varying the Al content from 0 to 12 at.%, carrying out a broad characterization involving experiments and ab initio molecular dynamic simulations (AIMD). We show that the addition of Al resulted in a change of average interatomic distances by ∼10 pm with the formation of shorter bonds (Al-Zr and Al-Cu), influencing the mechanical response (shear/elastic moduli and hardness) which increases by ∼15% for 12 at.% Al. Moreover, tensile tests on polymer substrate revealed a maximum value for the crack initiation strain of 2.1% for ZrCuAl9, while the strain-to-failure rapidly decreases at higher Al contents. The observed reduction in damage tolerance is correlated to a transition in atomic configuration. Specifically, a maximum in density of full and defective icosahedral cluster population is observed at 9 at.% Al, inducing a more shear-resistant behavior to the material. Thermal stability is investigated by high-energy and conventional x-ray diffraction and electrical resistivity measurements as a function of the temperature. Glass transition (Tg) and crystallization (Tx) temperature increase by Al addition reaching 450 and 500 °C, respectively for ZrCuAl12. The increase in thermal stability is related to the reduction in atomic mobility due to the formation of shorter chemical bonds, inhibiting atomic reconfiguration during crystallization. In conclusion, we provide guidelines to the design of compositional-tailored ZrCuAlx TFMGs with tuned mechanical properties and thermal stability with potential impact on industrial applications. © 2023view abstract doi: 10.1016/j.actamat.2023.119226 2023 • 309 Modeling of minimal systems based on ATP-Zn coordination for chemically fueled self-assembly
Rossi, E. and Ferrarini, A. and Sulpizi, M.
Physical Chemistry Chemical Physics 25 6102-6111 (2023)Following nature's example, there is currently strong interest in using adenosine 5′-triphosphate (ATP) as a fuel for the self-assembly of functional materials with transient/non-equilibrium behaviours. These hold great promise for applications, e.g. in catalysis and drug delivery. In a recent seminal work [Maiti et al., Nat. Chem., 2016, 8, 725], binding of ATP to the metallosurfactant zinc hexadecyl-1,4,7-triazacyclononane ([ZnC16 TACN]2+) was exploited to produce ATP-fueled transient vesicles. Crucial to the complex formation is the ability of ATP to bind to the metal ion. As a first step to unveil the key elements underlying this process, we investigate the interaction of ATP with Zn2+ and with methyl-1,4,7-triazacyclononane ([ZnCH3 TACN]2+), using all-atom molecular dynamics simulations. The free energy landscape of the complex formation is sampled using well-tempered metadynamics with three collective variables, corresponding to the coordination numbers of Zn2+ with the oxygen atoms of the three phosphate groups. We find that the structure of the ternary complex is controlled by direct triphosphate coordination to zinc, with a minor role played by the interactions between ATP and CH3 TACN which, however, may be important for the build-up of supramolecular assemblies. © 2023 The Royal Society of Chemistry.view abstract doi: 10.1039/d2cp05516c 2023 • 308 Molecular dynamics simulations of electrified interfaces including the metal polarisation
Ntim, Samuel and Sulpizi, Marialore
Physical Chemistry Chemical Physics 25 22619 – 22625 (2023)Understanding electrified interfaces requires an accurate description of the electric double layer which also takes into account the metal polarisation. Here we present a simple approach to the molecular dynamics simulation of electrified interfaces which combines fixed charges and a core-shell model for the description of the polarisable electron density on the metal electrode. The approach has been applied to the Au(111) surface in contact with a NaCl aqueous electrolyte solution in order to calculate the differential capacitance and to gain a detailed picture of the charging mechanism. Metal polarisation enhances the interfacial capacitance with a difference between the cathode and anode. In particular, we find that the influence of the metal polarisation on the electric double layer depends on the ion's solvation shell structure and, for the investigated interface, is more important at the cathode, where it modifies the sodium ion distribution. © 2023 The Royal Society of Chemistry.view abstract doi: 10.1039/d3cp01472j 2023 • 307 Numerical simulation of materials-oriented ultra-precision diamond cutting: review and outlook
Zhao, Liang and Zhang, Junjie and Zhang, Jianguo and Dai, Houfu and Hartmaier, Alexander and Sun, Tao
International Journal of Extreme Manufacturing 5 (2023)Ultra-precision diamond cutting is a promising machining technique for realizing ultra-smooth surface of different kinds of materials. While fundamental understanding of the impact of workpiece material properties on cutting mechanisms is crucial for promoting the capability of the machining technique, numerical simulation methods at different length and time scales act as important supplements to experimental investigations. In this work, we present a compact review on recent advancements in the numerical simulations of material-oriented diamond cutting, in which representative machining phenomena are systematically summarized and discussed by multiscale simulations such as molecular dynamics simulation and finite element simulation: the anisotropy cutting behavior of polycrystalline material, the thermo-mechanical coupling tool-chip friction states, the synergetic cutting responses of individual phase in composite materials, and the impact of various external energetic fields on cutting processes. In particular, the novel physics-based numerical models, which involve the high precision constitutive law associated with heterogeneous deformation behavior, the thermo-mechanical coupling algorithm associated with tool-chip friction, the configurations of individual phases in line with real microstructural characteristics of composite materials, and the integration of external energetic fields into cutting models, are highlighted. Finally, insights into the future development of advanced numerical simulation techniques for diamond cutting of advanced structured materials are also provided. The aspects reported in this review present guidelines for the numerical simulations of ultra-precision mechanical machining responses for a variety of materials. © 2023 The Author(s). Published by IOP Publishing Ltd on behalf of the IMMT.view abstract doi: 10.1088/2631-7990/acbb42 2022 • 306 Approximating the impact of nuclear quantum effects on thermodynamic properties of crystalline solids by temperature remapping
Dsouza, R. and Huber, L. and Grabowski, B. and Neugebauer, J.
Physical Review B 105 (2022)When computing finite-temperature properties of materials with atomistic simulations, nuclear quantum effects are often neglected or approximated at the quasiharmonic level. The inclusion of these effects beyond this level using approaches like the path integral method is often not feasible due to their large computational effort. We discuss and evaluate the performance of a temperature-remapping approach that links the finite-temperature quantum system to its best classical surrogate via a temperature map. This map, which is constructed using the internal energies of classical and quantum harmonic oscillators, is shown to accurately capture the impact of quantum effects on thermodynamic properties at an additional cost that is negligible compared to classical molecular dynamics simulations. Results from this approach show excellent agreement with previously reported path integral Monte Carlo simulation results for diamond cubic carbon and silicon. The approach is also shown to work well for obtaining thermodynamic properties of light metals and for the prediction of the fcc to bcc phase transition in calcium. © 2022 authors. Published by the American Physical Society. Published by the American Physical Society under the terms of the "https://creativecommons.org/licenses/by/4.0/"Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI. Open access publication funded by the Max Planck Society.view abstract doi: 10.1103/PhysRevB.105.184111 2022 • 305 Enhanced dynamics in deep thermal cycling of a model glass
Bruns, M. and Varnik, F.
Journal of Chemical Physics 156 (2022)We investigate the effect of low temperature (cryogenic) thermal cycling on dynamics of a generic model glass via molecular dynamics simulations. By calculating mean squared displacements after a varying number of cycles, a pronounced enhancement of dynamics is observed. This rejuvenation effect is visible already after the first cycle and accumulates upon further cycling in an intermittent way. Our data reveal an overall deformation (buckling of the slab-shaped system) modulated by a heterogeneous deformation field due to deep cryogenic thermal cycling. It is shown via strain maps that deformation localizes in the form of shear-bands, which gradually fill the entire sample in a random and intermittent manner, very much similar to the accumulation effect observed in dynamics. While spatial organization of local strain may be connected to the specific geometry, we argue that the heterogeneity of the structure is the main cause behind rejuvenation effects observed in the present study. © 2022 Author(s).view abstract doi: 10.1063/5.0094024 2022 • 304 Hydration in aqueous NaCl
Sahle, C.J. and de Clermont Gallerande, E. and Niskanen, J. and Longo, A. and Elbers, M. and Schroer, M.A. and Sternemann, C. and Jahn, S.
Physical Chemistry Chemical Physics 24 16075-16084 (2022)Atomistic details about the hydration of ions in aqueous solutions are still debated due to the disordered and statistical nature of the hydration process. However, many processes from biology, physical chemistry to materials sciences rely on the complex interplay between solute and solvent. Oxygen K-edge X-ray excitation spectra provide a sensitive probe of the local atomic and electronic surrounding of the excited sites. We used ab initio molecular dynamics simulations together with extensive spectrum calculations to relate the features found in experimental oxygen K-edge spectra of a concentration series of aqueous NaCl with the induced structural changes upon solvation of the salt and distill the spectral fingerprints of the first hydration shells around the Na+- and Cl−-ions. By this combined experimental and theoretical approach, we find the strongest spectral changes to indeed result from the first hydration shells of both ions and relate the observed shift of spectral weight from the post- to the main-edge to the origin of the post-edge as a shape resonance. © 2022 The Royal Society of Chemistry.view abstract doi: 10.1039/d2cp00162d 2022 • 303 Lower degree of dissociation of pyruvic acid at water surfaces than in bulk
Lesnicki, D. and Wank, V. and Cyran, J.D. and Backus, E.H.G. and Sulpizi, M.
Physical Chemistry Chemical Physics 24 13510-13513 (2022)Understanding the acid/base behavior of environmentally relevant organic acids is of key relevance for accurate climate modelling. Here we investigate the effect of pH on the (de)protonation state of pyruvic acid at the air-water interface and in bulk by using the analytical techniques surface-specific vibrational sum frequency generation and attenuated total reflection spectroscopy. To provide a molecular interpretation of the observed behavior, simulations are carried out using a free energy perturbation approach in combination with electronic structure-based molecular dynamics. In both the experimental and theoretical results we observe that the protonated form of pyruvic acid is preferred at the air-water interface. The increased proton affinity is the result of the specific microsolvation at the interface. © 2022 The Royal Society of Chemistryview abstract doi: 10.1039/d2cp01293f 2022 • 302 MEAM interatomic potentials of Ni, Re, and Ni-Re alloys for atomistic fracture simulations
Alam, M. and Lymperakis, L. and Groh, S. and Neugebauer, J.
Modelling and Simulation in Materials Science and Engineering 30 (2022)Second nearest neighbor modified embedded atom method (2NN-MEAM) interatomic potentials are developed for the Ni, Re, and Ni-Re binaries. To construct the potentials, density functional theory (DFT) calculations have been employed to calculate fundamental physical properties that play a dominant role in fracture. The potentials are validated to accurately reproduce material properties that correlate with material's fracture behavior. The thus constructed potentials were applied to perform large scale simulations of mode I fracture in Ni and Ni-Re binaries with low Re content. Substitutional Re did not alter the ductile nature of crack propagation, though it resulted in a monotonous increase of the critical stress intensity factor with Re content. © 2021 The Author(s). Published by IOP Publishing Ltd.view abstract doi: 10.1088/1361-651X/ac3a15 2022 • 301 Nanoporous SiOx plasma polymer films as carrier for liquid-infused surfaces
Gergs, T. and Monti, C. and Gaiser, S. and Amberg, M. and Schütz, U. and Mussenbrock, T. and Trieschmann, J. and Heuberger, M. and Hegemann, D.
Plasma Processes and Polymers 19 (2022)Liquid-infused surfaces are based upon the infusion of a liquid phase into a porous solid material to induce slippery and repellent character. In this context, porous SiOx plasma polymer films represent a relevant candidate for a robust nanoporous carrier layer. Intermittent low-pressure plasma etching of O2/hexamethyldisiloxane-derived coatings is investigated to enhance the intrinsic porosity inherent to residual hydrocarbons in the silica matrix. Simulations of the resulting Si–O ring network structure using reactive molecular dynamics indicate formation of interconnected voids with Si–OH functionalized pore walls allowing water penetration with almost Fickian diffusive behavior. The corresponding porosity of up to 18%, well agreeing with simulations, Fourier-transform infrared spectroscopy, and ellipsometry measurements, was found to be suitable for the liquid infusion of polyethylene glycol molecules into about 80 nm thick SiOx films providing ongoing lubricating properties, thus revealing their suitability as liquid-infused surfaces. © 2022 The Authors. Plasma Processes and Polymers published by Wiley-VCH GmbH.view abstract doi: 10.1002/ppap.202200049 2022 • 300 Neural Network Potentials: A Concise Overview of Methods
Kocer, E. and Ko, T.W. and Behler, J.
Annual Review of Physical Chemistry 73 163-186 (2022)In the past two decades, machine learning potentials (MLPs) have reached a level of maturity that now enables applications to large-scale atomistic simulations of a wide range of systems in chemistry, physics, and materials science. Different machine learning algorithms have been used with great success in the construction of these MLPs. In this review, we discuss an important group of MLPs relying on artificial neural networks to establish a mapping from the atomic structure to the potential energy. In spite of this common feature, there are important conceptual differences among MLPs, which concern the dimensionality of the systems, the inclusion of long-range electrostatic interactions, global phenomena like nonlocal charge transfer, and the type of descriptor used to represent the atomic structure, which can be either predefined or learnable. A concise overview is given along with a discussion of the open challenges in the field. © 2022 Annual Reviews Inc.. All rights reserved.view abstract doi: 10.1146/annurev-physchem-082720-034254 2022 • 299 Temperature Rise Inside Shear Bands in a Simple Model Glass
Lagogianni, A.E. and Varnik, F.
International Journal of Molecular Sciences 23 (2022)One of the key factors, which hampers the application of metallic glasses as structural components, is the localization of deformation in narrow bands of a few tens up to one hundred nanometers thickness, the so-called shear bands. Processes, which occur inside shear bands are of central importance for the question whether a catastrophic failure of the material is unavoidable or can be circumvented or, at least, delayed. Via molecular dynamics simulations, this study addresses one of these processes, namely the local temperature rise due to viscous heat generation. The major contribution to energy dissipation is traced back to the plastic work performed by shear stress during steady deformation. Zones of largest strain contribute the most to this process and coincide with high-temperature domains (hottest spots) inside the sample. Magnitude of temperature rise can reach a few percent of the sample’s glass transition temperature. Consequences of these observations are discussed in the context of the current research in the field. © 2022 by the authors.view abstract doi: 10.3390/ijms232012159 2022 • 298 Unexpectedly High Capacitance of the Metal Nanoparticle/Water Interface: Molecular-Level Insights into the Electrical Double Layer
Azimzadeh Sani, M. and Pavlopoulos, N.G. and Pezzotti, S. and Serva, A. and Cignoni, P. and Linnemann, J. and Salanne, M. and Gaigeot, M.-P. and Tschulik, K.
Angewandte Chemie - International Edition 61 (2022)The electrical double-layer plays a key role in important interfacial electrochemical processes from catalysis to energy storage and corrosion. Therefore, understanding its structure is crucial for the progress of sustainable technologies. We extract new physico-chemical information on the capacitance and structure of the electrical double-layer of platinum and gold nanoparticles at the molecular level, employing single nanoparticle electrochemistry. The charge storage ability of the solid/liquid interface is larger by one order-of-magnitude than predicted by the traditional mean-field models of the double-layer such as the Gouy–Chapman–Stern model. Performing molecular dynamics simulations, we investigate the possible relationship between the measured high capacitance and adsorption strength of the water adlayer formed at the metal surface. These insights may launch the active tuning of solid–solvent and solvent–solvent interactions as an innovative design strategy to transform energy technologies towards superior performance and sustainability. © 2021 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbHview abstract doi: 10.1002/anie.202112679 2021 • 297 A fully automated approach to calculate the melting temperature of elemental crystals
Zhu, L.-F. and Janssen, J. and Ishibashi, S. and Körmann, F. and Grabowski, B. and Neugebauer, J.
Computational Materials Science 187 (2021)The interface method is a well established approach for predicting melting points of materials using interatomic potentials. However, applying the interface method is tedious and involves significant human intervention. The whole procedure involves several successive tasks: estimate a rough melting point, set up the interface structure, run molecular dynamic calculations and analyze the data. Loop calculations are necessary if the predicted melting point is different from the estimated one by more than a certain convergence criterion, or if full melting/solidification occurs. In this case monitoring the solid–liquid phase transition in the interface structure becomes critical. As different initial random seeds for the molecular dynamic simulations within the interface method induce slightly different melting points, a few ten or hundred interface method calculations with different random seeds are necessary for performing a statistical analysis on these melting points. Considering all these technical details, the work load for manually executing and combining the various involved scripts and programs quickly becomes prohibitive. To simplify and automatize the whole procedure, we have implemented the interface method into pyiron (http://pyiron.org). Our fully automatized procedure allows to efficiently and precisely predict melting points of stable unaries represented by arbitrary potentials with only two user-specified parameters (interatomic potential file and element). For metastable or dynamically unstable unary phases, the crystal structure needs to be provided as an additional parameter. We have applied our automatized approach on fcc Al, Ni, dynamically unstable bcc Ti and hcp Mg and employed a large set of available interatomic potentials. Melting points for classical interatomic potentials of these metals have been obtained with a numerical precision well below 1 K. © 2020 The Authorsview abstract doi: 10.1016/j.commatsci.2020.110065 2021 • 296 An automatized workflow from molecular dynamic simulation to quantum chemical methods to identify elementary reactions and compute reaction constants
Schmitz, G. and Yönder, Ö. and Schnieder, B. and Schmid, R. and Hättig, C.
Journal of Computational Chemistry 42 2264-2282 (2021)We present an automatized workflow which, starting from molecular dynamics simulations, identifies reaction events, filters them, and prepares them for accurate quantum chemical calculations using, for example, Density Functional Theory (DFT) or Coupled Cluster methods. The capabilities of the automatized workflow are demonstrated by the example of simulations for the combustion of some polycyclic aromatic hydrocarbons (PAHs). It is shown how key elementary reaction candidates are filtered out of a much larger set of redundant reactions and refined further. The molecular species in question are optimized using DFT and reaction energies, barrier heights, and reaction rates are calculated. The setup is general enough to include at this stage configurational sampling, which can be exploited in the future. Using the introduced machinery, we investigate how the observed reaction types depend on the gas atmosphere used in the molecular dynamics simulation. For the re-optimization on the DFT level, we show how the additional information needed to switch from reactive force-field to electronic structure calculations can be filled in and study how well ReaxFF and DFT agree with each other and shine light on the perspective of using more accurate semi-empirical methods in the MD simulation. © 2021 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC.view abstract doi: 10.1002/jcc.26757 2021 • 295 Atomistic investigation of machinability of monocrystalline 3C–SiC in elliptical vibration-assisted diamond cutting
Zhao, L. and Zhang, J. and Zhang, J. and Hartmaier, A.
Ceramics International 47 2358-2366 (2021)Deformation-induced characteristics of surface layer strongly rely on loading condition-related operating deformation modes. In the current study we reveal the mechanisms governing machined surface formation of hard brittle monocrystalline 3C–SiC in ultrasonic elliptical vibration-assisted diamond cutting by molecular dynamics simulations. Simulation results show different deformation modes including phase transformation, dislocation activity, and crack nucleation and propagation, as well as their correlations with surface integrity in terms of machined surface morphology and subsurface damage. In particular, molecular dynamics simulations of ordinary cutting are also carried out, which demonstrate the effectiveness of applying ultrasonic vibration of cutting tool in decreasing machining force and suppressing crack events, i.e., promoting ductile-mode cutting for achieving high surface integrity. The physical mechanism governing the machining differences between the two machining processes are also revealed. Furthermore, the effect of cutting depth on machined surface integrity under vibration-assisted cutting and ordinary cutting is addressed. © 2020 Elsevier Ltd and Techna Group S.r.l.view abstract doi: 10.1016/j.ceramint.2020.09.078 2021 • 294 Decelerated aging in metallic glasses by low temperature thermal cycling
Bruns, M. and Hassani, M. and Varnik, F. and Hassanpour, A. and Divinski, S. and Wilde, G.
Physical Review Research 3 (2021)Differential scanning calorimetry measurements on different bulk metallic glasses show no measurable rejuvenation upon deeply cooled (cryogenic) thermal cycling. This applies both to as-quenched and well-annealed samples. Extensive molecular dynamics simulations of a generic model glass former corroborate these observations. We disentangle the effects of aging from those of thermal treatment and show that aging is slowed down but not stopped - neither reversed - during thermal cycling. These observations are corroborated further by a survey of energy distribution, which continues narrowing, albeit with a smaller rate. © 2021 authors.view abstract doi: 10.1103/PhysRevResearch.3.013234 2021 • 293 Finite-temperature interplay of structural stability, chemical complexity, and elastic properties of bcc multicomponent alloys from ab initio trained machine-learning potentials
Gubaev, K. and Ikeda, Y. and Tasnádi, F. and Neugebauer, J. and Shapeev, A.V. and Grabowski, B. and Körmann, F.
Physical Review Materials 5 (2021)An active learning approach to train machine-learning interatomic potentials (moment tensor potentials) for multicomponent alloys to ab initio data is presented. Employing this approach, the disordered body-centered cubic (bcc) TiZrHfTax system with varying Ta concentration is investigated via molecular dynamics simulations. Our results show a strong interplay between elastic properties and the structural ω phase stability, strongly affecting the mechanical properties. Based on these insights we systematically screen composition space for regimes where elastic constants show little or no temperature dependence (elinvar effect). © 2021 American Physical Society.view abstract doi: 10.1103/PhysRevMaterials.5.073801 2021 • 292 Impact of deep eutectic solvents and their constituents on the aqueous solubility of phloroglucinol dihydrate
Gajardo-Parra, N.F. and Do, H.T. and Yang, M. and Pérez-Correa, J.R. and Garrido, J.M. and Sadowski, G. and Held, C. and Canales, R.I.
Journal of Molecular Liquids 344 (2021)Phlorotannins are highly bioactive phenolic compounds mainly found in brown algae. Phloroglucinol is the basic unit from which phlorotannins polymerize. Deep eutectic solvents (DES) are potentially beneficial for increasing phenolics solubility, therefore good solvent candidates for phlorotannins extraction processes. Solubility measurements were performed for phloroglucinol in pure water and aqueous mixtures of DES or their constituents, i.e., different hydrogen bond donors (HBD) and choline chloride (ChCl). The stable crystal form of the phenolic in equilibrium was phloroglucinol dihydrate within the studied temperature range (293.15–313.15 K) and water weight fractions (≥0.25). The water + ChCl + HBD mixtures yielded higher solubility for phloroglucinol dihydrate than the corresponding water + HBD or water + ChCl mixtures. Solubility predicted with PC-SAFT was in quantitative agreement with the experimental data. The solubility behavior of phloroglucinol dihydrate in the different mixtures was related to the hydrogen bonds formed using molecular dynamics and PC-SAFT. © 2021 Elsevier B.V.view abstract doi: 10.1016/j.molliq.2021.117932 2021 • 291 Impact of single-pulse, low-intensity laser post-processing on structure and activity of mesostructured cobalt oxide for the oxygen evolution reaction
Budiyanto, E. and Zerebecki, S. and Weidenthaler, C. and Kox, T. and Kenmoe, S. and Spohr, E. and Debeer, S. and Rüdiger, O. and Reichenberger, S. and Barcikowski, S. and Tüysüz, H.
ACS Applied Materials and Interfaces (2021)Herein, we report nanosecond, single-pulse laser post-processing (PLPP) in a liquid flat jet with precise control of the applied laser intensity to tune structure, defect sites, and the oxygen evolution reaction (OER) activity of mesostructured Co3O4. High-resolution X-ray diffraction (XRD), Raman, and X-ray photoelectron spectroscopy (XPS) are consistent with the formation of cobalt vacancies at tetrahedral sites and an increase in the lattice parameter of Co3O4 after the laser treatment. X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) further reveal increased disorder in the structure and a slight decrease in the average oxidation state of the cobalt oxide. Molecular dynamics simulation confirms the surface restructuring upon laser post-treatment on Co3O4. Importantly, the defect-induced PLPP was shown to lower the charge transfer resistance and boost the oxygen evolution activity of Co3O4. For the optimized sample, a 2-fold increment of current density at 1.7 V vs RHE is obtained and the overpotential at 10 mA/cm2 decreases remarkably from 405 to 357 mV compared to pristine Co3O4. Post-mortem characterization reveals that the material retains its activity, morphology, and phase structure after a prolonged stability test. © XXX The Authors.view abstract doi: 10.1021/acsami.1c08034 2021 • 290 Influence of flexible side-chains on the breathing phase transition of pillared layer MOFs: A force field investigation
Keupp, J. and Dürholt, J.P. and Schmid, R.
Faraday Discussions 225 324-340 (2021)The prototypical pillared layer MOFs, formed by a square lattice of paddle-wheel units and connected by dinitrogen pillars, can undergo a breathing phase transition by a "wine-rack"type motion of the square lattice. We studied this behavior, which is not yet fully understood, using an accurate first principles parameterized force field (MOF-FF) for larger nanocrystallites on the example of Zn2(bdc)2(dabco) [bdc: benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)], and found clear indications for an interface between a closed and an open pore phase traveling through the system during the phase transformation [J. Keupp and R. Schmid, Adv. Theory Simul., 2019, 2, 1900117]. In conventional simulations in small supercells this mechanism is prevented by periodic boundary conditions (PBCs), enforcing a synchronous transformation of the entire crystal. Here, we extend this investigation to pillared layer MOFs with flexible side-chains, attached to the linker. Such functionalized (fu-)MOFs are experimentally known to have different properties with the side-chains acting as fixed guest molecules. First, in order to extend the parameterization for such flexible groups, a new parameterization strategy for MOF-FF had to be developed, using a multi-structure force based fit method. The resulting parameterization for a library of fu-MOFs is then validated with respect to a set of reference systems and shows very good accuracy. In the second step, a series of fu-MOFs with increasing side-chain length is studied with respect to the influence of the side-chains on the breathing behavior. For small supercells in PBCs a systematic trend of the closed pore volume with the chain length is observed. However, for a nanocrystallite model a distinct interface between a closed and an open pore phase is visible only for the short chain length, whereas for longer chains the interface broadens and a nearly concerted transformation is observed. Only by molecular dynamics simulations using accurate force fields can such complex phenomena can be studied on a molecular level. © 2021 The Royal Society of Chemistry.view abstract doi: 10.1039/d0fd00017e 2021 • 289 Insights into lithium manganese oxide-water interfaces using machine learning potentials
Eckhoff, M. and Behler, J.
Journal of Chemical Physics 155 (2021)Unraveling the atomistic and the electronic structure of solid-liquid interfaces is the key to the design of new materials for many important applications, from heterogeneous catalysis to battery technology. Density functional theory (DFT) calculations can, in principle, provide a reliable description of such interfaces, but the high computational costs severely restrict the accessible time and length scales. Here, we report machine learning-driven simulations of various interfaces between water and lithium manganese oxide (LixMn2O4), an important electrode material in lithium ion batteries and a catalyst for the oxygen evolution reaction. We employ a high-dimensional neural network potential to compute the energies and forces several orders of magnitude faster than DFT without loss in accuracy. In addition, a high-dimensional neural network for spin prediction is utilized to analyze the electronic structure of the manganese ions. Combining these methods, a series of interfaces is investigated by large-scale molecular dynamics. The simulations allow us to gain insights into a variety of properties, such as the dissociation of water molecules, proton transfer processes, and hydrogen bonds, as well as the geometric and electronic structure of the solid surfaces, including the manganese oxidation state distribution, Jahn-Teller distortions, and electron hopping. © 2021 Author(s).view abstract doi: 10.1063/5.0073449 2021 • 288 Isomeric effects in structure formation and dielectric dynamics of different octanols
Bolle, J. and Bierwirth, S.P. and Požar, M. and Perera, A. and Paulus, M. and Münzner, P. and Albers, C. and Dogan, S. and Elbers, M. and Sakrowski, R. and Surmeier, G. and Böhmer, R. and Tolan, M. and Sternemann, C.
Physical Chemistry Chemical Physics 23 24211-24221 (2021)The understanding of the microstructure of associated liquids promoted by hydrogen-bonding and constrained by steric hindrance is highly relevant in chemistry, physics, biology and for many aspects of daily life. In this study we use a combination of X-ray diffraction, dielectric spectroscopy and molecular dynamics simulations to reveal temperature induced changes in the microstructure of different octanol isomers,i.e., linear 1-octanol and branched 2-, 3- and 4-octanol. In all octanols, the hydroxyl groups form the basis of chain-, cyclic- or loop-like bonded structures that are separated by outwardly directed alkyl chains. This clustering is analyzed through the scattering pre-peaks observed from X-ray scattering and simulations. The charge ordering which pilots OH aggregation can be linked to the strength of the Debye process observed in dielectric spectroscopy. Interestingly, all methods used here converge to the same interpretation: as one moves from 1-octanol to the branched octanols, the cluster structure evolves from loose large aggregates to a larger number of smaller, tighter aggregates. All alcohols exhibit a peculiar temperature dependence of both the pre-peak and Debye process, which can be understood as a change in microstructure promoted by chain association with increased chain length possibly assisted by ring-opening effects. All these results tend to support the intuitive picture of the entropic constraint provided by branching through the alkyl tails and highlight its capital entropic role in supramolecular assembly. © the Owner Societies 2021.view abstract doi: 10.1039/d1cp02468j 2021 • 287 MD simulation study on defect evolution and doping efficiency of p-type doping of 3C-SiC by Al ion implantation with subsequent annealing
Wu, J. and Xu, Z. and Liu, L. and Hartmaier, A. and Rommel, M. and Nordlund, K. and Wang, T. and Janisch, R. and Zhao, J.
Journal of Materials Chemistry C 9 2258-2275 (2021)We use molecular dynamics (MD) simulation with numerical characterisation and statistical analysis to study the mechanisms of damage evolution and p-type doping efficiency by aluminum (Al) ion implantation into 3C silicon carbide (SiC) with subsequent annealing. By incorporating the electronic stopping power for implantation, a more accurate description of the atomic-scale mechanisms of damage evolution and distribution in SiC can be obtained. The simulation results show a novel observation that the recrystallization process occurs in the region below the subsurface layer, and develops from amorphous-crystalline interface to the damage center region, which is a new insight into previously published studies. During surface recrystallization, significant compressive stress concentration occurs, and more structural phase transition atoms and dislocations formed at the damage-rich-crystalline interface. Another point of interest is that for low-dose implantation, more implantation-induced defects hamper the doping efficiency. Correspondingly, the correlation between lattice damage and doping efficiency becomes weaker as the implant dose increases under the same annealing conditions. Our simulation also predicts that annealing after high temperature (HT) implantation is more likely to lead to the formation of carbon vacancies (VC). © The Royal Society of Chemistry 2021.view abstract doi: 10.1039/d0tc05374k 2021 • 286 Mechanism of amorphous phase stabilization in ultrathin films of monoatomic phase change material
Dragoni, D. and Behler, J. and Bernasconi, M.
Nanoscale 13 16146-16155 (2021)Elemental antimony has been recently proposed as a promising material for phase change memories with improved performances with respect to the most used ternary chalcogenide alloys. The compositional simplification prevents reliability problems due to demixing of the alloy during memory operation. This is made possible by the dramatic stabilization of the amorphous phase once Sb is confined in an ultrathin film 3-5 nm thick. In this work, we shed light on the microscopic origin of this effect by means of large scale molecular dynamics simulations based on an interatomic potential generated with a machine learning technique. The simulations suggest that the dramatic reduction of the crystal growth velocity in the film with respect to the bulk is due to the effect of nanoconfinement on the fast β relaxation dynamics while the slow α relaxation is essentially unaffected. © The Royal Society of Chemistry.view abstract doi: 10.1039/d1nr03432d 2021 • 285 Method to Construct Volcano Relations by Multiscale Modeling: Building Bridges between the Catalysis and Biosimulation Communities
Exner, K.S. and Ivanova, A.
Journal of Physical Chemistry B 125 2098-2104 (2021)Understanding the complex interactions of different building blocks within a sophisticated drug-delivery system (DDS), aimed at targeted transport of the drug to malignant cells, requires modeling techniques on different time and length scales. On the example of the anthracycline antibiotic doxorubicin (DOX), we investigate a potential DDS component, consisting of a gold nanoparticle and a short peptide sequence as carriers of DOX. The combination of atomistic molecular dynamics simulations and density functional theory calculations facilitates compiling a volcano plot, which allows deriving general conclusions on DDS constituents for chemotherapeutic agents within the class of anthracycline antibiotics: the nanoparticle and peptide carrier moieties need to be chosen in such a way that the anthracycline body of the drug is able to intercalate between both entities or between two (π-stacking) residues of the peptide. Using the popular volcano framework as a guideline, the present article connects the catalysis and biosimulation communities, thereby identifying a strategy to overcome the limiting volcano relation by tuning the coordination number of the drug in the DDS component. ©view abstract doi: 10.1021/acs.jpcb.1c00836 2021 • 284 Molecular Insight into the Swelling of a MOF: A Force-Field Investigation of Methanol Uptake in MIL-88B(Fe)-Cl
Siwaipram, S. and Bopp, P.A. and Keupp, J. and Pukdeejorhor, L. and Soetens, J.-C. and Bureekaew, S. and Schmid, R.
Journal of Physical Chemistry C (2021)Volume changes are observed in the metal-organic frameworks (MOFs) of the MIL-88 family when they are exposed to certain solvents. We investigate here, at the atomic level, the swelling behavior of MIL-88B absorbing strongly interacting guest molecules, methanol, for which the largest changes are found. The MOF is positively charged and possesses open metal sites at the trimetallic inorganic building units (M3O), with which the counterions and guests coordinate. We develop an extended MOF-FF-type interaction model and perform the first molecular dynamics (MD) simulations to describe the structural changes of the flexible MIL-88B(Fe)-Cl upon insertion of methanol. The newly developed interaction model according to the MOF-FF scheme consists of (I) the intra-MOF interactions, (II) a fully MOF-FF-compatible model for the methanol and the solvated Cl- ion, which was recently published, and (III) specific new terms developed for the interactions between a trimetallic building unit (Fe3O) connected with six benzoate rings and these species. We report the free energy versus volume profiles as a function of loading and temperature, which are matched with the evolution of the unit cell volume versus the methanol loading profile. We discuss radial pair distribution functions (rdf) and some three-dimensional distributions of the counterions around Fe3O. We find that the pore opening is accompanied by characteristic structural changes in the arrangements of the counterions near the central Fe3 units and also of the solvent coordinating these counterions: this illustrates the role of the solvated counterions in the swelling process. © 2021 American Chemical Society. All rights reserved.view abstract doi: 10.1021/acs.jpcc.1c01033 2021 • 283 On the origin of controlled anisotropic growth of monodisperse gold nanobipyramids
Meena, S.K. and Lerouge, F. and Baldeck, P. and Andraud, C. and Garavelli, M. and Parola, S. and Sulpizi, M. and Rivalta, I.
Nanoscale 13 15292-15300 (2021)We elucidate the crucial role of the cetyl trimethylammonium bromide (CTAB) surfactant in the anisotropic growth mechanism of gold nano-bipyramids, nano-objects with remarkable optical properties and high tunability. Atomistic molecular dynamics simulations predict different surface coverages of the CTAB (positively charged) heads and their (bromide) counterions as function of the gold exposed surfaces. High concentration of CTAB surfactant promotes formation of gold nanograins in solution that work as precursors for the smooth anisotropic growth of more elongated nano-bipyramidal objects. Nanobipyramids feature higher index facets with respect to nanorods, allowing higher CTAB coverages that stabilize their formation and leading to narrower inter-micelles channels that smooth down their anisotropic growth. Absorption spectroscopy and scanning electron microscopy confirmed the formation of nanograins and demonstrated the importance of surfactant concentration on driving the growth towards nano-bipyramids rather than nanorods. The outcome explains the formation of the monodisperse bipyramidal nano-objects, the origin of their controlled shapes and sizes along with their remarkable stability. © The Royal Society of Chemistry.view abstract doi: 10.1039/d1nr01768c 2021 • 282 On the size effect of additives in amorphous shape memory polymers
Zirdehi, E.M. and Dumlu, H. and Eggeler, G. and Varnik, F.
Materials 14 1-16 (2021)Small additive molecules often enhance structural relaxation in polymers. We explore this effect in a thermoplastic shape memory polymer via molecular dynamics simulations. The additiveto-monomer size ratio is shown to play a key role here. While the effect of additive-concentration on the rate of shape recovery is found to be monotonic in the investigated range, a non-monotonic dependence on the size-ratio emerges at temperatures close to the glass transition. This work thus identifies the additives’ size to be a qualitatively novel parameter for controlling the recovery process in polymer-based shape memory materials. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.view abstract doi: 10.3390/ma14020327 2021 • 281 Orientation-dependent plastic deformation mechanisms and competition with stress-induced phase transformation in microscale NiTi
Choi, W.S. and Pang, E.L. and Ko, W.-S. and Jun, H. and Bong, H.J. and Kirchlechner, C. and Raabe, D. and Choi, P.-P.
Acta Materialia 208 (2021)Understanding the orientation-dependent deformation behavior of NiTi shape-memory alloys at small length scales is of importance for designing nano- and micro-electromechanical systems. However, a complete understanding of the orientation- and size-dependent competition between the various modes of slip, deformation twinning, and martensitic transformation in NiTi shape-memory alloys is still lacking, especially in micron-scale specimens. In the present study, we perform micro-compression tests on [001]- and [112]-oriented micro-pillars of a solutionized Ti-49.9at.% Ni alloy. Post-mortem TEM analysis of the deformed pillars reveal that the operating plastic deformation modes are {011}<100> slip and {114}<221¯> deformation twinning, which compete with the martensitic transformation, depending on the crystal orientation. Furthermore, in both experiments and molecular dynamics simulations, we consistently find residual B19′ martensite in a herringbone microstructure composed of finely spaced (001)B19′ compound twins instead of the generally assumed [011]B19′ type II twins common in bulk samples, suggesting that the operative martensitic transformation mode may be size-dependent. Schmid factors in compression are calculated for all commonly reported slip, deformation twinning, and martensitic transformation modes as a function of crystallographic orientation, which rationalize the orientation-dependent competition between these deformation modes. © 2021 Acta Materialia Inc.view abstract doi: 10.1016/j.actamat.2021.116731 2021 • 280 Properties of α-Brass Nanoparticles II: Structure and Composition
Weinreich, J. and Paleico, M.L. and Behler, J.
Journal of Physical Chemistry C 125 14897-14909 (2021)Nanoparticles have become increasingly interesting for a wide range of applications because in principle it is possible to tailor their properties by controlling size, shape, and composition. One of these applications is heterogeneous catalysis, and a fundamental understanding of the structural details of the nanoparticles is essential for any knowledge-based improvement of reactivity and selectivity. In this work, we investigate the atomic structure of brass nanoparticles containing up to 5000 atoms as a typical example for a binary alloy consisting of Cu and Zn. As systems of this size are too large for electronic structure calculations, in our simulations, we use a recently parameterized machine learning potential providing close to density functional theory accuracy. This potential is employed for a structural characterization as a function of chemical composition by various types of simulations such as Monte Carlo in the semigrand canonical ensemble and simulated annealing molecular dynamics. Our analysis reveals that the distribution of both elements in the nanoparticles is inhomogeneous, and zinc accumulates in the outermost layer, while the first subsurface layer shows an enrichment of copper. Only for high zinc concentrations, alloying can be found in the interior of the nanoparticles, and regular patterns corresponding to crystalline bulk phases of α-brass can then be observed. The surfaces of the investigated clusters exhibit well-ordered single-crystal facets, which can give rise to grain boundaries inside the clusters. The melting temperature of the nanoparticles is found to decrease with increasing zinc-atom fraction, a trend which is well known also for the bulk phase diagram of brass. © 2021 The Authors. Published by American Chemical Society.view abstract doi: 10.1021/acs.jpcc.1c02314 2021 • 279 Rheology based estimates of self- And collective diffusivities in viscous liquids
Gainaru, C. and Ahlmann, S. and Röwekamp, L.S. and Moch, K. and Bierwirth, S.P. and Böhmer, R.
Journal of Chemical Physics 155 (2021)The self-diffusion coefficient of viscous liquids is estimated on the basis of a simple analysis of their rheological shear spectra. To this end, the Almond-West approach, previously employed to access single-particle diffusivities in ionic conductors, is generalized for application to molecular dynamics in supercooled liquids. Rheology based estimates, presented for indomethacin, ortho-terphenyl, and trinaphthylbenzene, reveal relatively small, yet systematic differences when compared with diffusivity data directly measured for these highly viscous liquids. These deviations are discussed in terms of mechanical Haven ratios, introduced to quantify the magnitude of collective translational effects that have an impact on the viscous flow. © 2021 Author(s).view abstract doi: 10.1063/5.0055811 2021 • 278 Role of pH in the synthesis and growth of gold nanoparticles using L-asparagine: A combined experimental and simulation study
Baez-Cruz, R. and Baptista, L.A. and Ntim, S. and Manidurai, P. and Espinoza, S. and Ramanan, C. and Cortes-Huerto, R. and Sulpizi, M.
Journal of Physics Condensed Matter 33 (2021)The use of biomolecules as capping and reducing agents in the synthesis of metallic nanoparticles constitutes a promising framework to achieve desired functional properties with minimal toxicity. The system's complexity and the large number of variables involved represent a challenge for theoretical and experimental investigations aiming at devising precise synthesis protocols. In this work, we use L-asparagine (Asn), an amino acid building block of large biomolecular systems, to synthesise gold nanoparticles (AuNPs) in aqueous solution at controlled pH. The use of Asn offers a primary system that allows us to understand the role of biomolecules in synthesising metallic nanoparticles. Our results indicate that AuNPs synthesised in acidic (pH 6) and basic (pH 9) environments exhibit somewhat different morphologies.We investigate these AuNPs via Raman scattering experiments and classical molecular dynamics simulations of zwitterionic and anionic Asn states adsorbing on (111)-, (100)-, (110)-, and (311)-oriented gold surfaces. A combined analysis suggests that the underlying mechanism controlling AuNPs geometry correlates with amine's preferential adsorption over ammonium groups, enhanced upon increasing pH. Our simulations reveal that Asn (both zwitterionic and anionic) adsorption on gold (111) is essentially different from adsorption on more open surfaces. Water molecules strongly interact with the gold face-centred-cubic lattice and create traps, on the more open surfaces, that prevent the Asn from diffusing. These results indicate that pH is a relevant parameter in green-synthesis protocols with the capability to control the nanoparticle's geometry, and pave the way to computational studies exploring the effect of water monolayers on the adsorption of small molecules on wet gold surfaces. © 2021 The Author(s).view abstract doi: 10.1088/1361-648X/abf6e3 2021 • 277 Specific inhibition of the Survivin–CRM1 interaction by peptide-modified molecular tweezers
Meiners, A. and Bäcker, S. and Hadrović, I. and Heid, C. and Beuck, C. and Ruiz-Blanco, Y.B. and Mieres-Perez, J. and Pörschke, M. and Grad, J.-N. and Vallet, C. and Hoffmann, D. and Bayer, P. and Sánchez-García, E. and Schra...
Nature Communications 12 (2021)Survivin’s dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. This protein–protein interaction represents an attractive target in cancer research and therapy. Here, we report a sophisticated strategy addressing Survivin’s nuclear export signal (NES), the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine. These were covalently connected to small peptides resembling the natural, self-complementary dimer interface which largely overlaps with the NES. Several biochemical methods demonstrated sequence-selective NES recognition and interference with the critical receptor interaction. These data were strongly supported by molecular dynamics simulations and multiscale computational studies. Rational design of lysine tweezers equipped with a peptidic recognition element thus allowed to address a previously unapproachable protein surface area. As an experimental proof-of-principle for specific transport signal interference, this concept should be transferable to any protein epitope with a flanking well-accessible lysine. © 2021, The Author(s).view abstract doi: 10.1038/s41467-021-21753-9 2021 • 276 Stripping away ion hydration shells in electrical double-layer formation: Water networks matter
Alfarano, S.R. and Pezzotti, S. and Stein, C.J. and Lin, Z. and Sebastiani, F. and Funke, S. and Hoberg, C. and Kolling, I. and Ma, C.Y. and Mauelshagen, K. and Ockelmann, T. and Schwaab, G. and Fu, L. and Brubach, J.-B. and Roy, ...
Proceedings of the National Academy of Sciences of the United States of America 118 (2021)The double layer at the solid/electrolyte interface is a key concept in electrochemistry. Here, we present an experimental study combined with simulations, which provides a molecular picture of the double-layer formation under applied voltage. By THz spectroscopy we are able to follow the stripping away of the cation/anion hydration shells for an NaCl electrolyte at the Au surface when decreasing/increasing the bias potential. While Na+ is attracted toward the electrode at the smallest applied negative potentials, stripping of the Cl2 hydration shell is observed only at higher potential values. These phenomena are directly measured by THz spectroscopy with ultrabright synchrotron light as a source and rationalized by accompanying molecular dynamics simulations and electronic-structure calculations. © 2021 National Academy of Sciences. All rights reserved.view abstract doi: 10.1073/pnas.2108568118 2021 • 275 Studying the mechanism of phase separation in aqueous solutions of globular proteins via molecular dynamics computer simulations
Brudar, S. and Gujt, J. and Spohr, E. and Hribar-Lee, B.
Physical chemistry chemical physics : PCCP 23 415-424 (2021)Proteins are the most abundant biomacromolecules in living cells, where they perform vital roles in virtually every biological process. To maintain their function, proteins need to remain in a stable (native) state. Inter- and intramolecular interactions in aqueous protein solutions govern the fate of proteins, as they can provoke their unfolding or association into aggregates. The initial steps of protein aggregation are difficult to capture experimentally, therefore we used molecular dynamics simulations in this study. We investigated the initial phase of aggregation of two different lysozymes, hen egg-white (HEWL) and T4 WT* lysozyme and also human lens γ-D crystallin by using atomistic simulations. We monitored the phase stability of their aqueous solutions by calculating time-dependent density fluctuations. We found that all proteins remained in their compact form despite aggregation. With an extensive analysis of intermolecular residue-residue interactions we discovered that arginine is of paramount importance in the initial stage of aggregation of HEWL and γ-D crystallin, meanwhile lysine was found to be the most involved amino acid in forming initial contacts between T4 WT* molecules.view abstract doi: 10.1039/d0cp05160h 2021 • 274 Supramolecular Enhancement of a Natural 14-3-3 Protein Ligand
Guillory, X. and Hadrović, I. and De Vink, P.J. and Sowislok, A. and Brunsveld, L. and Schrader, T. and Ottmann, C.
Journal of the American Chemical Society 143 13495-13500 (2021)Rational design of protein-protein interaction (PPI) inhibitors is challenging. Connecting a general supramolecular protein binder with a specific peptidic ligand provides a novel conceptual approach. Thus, lysine-specific molecular tweezers were conjugated to a peptide-based 14-3-3 ligand and produced a strong PPI inhibitor with 100-fold elevated protein affinity. X-ray crystal structure elucidation of this supramolecular directed assembly provides unique molecular insight into the binding mode and fully aligns with Molecular Dynamics (MD) simulations. This new supramolecular chemical biology concept opens the path to novel chemical tools for studying PPIs. © 2021 American Chemical Society.view abstract doi: 10.1021/jacs.1c07095 2021 • 273 The relationship between charge and molecular dynamics in viscous acid hydrates
Ahlmann, S. and Münzner, P. and Moch, K. and Sokolov, A.P. and Böhmer, R. and Gainaru, C.
Journal of Chemical Physics 155 (2021)Oscillatory shear rheology has been employed to access the structural rearrangements of deeply supercooled sulfuric acid tetrahydrate (SA4H) and phosphoric acid monohydrate, the latter in protonated (PA1H) and deuterated (PA1D) forms. Their viscoelastic responses are analyzed in relation to their previously investigated electric conductivity. The comparison of the also presently reported dielectric response of deuterated sulfuric acid tetrahydrate (SA4D) and that of its protonated analog SA4H reveals an absence of isotope effects for the charge transport in this hydrate. This finding clearly contrasts with the situation known for PA1H and PA1D. Our analyses also demonstrate that the conductivity relaxation profiles of acid hydrides closely resemble those exhibited by classical ionic electrolytes, even though the charge transport in phosphoric acid hydrates is dominated by proton transfer processes. At variance with this dielectric simplicity, the viscoelastic responses of these materials depend on their structural compositions. While SA4H displays a “simple liquid”-like viscoelastic behavior, the mechanical responses of PA1H and PA1D are more complex, revealing relaxation modes, which are faster than their ubiquitous structural rearrangements. Interestingly, the characteristic rates of these fast mechanical relaxations agree well with the characteristic frequencies of the charge rearrangements probed in the dielectric investigations, suggesting appearance of a proton transfer in mechanical relaxation of phosphoric acid hydrates. These findings open the exciting perspective of exploiting shear rheology to access not only the dynamics of the matrix but also that of the charge carriers in highly viscous decoupled conductors. © 2021 Author(s).view abstract doi: 10.1063/5.0055179 2021 • 272 The relaxation behavior of supercooled and glassy imidacloprid
Mansuri, A. and Münzner, P. and Feuerbach, T. and Vermeer, A.W.P. and Hoheisel, W. and Böhmer, R. and Thommes, M. and Gainaru, C.
Journal of Chemical Physics 155 (2021)Employing dielectric spectroscopy, oscillatory shear rheology, and calorimetry, the present work explores the molecular dynamics of the widely used insecticide imidacloprid above and below its glass transition temperature. In its supercooled liquid regime, the applied techniques yield good agreement regarding the characteristic structural (alpha) relaxation times of this material. In addition, the generalized Gemant-DiMarzio-Bishop model provides a good conversion between the frequency-dependent dielectric and shear mechanical responses in its viscous state, allowing for an assessment of imidacloprid's molecular hydrodynamic radius. In order to characterize the molecular dynamics in its glassy regime, we employ several approaches. These include the application of frequency-temperature superposition (FTS) to its isostructural dielectric and rheological responses as well as use of dielectric and calorimetric physical aging and the Adam-Gibbs-Vogel model. While the latter approach and dielectric FTS provide relaxation times that are close to each other, the other methods predict notably longer times that are closer to those reflecting a complete recovery of ergodicity. This seemingly conflicting dissimilarity demonstrates that the molecular dynamics of glassy imidacloprid strongly depends on its thermal history, with high relevance for the use of this insecticide as an active ingredient in technological applications. © 2021 Author(s).view abstract doi: 10.1063/5.0067404 2021 • 271 Three-Dimensional Analysis of the Natural-Organic-Matter Distribution in the Cake Layer to Precisely Reveal Ultrafiltration Fouling Mechanisms
Wu, S. and Hua, X. and Ma, B. and Fan, H. and Miao, R. and Ulbricht, M. and Hu, C. and Qu, J.
Environmental Science and Technology 55 5442-5452 (2021)Cake layer formation is the dominant ultrafiltration membrane fouling mechanism after long-term operation. However, precisely analyzing the cake-layer structure still remains a challenge due to its thinness (micro/nano scale). Herein, based on the excellent depth-resolution and foulant-discrimination of time-of-flight secondary ion mass spectrometry, a three-dimensional analysis of the cake-layer structure caused by natural organic matter was achieved at lower nanoscale for the first time. When humic substances or polysaccharides coexisted with proteins separately, a homogeneous cake layer was formed due to their interactions. Consequently, membrane fouling resistances induced by proteins were reduced by humic substances or polysaccharides, leading to a high flux. However, when humic substances and polysaccharides coexisted, a sandwich-like cake layer was formed owing to the asynchronous deposition based on molecular dynamics simulations. As a result, membrane fouling resistances were superimposed, and the flux was low. Furthermore, it is interesting that cake-layer structures were relatively stable under common UF operating conditions (i.e., concentration and stirring). These findings better elucidate membrane fouling mechanisms of different natural-organic-matter mixtures. Moreover, it is demonstrated that membrane fouling seems lower with a more homogeneous cake layer, and humic substances or polysaccharides play a critical role. Therefore, regulating the cake-layer structure by feed pretreatment scientifically based on proven mechanisms should be an efficient membrane-fouling-control strategy. © 2021 American Chemical Society.view abstract doi: 10.1021/acs.est.1c00435 2021 • 270 Twins – A weak link in the magnetic hardening of ThMn12-type permanent magnets
Ener, S. and Skokov, K.P. and Palanisamy, D. and Devillers, T. and Fischbacher, J. and Eslava, G.G. and Maccari, F. and Schäfer, L. and Diop, L.V.B. and Radulov, I. and Gault, B. and Hrkac, G. and Dempsey, N.M. and Schrefl, T. an...
Acta Materialia 214 (2021)Nd2Fe14B-type materials exhibit the highest energy product around room temperature and hence dominate the high-performance permanent magnet market. Intensive research efforts aim at alternative material systems containing less critical elements with similar or better magnetic properties. Nd- and Sm-based compounds with a ThMn12-type structure exhibit intrinsic properties comparable or even superior to Nd2Fe14B. However, it has not been possible to achieve technically relevant coercivity and remanent magnetization in ThMn12-based bulk sintered magnets. Using SmFe11Ti as a prototypical representative, we demonstrate that one important reason for the poor performance is the formation of twins inside micro-crystalline grains. The nature of the twins in SmFe11Ti was investigated in twinned “single crystals” and both bulk and thin film poly-crystalline samples, using advanced electron microscopy and atom probe tomography as well as simulations and compared with benchmark Nd2Fe14B. Both micro-twins and nano-twins show a twin orientation of 57±2° and an enrichment in Sm, which could affect domain wall motion in this material. Micromagnetic simulations indicate that twins act as nucleation centers, representing the magnetically weakest link in the microstructure. The relation between twin formation energies and geometrical features are briefly discussed using molecular dynamic simulations. © 2021view abstract doi: 10.1016/j.actamat.2021.116968 2020 • 269 A flexible and adaptive grid algorithm for global optimization utilizing basin hopping Monte Carlo
Paleico, M.L. and Behler, J.
Journal of Chemical Physics 152 (2020)Global optimization is an active area of research in atomistic simulations, and many algorithms have been proposed to date. A prominent example is basin hopping Monte Carlo, which performs a modified Metropolis Monte Carlo search to explore the potential energy surface of the system of interest. These simulations can be very demanding due to the high-dimensional configurational search space. The effective search space can be reduced by utilizing grids for the atomic positions, but at the cost of possibly biasing the results if fixed grids are employed. In this paper, we present a flexible grid algorithm for global optimization that allows us to exploit the efficiency of grids without biasing the simulation outcome. The method is general and applicable to very heterogeneous systems, such as interfaces between two materials of different crystal structures or large clusters supported at surfaces. As a benchmark case, we demonstrate its performance for the well-known global optimization problem of Lennard-Jones clusters containing up to 100 particles. Despite the simplicity of this model potential, Lennard-Jones clusters represent a challenging test case since the global minima for some "magic" numbers of particles exhibit geometries that are very different from those of clusters with only a slightly different size. © 2020 Author(s).view abstract doi: 10.1063/1.5142363 2020 • 268 Amorphization-governed elasto-plastic deformation under nanoindentation in cubic (3C) silicon carbide
Zhao, L. and Alam, M. and Zhang, J. and Janisch, R. and Hartmaier, A.
Ceramics International 46 12470-12479 (2020)Amorphization plays an important role in ceramic deformation under mechanical loading. In the present work, we investigate the elasto-plastic deformation mechanisms of monocrystalline cubic silicon carbide (3C–SiC) in spherical nanoindentation by means of molecular dynamics simulations. The indentation-induced amorphization and its interactions with other deformation modes are emphasized. Initially, the suitable empirical potential capable of accurately characterizing the mechanical and defect properties of monocrystalline 3C–SiC, as well as the propensity of phase transformation from 3C–SiC to amorphous SiC, is rationally selected by benchmarking of different empirical potentials with experimental data and density functional theory calculations. Subsequently, the inhomogeneous elastic-plastic transitions during nanoindentation of monocrystalline 3C–SiC, as well as their dependence on crystallographic orientation, are investigated. Phase transformations including amorphization are analyzed using combined methods based on radial distribution function and bond angle distribution. Our simulation results demonstrate that before plasticity initiation-related “pop-in” event, each indented-monocrystalline 3C–SiC experiences a pure quasi-elastic deformation governed by the formation of amorphous structures. And this process of amorphization is fully reversible for small indentation depths. Further amorphization and dislocation nucleation jointly dominate the incipient plasticity in 3C–SiC nanoindentation. It is found that the indentation-induced defect zone composed of amorphous phase and dislocations is more pronounced in 3C–SiC(010) than that in the other two orientations of (110) and (111). © 2020 Elsevier Ltd and Techna Group S.r.l.view abstract doi: 10.1016/j.ceramint.2020.02.009 2020 • 267 Atomistic deformation behavior of single and twin crystalline Cu nanopillars with preexisting dislocations
Ko, W.-S. and Stukowski, A. and Hadian, R. and Nematollahi, A. and Jeon, J.B. and Choi, W.S. and Dehm, G. and Neugebauer, J. and Kirchlechner, C. and Grabowski, B.
Acta Materialia 197 54-68 (2020)Molecular dynamics simulations are performed to investigate the impact of a coherent Σ3 (111) twin boundary on the plastic deformation behavior of Cu nanopillars. Our work reveals that the mechanical response of pillars with and without the twin boundary is decisively driven by the characteristics of initial dislocation sources. In the condition of comparably large pillar size and abundant initial mobile dislocations, overall yield and flow stresses are controlled by the longest, available mobile dislocation. An inverse correlation of the yield and flow stresses with the length of the longest dislocation is established and compared to experimental data. The experimentally reported subtle differences in yield and flow stresses between pillars with and without the twin boundary are likely related to the maximum lengths of the mobile dislocations. In the condition of comparably small pillar size, for which a reduction of mobile dislocations during heat treatment and mechanical loading occurs, the mechanical response of pillars with and without the twin boundary can be clearly distinguished. Dislocation starvation during deformation is more pronounced in pillars without the twin boundary than in pillars with the twin boundary because the twin boundary acts as a pinning surface for the dislocation network. © 2020 Acta Materialia Inc.view abstract doi: 10.1016/j.actamat.2020.07.029 2020 • 266 Atomistic description of self-diffusion in molybdenum: A comparative theoretical study of non-Arrhenius behavior
Smirnova, D. and Starikov, S. and Leines, G.D. and Liang, Y. and Wang, N. and Popov, M.N. and Abrikosov, I.A. and Sangiovanni, D.G. and Drautz, R. and Mrovec, M.
Physical Review Materials 4 (2020)According to experimental observations, the temperature dependence of self-diffusion coefficient in most body-centered cubic metals (bcc) exhibits non-Arrhenius behavior. The origin of this behavior is likely related to anharmonic vibrational effects at elevated temperatures. However, it is still debated whether anharmonicity affects more the formation or migration of monovacancies, which are known to govern the self-diffusion. In this extensive atomistic simulation study we investigated thermodynamic properties of monovacancies in bcc molybdenum, here taken as a representative model system, from zero temperature to the melting point. We combined first-principles calculations and classical simulations based on three widely used interatomic potentials for Mo. In our analysis we employ static and dynamic atomistic calculations as well as statistical sampling techniques and thermodynamic integration to achieve thorough information about temperature variations of vacancy formation and migration free energies and diffusivities. In addition, we carry out large-scale molecular dynamics simulations that enable direct observation of high-temperature self-diffusion at the atomic scale. By scrutinizing the results obtained by different models and methods, we conclude that the peculiar self-diffusion behavior is likely caused by strong temperature dependence of the vacancy formation energy. © 2020 American Physical Society.view abstract doi: 10.1103/PhysRevMaterials.4.013605 2020 • 265 Atomistic simulations of thermal conductivity in GeTe nanowires
Bosoni, E. and Campi, D. and Donadio, D. and Sosso, G.C. and Behler, J. and Bernasconi, M.
Journal of Physics D: Applied Physics 53 (2020)The thermal conductivity of GeTe crystalline nanowires has been computed by means of non-equilibrium molecular dynamics simulations employing a machine learning interatomic potential. This material is of interest for application in phase change non-volatile memories. The resulting lattice thermal conductivity of an ultrathin nanowire (7.3 nm diameter) of 1.57 W m-1 K-1 is sizably lower than the corresponding bulk value of 3.15 W m-1 K-1 obtained within the same framework. The analysis of the phonon dispersion relations and lifetimes reveals that the lower thermal conductivity in the nanowire is mostly due to a reduction in the phonon group velocities. We further predict the presence of a minimum in the lattice thermal conductivity for thicker nanowires. © 2019 IOP Publishing Ltd.view abstract doi: 10.1088/1361-6463/ab5478 2020 • 264 Element-specific displacements in defect-enriched TiO2: Indication of a flash sintering mechanism
Jongmanns, M. and Wolf, D.E.
Journal of the American Ceramic Society 103 589-596 (2020)Flash sintering experiments of ceramics indicate the formation of a state far from equilibrium. It is hypothesized that this state is enriched by Frenkel defects. The possibility is investigated that such lattice defects are being generated by a proliferation of lattice vibrations that lie close to the Brillouin zone edge. We show by means of Molecular Dynamics simulations of rutile TiO2 that this mechanism generates Frenkel defects in concentrations far beyond equilibrium. These defects deform the whole lattice in a way that the mean-square displacements of the vibration amplitudes of the Ti and O atoms are specifically enhanced. This finding compares well to atomic displacement data of flash sintered rutile TiO2 reported recently. © 2019 The Authors. Journal of the American Ceramic Society published by Wiley Periodicals, Inc. on behalf of American Ceramic Society (ACERS)view abstract doi: 10.1111/jace.16696 2020 • 263 Fast diffusion mechanism in Li4P2S6: Via a concerted process of interstitial Li ions
Stamminger, A.R. and Ziebarth, B. and Mrovec, M. and Hammerschmidt, T. and Drautz, R.
RSC Advances 10 10715-10722 (2020)The synthesis of Li superionic conductor Li7P3S11 may be accompanied by the formation of a detrimental Li4P2S6 phase due to a high mixing sensitivity of precursor materials. This phase exhibits a poor ionic conductivity whose origins are not fully understood. Recently Dietrich et al. investigated the energetics of Li ion migration in Li4P2S6 with nudged elastic band (NEB) calculations. The observed large migration barrier of 0.51 eV for purely interstitial diffusion leads to an interpretation of the low ionic conductivity by kinetic limitations. Based on ab initio molecular dynamics simulations (AIMD) we propose a new and energetically much more favorable diffusion path available to interstitial Li ion charge carriers that has not been considered so far. It consists of a concerted process in which a second lithium atom is pushed out from its equilibrium lattice position by the diffusing lithium ion. A detailed analysis with NEB calculations shows that the energy barrier for this concerted diffusion is only 0.08 eV, i.e. an order of magnitude lower than the previously reported value for purely interstitial diffusion. Therefore, the observed low ionic conductivity of Li4P2S6 is likely not originating from kinetic limitations due to high diffusion barriers but rather from thermodynamic reasons associated with a low concentration of free charge carriers. We therefore expect that increasing the charge carrier concentration by doping is a viable design route to optimize the ionic conductivity of this material. © 2020 The Royal Society of Chemistry.view abstract doi: 10.1039/d0ra00932f 2020 • 262 Freestanding and Supported MoS2Monolayers under Cluster Irradiation: Insights from Molecular Dynamics Simulations
Ghaderzadeh, S. and Ladygin, V. and Ghorbani-Asl, M. and Hlawacek, G. and Schleberger, M. and Krasheninnikov, A.V.
ACS Applied Materials and Interfaces 12 37454-37463 (2020)Two-dimensional (2D) materials with nanometer-size holes are promising systems for DNA sequencing, water purification, and molecule selection/separation. However, controllable creation of holes with uniform sizes and shapes is still a challenge, especially when the 2D material consists of several atomic layers as, e.g., MoS2, the archetypical transition metal dichalcogenide. We use analytical potential molecular dynamics simulations to study the response of 2D MoS2 to cluster irradiation. We model both freestanding and supported sheets and assess the amount of damage created in MoS2 by the impacts of noble gas clusters in a wide range of cluster energies and incident angles. We show that cluster irradiation can be used to produce uniform holes in 2D MoS2 with the diameter being dependent on cluster size and energy. Energetic clusters can also be used to displace sulfur atoms preferentially from either top or bottom layers of S atoms in MoS2 and also clean the surface of MoS2 sheets from adsorbents. Our results for MoS2, which should be relevant to other 2D transition metal dichalcogenides, suggest new routes toward cluster beam engineering of devices based on 2D inorganic materials. Copyright © 2020 American Chemical Society.view abstract doi: 10.1021/acsami.0c09255 2020 • 261 Hydration in aqueous osmolyte solutions: The case of TMAO and urea
Sahle, C.J. and Schroer, M.A. and Niskanen, J. and Elbers, M. and Jeffries, C.M. and Sternemann, C.
Physical Chemistry Chemical Physics 22 11614-11624 (2020)The hydration and hydrogen-bond topology of small water solvated molecules such as the naturally occurring organic osmolytes trimethylamine N-oxide (TMAO) and urea are under intense investigation. We aim at furthering the understanding of this complex hydration by combining experimental oxygen K-edge excitation spectra with results from spectra calculated via the Bethe-Salpeter equation based on structures obtained from ab initio molecular dynamics simulations. Comparison of experimental and calculated spectra allows us to extract detailed information about the immediate surrounding of the solute molecules in the solvated state. We quantify and localize the influence of the solute on the hydrogen bond network of the water solvent and find spectroscopic fingerprints of a clear directional asymmetry around TMAO with strong and local kosmotropic influence around TMAO's NO head group and slight chaotropic influence around the hydrophobic methyl groups. The influence of urea on the local water network is qualitatively similar to that of TMAO but weaker in magnitude. The strongest influence of both molecules on the shape of the oxygen K-edge spectra is found in the first hydration shells. This journal is © the Owner Societies.view abstract doi: 10.1039/c9cp06785j 2020 • 260 Identifying a gold nanoparticle as a proactive carrier for transport of a doxorubicin-peptide complex
Exner, K.S. and Ivanova, A.
Colloids and Surfaces B: Biointerfaces 194 (2020)Efficient drug delivery to malignant cells in the human organism requires the application of drug-delivery systems (DDS) that consist of several building blocks, such as a biomolecule to bind the drug as well as a carrier for transport. In the present study, we investigate a potential DDS component for the cytostatic doxorubicin (DOX) that consists of a gold nanoparticle (Au-NP) and a short drug-binding peptide sequence. Combining molecular dynamics simulations with density functional theory calculations allows resolving the adsorption configurations of DOX at simulated physiological conditions as well as the interaction energies between the building blocks of the DDS. Interestingly, it turns out that the task of the Au-NP is not limited to being a passive carrier. The nanoparticle is directly involved in the stabilization of the drug by intercalating DOX together with a tryptophan residue from the peptide. Another favored adsorption configuration corresponds to an intercalation complex of DOX with two tryptophan residues, reminiscent of the intercalation of DOX between DNA bases. The insights gained in the present study allow deriving general conclusions about the surface chemistry of DOX: its tendency to intercalate seems not to depend on its π-stacking partners (organic or inorganic), as long as they can be properly arranged around the drug. Hence, DOX may be stabilized sufficiently during its delivery if intercalation within the carrier moieties is possible. This finding may assist the construction of a more complex DDS for DOX in the future, for which the investigated drug-peptide-nanoparticle conjugate may serve as a prototype. © 2020 Elsevier B.V.view abstract doi: 10.1016/j.colsurfb.2020.111155 2020 • 259 Linking Fluid Densimetry and Molecular Simulation: Adsorption Behavior of Carbon Dioxide on Planar Gold Surfaces
Tietz, C. and Sekulla, M. and Yang, X. and Schmid, R. and Richter, M.
Industrial and Engineering Chemistry Research 59 13283-13289 (2020)Phase equilibria of fluid substances and their mixtures are important in numerous scientific as well as industrial applications and are, therefore, a major focus of thermophysical property research. For the development and improvement of thermophysical property models, reliable experimental data are crucial. However, measurements of thermophysical properties in the vicinity of the dew line can be substantially distorted by surface phenomena such as adsorption and capillary condensation on the quasi nonporous metal surfaces of the experimental apparatuses. To support the qualitative understanding of these phenomena on an atomistic level and to estimate their impact on experiments, we performed classical molecular dynamics (MD) simulations. As a first proof-of-concept investigation, we focused on pure CO2 on an idealized face-centered cubic (fcc) {111} gold surface. The results, in the form of an adsorption isotherm at T = 283.15 K, are compared to sorption measurements using a specially designed gold sinker incorporated in an optimized gravimetric sorption analyzer. This first comparison between atomistic MD simulations and gravimetric experiments helps in assessing the applicability of our simulation technique and paves the way for a deeper understanding of the relevant surface phenomena occurring in our apparatus. © 2020 American Chemical Society.view abstract doi: 10.1021/acs.iecr.0c01423 2020 • 258 Observations of grain-boundary phase transformations in an elemental metal
Meiners, T. and Frolov, T. and Rudd, R.E. and Dehm, G. and Liebscher, C.H.
Nature 579 375-378 (2020)The theory of grain boundary (the interface between crystallites, GB) structure has a long history1 and the concept of GBs undergoing phase transformations was proposed 50 years ago2,3. The underlying assumption was that multiple stable and metastable states exist for different GB orientations4–6. The terminology ‘complexion’ was recently proposed to distinguish between interfacial states that differ in any equilibrium thermodynamic property7. Different types of complexion and transitions between complexions have been characterized, mostly in binary or multicomponent systems8–19. Simulations have provided insight into the phase behaviour of interfaces and shown that GB transitions can occur in many material systems20–24. However, the direct experimental observation and transformation kinetics of GBs in an elemental metal have remained elusive. Here we demonstrate atomic-scale GB phase coexistence and transformations at symmetric and asymmetric [11 1 ¯] tilt GBs in elemental copper. Atomic-resolution imaging reveals the coexistence of two different structures at Σ19b GBs (where Σ19 is the density of coincident sites and b is a GB variant), in agreement with evolutionary GB structure search and clustering analysis21,25,26. We also use finite-temperature molecular dynamics simulations to explore the coexistence and transformation kinetics of these GB phases. Our results demonstrate how GB phases can be kinetically trapped, enabling atomic-scale room-temperature observations. Our work paves the way for atomic-scale in situ studies of metallic GB phase transformations, which were previously detected only indirectly9,15,27–29, through their influence on abnormal grain growth, non-Arrhenius-type diffusion or liquid metal embrittlement. © 2020, The Author(s), under exclusive licence to Springer Nature Limited.view abstract doi: 10.1038/s41586-020-2082-6 2020 • 257 Performance and Cost Assessment of Machine Learning Interatomic Potentials
Zuo, Y. and Chen, C. and Li, X. and Deng, Z. and Chen, Y. and Behler, J. and Csányi, G. and Shapeev, A.V. and Thompson, A.P. and Wood, M.A. and Ong, S.P.
Journal of Physical Chemistry A 124 731-745 (2020)Machine learning of the quantitative relationship between local environment descriptors and the potential energy surface of a system of atoms has emerged as a new frontier in the development of interatomic potentials (IAPs). Here, we present a comprehensive evaluation of machine learning IAPs (ML-IAPs) based on four local environment descriptors - atom-centered symmetry functions (ACSF), smooth overlap of atomic positions (SOAP), the spectral neighbor analysis potential (SNAP) bispectrum components, and moment tensors - using a diverse data set generated using high-throughput density functional theory (DFT) calculations. The data set comprising bcc (Li, Mo) and fcc (Cu, Ni) metals and diamond group IV semiconductors (Si, Ge) is chosen to span a range of crystal structures and bonding. All descriptors studied show excellent performance in predicting energies and forces far surpassing that of classical IAPs, as well as predicting properties such as elastic constants and phonon dispersion curves. We observe a general trade-off between accuracy and the degrees of freedom of each model and, consequently, computational cost. We will discuss these trade-offs in the context of model selection for molecular dynamics and other applications. © 2020 American Chemical Society.view abstract doi: 10.1021/acs.jpca.9b08723 2020 • 256 Phase diagram of grain boundary facet and line junctions in silicon
Alam, M. and Lymperakis, L. and Neugebauer, J.
Physical Review Materials 4 (2020)The presence of facets and line junctions connecting facets on grain boundaries (GBs) has a strong impact on the properties of structural, functional, and optoelectronic materials: They govern the mobility of interfaces, the segregation of impurities, as well the electronic properties. In the present paper, we employ density-functional theory and modified embedded atom method calculations to systematically investigate the energetics and thermodynamic stability of these defects. As a prototype system, we consider ς3 tilt GBs in Si. By analyzing the energetics of different faceted GBs, we derive a diagram that describes and predicts the reconstruction of these extended defects as a function of facet length and boundary inclination angle. The phase diagram sheds light upon the fundamental mechanisms causing GB faceting phenomena. It demonstrates that the properties of faceting are not determined solely by anisotropic GB energies but by a complex interplay between geometry and microstructure, boundary energies as well as long-range strain interactions. © 2020 authors. Published by the American Physical Society. Open access publication funded by the Max Planck Society.view abstract doi: 10.1103/PhysRevMaterials.4.083604 2020 • 255 Predicting oxidation and spin states by high-dimensional neural networks: Applications to lithium manganese oxide spinels
Eckhoff, M. and Lausch, K.N. and Blöchl, P.E. and Behler, J.
Journal of Chemical Physics 153 (2020)Lithium ion batteries often contain transition metal oxides such as LixMn2O4 (0 ≤ x ≤ 2). Depending on the Li content, different ratios of MnIII to MnIV ions are present. In combination with electron hopping, the Jahn-Teller distortions of the MnIIIO6 octahedra can give rise to complex phenomena such as structural transitions and conductance. While for small model systems oxidation and spin states can be determined using density functional theory (DFT), the investigation of dynamical phenomena by DFT is too demanding. Previously, we have shown that a high-dimensional neural network potential can extend molecular dynamics (MD) simulations of LixMn2O4 to nanosecond time scales, but these simulations did not provide information about the electronic structure. Here, we extend the use of neural networks to the prediction of atomic oxidation and spin states. The resulting high-dimensional neural network is able to predict the spins of the Mn ions with an error of only 0.03 We find that the Mn eg electrons are correctly conserved and that the number of Jahn-Teller distorted MnIIIO6 octahedra is predicted precisely for different Li loadings. A charge ordering transition is observed between 280 K and 300 K, which matches resistivity measurements. Moreover, the activation energy of the electron hopping conduction above the phase transition is predicted to be 0.18 eV, deviating only 0.02 eV from experiment. This work demonstrates that machine learning is able to provide an accurate representation of both the geometric and the electronic structure dynamics of LixMn2O4 on time and length scales that are not accessible by ab initio MD. © 2020 Author(s).view abstract doi: 10.1063/5.0021452 2020 • 254 Pressure-dependent electronic structure calculations using integral equation-based solvation models
Pongratz, T. and Kibies, P. and Eberlein, L. and Tielker, N. and Hölzl, C. and Imoto, S. and Beck Erlach, M. and Kurrmann, S. and Schummel, P.H. and Hofmann, M. and Reiser, O. and Winter, R. and Kremer, W. and Kalbitzer, H.R. and...
Biophysical Chemistry 257 (2020)Recent methodological progress in quantum-chemical calculations using the “embedded cluster reference interaction site model” (EC-RISM) integral equation theory is reviewed in the context of applying it as a solvation model for calculating pressure-dependent thermodynamic and spectroscopic properties of molecules immersed in water. The methodology is based on self-consistent calculations of electronic and solvation structure around dissolved molecules where pressure enters the equations via an appropriately chosen solvent response function and the pure solvent density. Besides specification of a dispersion-repulsion force field for solute-solvent interactions, the EC-RISM approach derives the electrostatic interaction contributions directly from the wave function. We further develop and apply the method to a variety of benchmark cases for which computational or experimental reference data are either available in the literature or are generated specifically for this purpose in this work. Starting with an enhancement to predict hydration free energies at non-ambient pressures, which is the basis for pressure-dependent molecular population estimation, we demonstrate the performance on the calculation of the autoionization constant of water. Spectroscopic problems are addressed by studying the biologically relevant small osmolyte TMAO (trimethylamine N-oxide). Pressure-dependent NMR shifts are predicted and compared to experiments taking into account proper computational referencing methods that extend earlier work. The experimentally observed IR blue-shifts of certain vibrational bands of TMAO as well as of the cyanide anion are reproduced by novel methodology that allows for weighing equilibrium and non-equilibrium solvent relaxation effects. Taken together, the model systems investigated allow for an assessment of the reliability of the EC-RISM approach for studying pressure-dependent biophysical processes. © 2019 Elsevier B.V.view abstract doi: 10.1016/j.bpc.2019.106258 2020 • 253 Prismatic Slip in Magnesium
Stricker, M. and Curtin, W.A.
Journal of Physical Chemistry C 124 27230-27240 (2020)Magnesium is the lowest-density structural metal but has low ductility that limits applications. The low ductility is related to the hexagonally close-packed crystal structure where activation of nonbasal slip is required for general plasticity. Here, our recent neural network potential (NNP) for Mg, trained using Kohn-Sham density functional theory (DFT), is used to examine slip of a dislocations on the prismatic plane. The generalized stacking fault surface energies (GSFEs) for basal and prismatic slip are computed and agree better with Kohn-Sham density functional theory (KS-DFT) than orbital-free density functional theory (OF-DFT) and modified embedded atom method (MEAM), which predict spurious minima. Consistent with the generalized stacking fault energy (GSFE), direct simulations of the prismatic a»screw dislocation show it is unstable to dissociate into the a basal screw dislocation; this is mostly consistent with OF-DFT while MEAM predicts stability. Prismatic slip is thus achieved by a double-cross-slip process of the stable basal dislocations driven by a resolved shear stress on the orthogonal prismatic plane; this is consistent with the process deduced from experiments. The Nudged Elastic Band method is used with the NNP to examine the atomistic path and the stress-dependent enthalpy barrier for this mechanism; this requires many tens of thousands of atoms. The basal-prismatic cross-slip occurs in increments of c/2 via basal constriction, cross-slip on the prism plane, cross-slip back onto the basal plane, and lateral motion of the created jogs to extend the new basal dislocation. Comparisons with experimental deductions show some agreement and some notable disagreement. Resolution of the differences points toward further large-scale studies that require the accuracy and efficiency of KS-DFT-trained NNP, an approach that is also naturally extendable to the important domain of Mg alloys. © 2020 American Chemical Society. All rights reserved.view abstract doi: 10.1021/acs.jpcc.0c09665 2020 • 252 Properties of α-Brass Nanoparticles. 1. Neural Network Potential Energy Surface
Weinreich, J. and Römer, A. and Paleico, M.L. and Behler, J.
Journal of Physical Chemistry C 124 12682-12695 (2020)Binary metal clusters are of high interest for applications in heterogeneous catalysis and have received much attention in recent years. To gain insights into their structure and composition at the atomic scale, computer simulations can provide valuable information if reliable interatomic potentials are available. In this paper we describe the construction of a high-dimensional neural network potential (HDNNP) intended for simulations of large brass nanoparticles with thousands of atoms, which is also applicable to bulk α-brass and its surfaces. The HDNNP, which is based on reference data obtained from density-functional theory calculations, is very accurate with a root-mean-square error of 1.7 meV/atom for total energies and 39 meV Å-1 for the forces of structures not included in the training set. The potential has been thoroughly validated for a wide range of energetic and structural properties of bulk α-brass, its surfaces as well as clusters of different size and composition demonstrating its suitability for large-scale molecular dynamics and Monte Carlo simulations with first-principles accuracy. © 2020 American Chemical Society.view abstract doi: 10.1021/acs.jpcc.0c00559 2020 • 251 Reorientational dynamics of trimethoxyboroxine: A molecular glass former studied by dielectric spectroscopy and 11B nuclear magnetic resonance
Hoffmann, L. and Beerwerth, J. and Greim, D. and Senker, J. and Sternemann, C. and Hiller, W. and Böhmer, R.
Journal of Chemical Physics 152 (2020)In this work, trimethoxyboroxine (TMB) is identified as a small-molecule glass former. In its viscous liquid as well as glassy states, static and dynamic properties of TMB are explored using various techniques. It is found that, on average, the structure of the condensed TMB molecules deviates from threefold symmetry so that TMB's electric dipole moment is nonzero, thus rendering broadband dielectric spectroscopy applicable. This method reveals the super-Arrhenius dynamics that characterizes TMB above its glass transition, which occurs at about 204 K. To extend the temperature range in which the molecular dynamics can be studied, 11B nuclear magnetic resonance experiments are additionally carried out on rotating and stationary samples: Exploiting dynamic second-order shifts, spin-relaxation times, line shape effects, as well as stimulated-echo and two-dimensional exchange spectroscopy, a coherent picture regarding the dynamics of this glass former is gained. © 2020 Author(s).view abstract doi: 10.1063/1.5129769 2020 • 250 Roadmap on multiscale materials modeling
Van Der Giessen, E. and Schultz, P.A. and Bertin, N. and Bulatov, V.V. and Cai, W. and Csányi, G. and Foiles, S.M. and Geers, M.G.D. and González, C. and Hütter, M. and Kim, W.K. and Kochmann, D.M. and Llorca, J. and Mattsson, ...
Modelling and Simulation in Materials Science and Engineering 28 (2020)Modeling and simulation is transforming modern materials science, becoming an important tool for the discovery of new materials and material phenomena, for gaining insight into the processes that govern materials behavior, and, increasingly, for quantitative predictions that can be used as part of a design tool in full partnership with experimental synthesis and characterization. Modeling and simulation is the essential bridge from good science to good engineering, spanning from fundamental understanding of materials behavior to deliberate design of new materials technologies leveraging new properties and processes. This Roadmap presents a broad overview of the extensive impact computational modeling has had in materials science in the past few decades, and offers focused perspectives on where the path forward lies as this rapidly expanding field evolves to meet the challenges of the next few decades. The Roadmap offers perspectives on advances within disciplines as diverse as phase field methods to model mesoscale behavior and molecular dynamics methods to deduce the fundamental atomic-scale dynamical processes governing materials response, to the challenges involved in the interdisciplinary research that tackles complex materials problems where the governing phenomena span different scales of materials behavior requiring multiscale approaches. The shift from understanding fundamental materials behavior to development of quantitative approaches to explain and predict experimental observations requires advances in the methods and practice in simulations for reproducibility and reliability, and interacting with a computational ecosystem that integrates new theory development, innovative applications, and an increasingly integrated software and computational infrastructure that takes advantage of the increasingly powerful computational methods and computing hardware. © 2020 The Author(s). Published by IOP Publishing Ltd.view abstract doi: 10.1088/1361-651X/ab7150 2020 • 249 Role of image charges in ionic liquid confined between metallic interfaces
Ntim, S. and Sulpizi, M.
Physical Chemistry Chemical Physics 22 10786-10791 (2020)The peculiar properties of ionic liquids in confinement have not only become essential for energy storage, catalysis and tribology, but still pose fundamental questions. Recently, an anomalous liquid-solid phase transition has been observed in atomic force microscopy experiments for 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]), the transition being more pronounced for metallic surfaces. Image charges have been suggested as the key element driving the anomalous freezing. Using atomistic molecular dynamics simulations, we investigate the impact of image charges on structure, dynamics and thermodynamics of [BMIM][BF4] confined between gold electrodes. Our results not only unveil a minor role played by the metal polarisation, but also provide a novel description of the interfacial layer. Although no diffuse layer can be defined in terms of the electrostatic potential, long range effects are clearly visible in the dynamical properties up to 10 nanometers away from the surface, and are expected to influence viscous forces in the experiments. This journal is © the Owner Societies.view abstract doi: 10.1039/d0cp00409j 2020 • 248 Temperature effects on the ionic conductivity in concentrated alkaline electrolyte solutions
Shao, Y. and Hellström, M. and Yllö, A. and Mindemark, J. and Hermansson, K. and Behler, J. and Zhang, C.
Physical Chemistry Chemical Physics 22 10426-10430 (2020)Alkaline electrolyte solutions are important components in rechargeable batteries and alkaline fuel cells. As the ionic conductivity is thought to be a limiting factor in the performance of these devices, which are often operated at elevated temperatures, its temperature dependence is of significant interest. Here we use NaOH as a prototypical example of alkaline electrolytes, and for this system we have carried out reactive molecular dynamics simulations with an experimentally verified high-dimensional neural network potential derived from density-functional theory calculations. It is found that in concentrated NaOH solutions elevated temperatures enhance both the contributions of proton transfer to the ionic conductivity and deviations from the Nernst-Einstein relation. These findings are expected to be of practical relevance for electrochemical devices based on alkaline electrolyte solutions. This journal is © the Owner Societies.view abstract doi: 10.1039/c9cp06479f 2020 • 247 Vapor Pressure Assessment of Sulfolane-Based Eutectic Solvents: Experimental, PC-SAFT, and Molecular Dynamics
Lima, F. and Dietz, C.H.J.T. and Silvestre, A.J.D. and Branco, L.C. and Canongia Lopes, J. and Gallucci, F. and Shimizu, K. and Held, C. and Marrucho, I.M.
Journal of Physical Chemistry B 124 10386-10397 (2020)Since their discovery, deep eutectic solvents (DES) have been explored in multiple applications. However, the complete physicochemical characterization is still nonexistent for many of the proposed and used DES. In particular, vapor pressure, which is a crucial property for the application of DES as solvents, is very rarely available. In this work, the measurement of the total and partial pressures of two sulfolane-based DES, tetrabutylammonium bromide:sulfolane and tetrabutylphosphonium bromide:sulfolane, in several proportions, from 40 to 100 °C and atmospheric pressure, was performed using headspace gas chromatography mass spectrometry, HS-GC-MS. A large decrease on the total pressure was recorded which, together with the finding that total pressures showed negative deviations from Raoult's law, is indicative of the favorable, strong interactions between the two components within the DES. Additionally, the study of vapor pressure change with DES molar composition was carried out, and surprisingly, the existence of inflection points in the pressure curve was observed. Experimental results were modeled using the PC-SAFT equation of state, and in addition, MD simulations were performed to provide a molecular understanding of the pressure data. Considering the different results and insights obtained from the used strategies, it can be concluded that both DES systems have especially strong interactions between salt and sulfolane, at high sulfolane content, due to the different structural rearrangement of the liquid state. © 2020 American Chemical Society.view abstract doi: 10.1021/acs.jpcb.0c04837 2019 • 246 A new class of supramolecular ligands stabilizes 14-3-3 protein-protein interactions by up to two orders of magnitude
Gigante, A. and Grad, J.-N. and Briels, J. and Bartel, M. and Hoffmann, D. and Ottmann, C. and Schmuck, C.
Chemical Communications 55 111-114 (2019)We report the first supramolecular stabilizers of the interaction between 14-3-3ζ and two of its effectors, Tau and C-Raf, which are involved in neurodegenerative diseases and proliferative signal transduction, respectively. These supramolecular ligands open up an opportunity to modulate functions of 14-3-3 with these effectors. © The Royal Society of Chemistry.view abstract doi: 10.1039/c8cc07946c 2019 • 245 Ab initio based method to study structural phase transitions in dynamically unstable crystals, with new insights on the β to ω transformation in titanium
Korbmacher, D. and Glensk, A. and Duff, A.I. and Finnis, M.W. and Grabowski, B. and Neugebauer, J.
Physical Review B 100 (2019)We present an approach that enables an efficient and accurate study of dynamically unstable crystals over the full temperature range. The approach is based on an interatomic potential fitted to ab initio molecular dynamics energies for both the high- and low-temperature stable phases. We verify by comparison to explicit ab initio simulations that such a bespoke potential, for which we use here the functional form of the embedded atom method, provides accurate transformation temperatures and atomistic features of the transformation. The accuracy of the potential makes it an ideal tool to study the important impact of finite size and finite time effects. We apply our approach to the dynamically unstable β (bcc) titanium phase and study in detail the transformation to the low-temperature stable hexagonal ω phase. We find a large set of previously unreported linear-chain disordered (LCD) structures made up of three types of [111]β linear-chain defects that exhibit randomly disordered arrangements in the (111)β plane. © 2019 American Physical Society.view abstract doi: 10.1103/PhysRevB.100.104110 2019 • 244 Ab initio thermodynamics of liquid and solid water
Cheng, B. and Engel, E.A. and Behler, J. and Dellago, C. and Ceriotti, M.
Proceedings of the National Academy of Sciences of the United States of America 116 1110-1115 (2019)Thermodynamic properties of liquid water as well as hexagonal (Ih) and cubic (Ic) ice are predicted based on density functional theory at the hybrid-functional level, rigorously taking into account quantum nuclear motion, anharmonic fluctuations, and proton disorder. This is made possible by combining advanced free-energy methods and state-of-the-art machine-learning techniques. The ab initio description leads to structural properties in excellent agreement with experiments and reliable estimates of the melting points of light and heavy water. We observe that nuclear-quantum effects contribute a crucial 0.2 meV/H 2 O to the stability of ice Ih, making it more stable than ice Ic. Our computational approach is general and transferable, providing a comprehensive framework for quantitative predictions of ab initio thermodynamic properties using machine-learning potentials as an intermediate step. © 2019 National Academy of Sciences. All rights reserved.view abstract doi: 10.1073/pnas.1815117116 2019 • 243 Accurate Probabilities for Highly Activated Reaction of Polyatomic Molecules on Surfaces Using a High-Dimensional Neural Network Potential: CHD 3 + Cu(111)
Gerrits, N. and Shakouri, K. and Behler, J. and Kroes, G.-J.
Journal of Physical Chemistry Letters 10 1763-1768 (2019)An accurate description of reactive scattering of molecules on metal surfaces often requires the modeling of energy transfer between the molecule and the surface phonons. Although ab initio molecular dynamics (AIMD) can describe this energy transfer, AIMD is at present untractable for reactions with reaction probabilities smaller than 1%. Here, we show that it is possible to use a neural network potential to describe a polyatomic molecule reacting on a mobile metal surface with considerably reduced computational effort compared to AIMD. The highly activated reaction of CHD 3 on Cu(111) is used as a test case for this method. It is observed that the reaction probability is influenced considerably by dynamical effects such as the bobsled effect and surface recoil. A special dynamical effect for CHD 3 + Cu(111) is that a higher vibrational efficacy is obtained for two quanta in the CH stretch mode than for a single quantum. Copyright © 2019 American Chemical Society.view abstract doi: 10.1021/acs.jpclett.9b00560 2019 • 242 Atomistic phase field chemomechanical modeling of dislocation-solute-precipitate interaction in Ni–Al–Co
Mianroodi, J.R. and Shanthraj, P. and Kontis, P. and Cormier, J. and Gault, B. and Svendsen, B. and Raabe, D.
Acta Materialia 175 250-261 (2019)Dislocation-precipitate interaction and solute segregation play important roles in controlling the mechanical behavior of Ni-based superalloys at high temperature. In particular, the increased mobility of solutes at high temperature leads to increased dislocation-solute interaction. For example, atom probe tomography (APT) results [1] for single crystal MC2 superalloy indicate significant segregation of solute elements such as Co and Cr to dislocations and stacking faults in γ′ precipitates. To gain further insight into solute segregation, dislocation-solute interaction, and its effect on the mechanical behavior in such Ni-superalloys, finite-deformation phase field chemomechanics [2] is applied in this work to develop a model for dislocation-solute-precipitate interaction in the two-phase γ-γ′ Ni-based superalloy model system Ni–Al–Co. Identification and quantification of this model is based in particular on the corresponding Ni–Al–Co embedded atom method (EAM) potential [3]. Simulation results imply both Cottrell- and Suzuki-type segregation of Co in γ and γ'. Significant segregation of Co to dislocation cores and faults in γ′ is also predicted, in agreement with APT results. Predicted as well is the drag of Co by γ dislocations entering and shearing γ'. Since solute elements such as Co generally prefer the γ phase, Co depletion in γ′ could be reversed by such dislocation drag. The resulting change in precipitate chemistry may in turn affect its stability and play a role in precipitate coarsening and rafting. © 2019 Acta Materialia Inc.view abstract doi: 10.1016/j.actamat.2019.06.008 2019 • 241 Deciphering Charge Transfer and Electronic Polarization Effects at Gold Nanocatalysts on Reduced Titania Support
Yoo, S.-H. and Siemer, N. and Todorova, M. and Marx, D. and Neugebauer, J.
Journal of Physical Chemistry C 123 5495-5506 (2019)Gold nanoparticles supported on reduced TiO2 (110) surfaces are widely used as catalysts for oxidation reactions. Despite extensive studies, the role of oxygen vacancies in such systems remains elusive and is controversially discussed. Combining ab initio molecular dynamics simulations with methods originally developed to describe defects in semiconductor physics we study how the electronic charge originally located at the vacancy modifies the charge on the cluster. Despite differences resulting from the employed level of density functional theory (namely semilocal/GGA, GGA + U, and hybrid functionals), we consistently find that the Au clusters remain either neutral or acquire a positive charge. The intuitively expected electron transfer from the oxygen vacancy to the gold cluster can be safely ruled out. Analyzing these findings, we discuss the role of the oxygen vacancy in the bonding between Au clusters and support and the catalytic activity of the system. © 2019 American Chemical Society.view abstract doi: 10.1021/acs.jpcc.8b12015 2019 • 240 Development of a MOF-FF-compatible interaction model for liquid methanol and Cl− in methanol
Siwaipram, S. and Bopp, P.A. and Soetens, J.-C. and Schmid, R. and Bureekaew, S.
Journal of Molecular Liquids 285 526-534 (2019)If complex systems are to be studied in molecular simulation, one usually attempts to combine existing interaction models in order to describe the new system. This is, however, not always feasible. We thus propose here a new pairwise-additive interaction model for liquid methanol and solvated Cl− to be used to study the immersion of Metal-Organic Frameworks (MOFs) in methanol. Practically, it entails that all interactions must be written to be compatible with the family of MOF-FF models, which have been specifically developed and then widely employed in molecular simulations of such MOFs, in particular flexible ones. The new model for liquid methanol has been mostly tailored to provide densities and dielectric constants as close to experiment as possible in a large temperature domain. This is important since the flexible MOFs modify their shapes according to their loading with guest molecules of various types, and also according to the thermodynamic conditions. The model yields excellent agreement for the density-temperature, dielectric constant-temperature, and self-diffusion-temperature relationships, properties. Other properties such as e.g. the compressibilities or thermal expansion coefficients are of the correct order of magnitude. Since some MOF frameworks are electrically charged, counterions will be present in these cases. The interactions of Cl− with the liquid are thus also considered here. The solvation of this ion is also found to be satisfactory when compared to other MD studies. © 2019 Elsevier B.V.view abstract doi: 10.1016/j.molliq.2019.04.068 2019 • 239 Electronic and optical properties of pristine, N- and S-doped water-covered TiO 2 nanotube surfaces
Kenmoe, S. and Lisovski, O. and Piskunov, S. and Zhukovskii, Y.F. and Spohr, E.
Journal of Chemical Physics 150 (2019)For rational design and improvement of electronic and optical properties of water-splitting photocatalysts, the ability to control the band edge positions relative to the water redox potentials and the photoresponse as a function of environmental conditions is essential. We combine ab initio molecular dynamics simulations with ab initio many-body theoretical calculations to predict the bandgap and band edge energies, as well as the absorption spectrum of pristine and N- and S-doped TiO 2 nanotubes using the DFT+U and G 0 W 0 approaches. Both levels of theory show similar trends, and N+S-codoping appears to be the optimal system for photocatalytic water splitting both in dry and humid conditions. However, the effect is rather moderate. Compared to DFT+U, the enhanced many-body effects in the G 0 W 0 calculations push the absolute energies of the band edges to higher values and yield increased quasi-particle bandgaps in better agreement with experiment. In dry and humid conditions, the electronic bandgap for all systems is found to be in the range of 6.0-6.2 eV with a redshift from electronic gap to optical gap. The absorption spectra show an optical anisotropy and different absorption thresholds for different light polarizations. © 2019 Author(s).view abstract doi: 10.1063/1.5050090 2019 • 238 Engineering atomic-level complexity in high-entropy and complex concentrated alloys
Oh, H.S. and Kim, S.J. and Odbadrakh, K. and Ryu, W.H. and Yoon, K.N. and Mu, S. and Körmann, F. and Ikeda, Y. and Tasan, C.C. and Raabe, D. and Egami, T. and Park, E.S.
Nature Communications 10 (2019)Quantitative and well-targeted design of modern alloys is extremely challenging due to their immense compositional space. When considering only 50 elements for compositional blending the number of possible alloys is practically infinite, as is the associated unexplored property realm. In this paper, we present a simple property-targeted quantitative design approach for atomic-level complexity in complex concentrated and high-entropy alloys, based on quantum-mechanically derived atomic-level pressure approximation. It allows identification of the best suited element mix for high solid-solution strengthening using the simple electronegativity difference among the constituent elements. This approach can be used for designing alloys with customized properties, such as a simple binary NiV solid solution whose yield strength exceeds that of the Cantor high-entropy alloy by nearly a factor of two. This study provides general design rules that enable effective utilization of atomic level information to reduce the immense degrees of freedom in compositional space without sacrificing physics-related plausibility. © 2019, The Author(s).view abstract doi: 10.1038/s41467-019-10012-7 2019 • 237 First-principles characterization of reversible martensitic transformations
Ferrari, A. and Sangiovanni, D.G. and Rogal, J. and Drautz, R.
Physical Review B 99 (2019)Reversible martensitic transformations (MTs) are the origin of many fascinating phenomena, including the famous shape memory effect. In this work, we present a fully ab initio procedure to characterize MTs in alloys and to assess their reversibility. Specifically, we employ ab initio molecular dynamics data to parametrize a Landau expansion for the free energy of the MT. This analytical expansion makes it possible to determine the stability of the high- and low-temperature phases, to obtain the Ehrenfest order of the MT, and to quantify its free energy barrier and latent heat. We apply our model to the high-temperature shape memory alloy Ti-Ta, for which we observe remarkably small values for the metastability region (the interval of temperatures in which the high- and low-temperature phases are metastable) and for the barrier: these small values are necessary conditions for the reversibility of MTs and distinguish shape memory alloys from other materials. © 2019 American Physical Society.view abstract doi: 10.1103/PhysRevB.99.094107 2019 • 236 Heterogeneous Interactions between Gas-Phase Pyruvic Acid and Hydroxylated Silica Surfaces: A Combined Experimental and Theoretical Study
Fang, Y. and Lesnicki, D. and Wall, K.J. and Gaigeot, M.-P. and Sulpizi, M. and Vaida, V. and Grassian, V.H.
Journal of Physical Chemistry A 123 983-991 (2019)The adsorption of gas-phase pyruvic acid (CH 3 COCOOH) on hydroxylated silica particles has been investigated at 296 K using transmission Fourier transform infrared (FTIR) spectroscopy and theoretical simulations. Under dry conditions (<1% relative humidity, RH), both the trans-cis (Tc) and trans-trans (Tt) pyruvic acid conformers are observed on the surface as well as the (hydrogen bonded) pyruvic acid dimer. The detailed surface interactions were further understood through ab initio molecular dynamics simulations. Under higher relative humidity conditions (above 10% RH), adsorbed water competes for surface adsorption sites. Adsorbed water is also observed to change the relative populations of the different adsorbed pyruvic acid configurations. Overall, this study provides valuable insights into the interaction of pyruvic acid with hydroxylated silica surfaces on the molecular level from both experimental and theoretical analyses. Furthermore, these results highlight the importance of the environment (relative humidity and coadsorbed water) in the adsorption, partitioning, and configurations of pyruvic acid at the surface. Copyright © 2019 American Chemical Society.view abstract doi: 10.1021/acs.jpca.8b10224 2019 • 235 How [FeFe]-Hydrogenase Facilitates Bidirectional Proton Transfer
Senger, M. and Eichmann, V. and Laun, K. and Duan, J. and Wittkamp, F. and Knör, G. and Apfel, U.-P. and Happe, T. and Winkler, M. and Heberle, J. and Stripp, S.T.
Journal of the American Chemical Society 141 17394-17403 (2019)Hydrogenases are metalloenzymes that catalyze the conversion of protons and molecular hydrogen, H2. [FeFe]-hydrogenases show particularly high rates of hydrogen turnover and have inspired numerous compounds for biomimetic H2 production. Two decades of research on the active site cofactor of [FeFe]-hydrogenases have put forward multiple models of the catalytic proceedings. In comparison, our understanding of proton transfer is poor. Previously, residues were identified forming a hydrogen-bonding network between active site cofactor and bulk solvent; however, the exact mechanism of catalytic proton transfer remained inconclusive. Here, we employ in situ infrared difference spectroscopy on the [FeFe]-hydrogenase from Chlamydomonas reinhardtii evaluating dynamic changes in the hydrogen-bonding network upon photoreduction. While proton transfer appears to be impaired in the oxidized state (Hox), the presented data support continuous proton transfer in the reduced state (Hred). Our analysis allows for a direct, molecular unique assignment to individual amino acid residues. We found that transient protonation changes of glutamic acid residue E141 and, most notably, arginine R148 facilitate bidirectional proton transfer in [FeFe]-hydrogenases. © 2019 American Chemical Society.view abstract doi: 10.1021/jacs.9b09225 2019 • 234 Ionic Conductivity and Its Dependence on Structural Disorder in Halogenated Argyrodites Li6PS5X (X = Br, Cl, I)
Stamminger, A.R. and Ziebarth, B. and Mrovec, M. and Hammerschmidt, T. and Drautz, R.
Chemistry of Materials (2019)Halogenated argyrodites Li6PS5Br, Li6PS5Cl, and Li6PS5I exhibit large differences in the measured Li ionic conductivities. Crystallographic analysis has shown that these differences may be related to occupations of specific Wyckoff sites in different argyrodite types, but detailed understanding of the relationship between the atomic structure and operating diffusion mechanisms is still lacking. In this work, we employed ab initio molecular dynamics simulations to calculate the Li diffusivity for different argyrodite structure types. Our calculations show that the Li diffusivity does not depend implicitly on the type of halogen but is rather governed by the degree of structural disorder. Assuming disordered structures to arise naturally from the ordered structure type by thermally activated antisite defects, we are able to explain the degree of disorder found for the different types of halogens from the calculated defect formation energies. Comparing the calculated formation energies to the ionic radii of the halogen atoms, we find a strong correlation between the radii and energies required for introducing the antisite defects. © 2019 American Chemical Society.view abstract doi: 10.1021/acs.chemmater.9b02047 2019 • 233 Mass transport properties of quasiharmonic vs. anharmonic transition-metal nitrides
Sangiovanni, D.G.
Thin Solid Films 688 (2019)I present a development of the color-diffusion algorithm, used in non-equilibrium (accelerated) ab initio molecular dynamics simulations of point-defect migration in crystals [Sangiovanni et al., Phys. Rev. B 93, 094305 (2016)], to determine the temperature dependence of anion vacancy jump frequencies in rocksalt-structure (B1) TiN and VN characterized by quasiharmonic (TiN) vs. strongly anharmonic (VN) lattice dynamics. Over a temperature range [≈0.6·Tm < T < ≈0.9·Tm] relatively close to the materials melting points Tm, the simulations reveal that anion vacancy migration in TiN and VN exhibits an Arrhenius-like behavior, described by activation energies Ea TiN = 4.2 ± 0.3 eV and Ea VN = 3.1 ± 0.3 eV, and attempt frequencies νTiN = 8·1015±0.7 s−1 and νVN = 2·1017±0.8 s−1. A comparison of activation energies Ea extracted by Arrhenius linear regression at elevated temperatures with ab initio Ea0K values calculated at 0 Kelvin reveals that, while the nitrogen migration energy Ea TiN varies modestly with temperature {∆Ea TiN = [Ea(Tm) – Ea(0 K)]/Ea(0 K) ≈ 0.1}, the changes in Ea VN vs. T are considerable (∆Ea VN ≈ 1). The temperature-induced variations in vacancy migration energies and diffusivities are discussed in relation to the TiN and VN vibrational properties determined via ab initio molecular dynamics at different temperatures. It is argued that static 0-K calculations, which account for thermal expansion effects within the framework of quasiharmonic transition-state theory, accurately reproduce the finite-temperature mass transport properties of TiN. Conversely, the use of molecular dynamics simulations, which explicit treat lattice vibrations at any temperature of interest, is necessary to achieve reliable atomic diffusivities in B1 VN, a crystal phase dynamically stabilized by anharmonic vibrations [Mei et al., Phys. Rev. B 91, 054101 (2015)]. © 2019 Elsevier B.V.view abstract doi: 10.1016/j.tsf.2019.05.016 2019 • 232 MD simulation of stress-assisted nanometric cutting mechanism of 3C silicon carbide
Liu, L. and Xu, Z. and Tian, D. and Hartmaier, A. and Luo, X. and Zhang, J. and Nordlund, K. and Fang, F.
Industrial Lubrication and Tribology 71 686-691 (2019)Purpose: This paper aims to reveal the mechanism for improving ductile machinability of 3C-silicon carbide (SiC) and associated cutting mechanism in stress-assisted nanometric cutting. Design/methodology/approach: Molecular dynamics simulation of nano-cutting 3C-SiC is carried out in this paper. The following two scenarios are considered: normal nanometric cutting of 3C-SiC; and stress-assisted nanometric cutting of 3C-SiC for comparison. Chip formation, phase transformation, dislocation activities and shear strain during nanometric cutting are analyzed. Findings: Negative rake angle can produce necessary hydrostatic stress to achieve ductile removal by the extrusion in ductile regime machining. In ductile-brittle transition, deformation mechanism of 3C-SiC is combination of plastic deformation dominated by dislocation activities and localization of shear deformation. When cutting depth is greater than 10 nm, material removal is mainly achieved by shear. Stress-assisted machining can lead to better quality of machined surface. However, there is a threshold for the applied stress to fully gain advantages offered by stress-assisted machining. Stress-assisted machining further enhances plastic deformation ability through the active dislocations’ movements. Originality/value: This work describes a stress-assisted machining method for improving the surface quality, which could improve 3C-SiC ductile machining ability. © 2019, Emerald Publishing Limited.view abstract doi: 10.1108/ILT-03-2019-0096 2019 • 231 Molecular Dynamics Simulations of the “Breathing” Phase Transformation of MOF Nanocrystallites
Keupp, J. and Schmid, R.
Advanced Theory and Simulations 2 (2019)The displacive phase transformation of metal-organic frameworks (MOFs), referred to as “breathing,” is computationally investigated intensively within periodic boundary conditions (PBC). In contrast, the first-principles parameterized force field MOF-FF is used to investigate the thermal- and pressure-induced transformations for non-periodic nanocrystallites of DMOF-1 (Zn2(bdc)2(dabco); bdc: 1,4-benzenedicarboxylate; dabco: 1,4-diazabicyclo[2.2.2]octane) as a model system to investigate the effect of the PBC approximation on the systems' kinetics and thermodynamics and to assess whether size effects can be captured by this kind of simulation. By the heating of differently sized closed pore nanocrystallites, a spontaneous opening is observed with an interface between the closed and open pore phase moving rapidly through the system. The nucleation temperature for the opening transition rises with size. By enforcing the phase transition with a distance restraint, the free energy can be quantified via umbrella sampling. The apparent barrier is substantially lower than for a concerted process under PBC. Interestingly, the barrier reduces with the size of the nanocrystallite, indicating a hindering surface effect. The results demonstrate that the actual free energy barriers and the importance of surface effects for the transformation under real conditions can only be studied beyond PBC. © 2019 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheimview abstract doi: 10.1002/adts.201900117 2019 • 230 Non-monotonic effect of additive particle size on the glass transition in polymers
Zirdehi, E.M. and Varnik, F.
Journal of Chemical Physics 150 (2019)Effect of small additive molecules on the structural relaxation of polymer melts is investigated via molecular dynamics simulations. At a constant external pressure and a fixed number concentration of added molecules, the variation of the particle diameter leads to a non-monotonic change of the relaxation dynamics of the polymer melt. For non-entangled chains, this effect is rationalized in terms of an enhanced added-particle-dynamics which competes with a weaker coupling strength upon decreasing the particle size. Interestingly, cooling simulations reveal a non-monotonic effect on the glass transition temperature also for entangled chains, where the effect of additives on polymer dynamics is more intricate. This observation underlines the importance of monomer-scale packing effects on the glass transition in polymers. In view of this fact, size-adaptive thermosensitive core-shell colloids would be a promising candidate route to explore this phenomenon experimentally. © 2019 Author(s).view abstract doi: 10.1063/1.5063476 2019 • 229 One-dimensional vs. two-dimensional proton transport processes at solid-liquid zinc-oxide-water interfaces
Hellström, M. and Quaranta, V. and Behler, J.
Chemical Science 10 1232-1243 (2019)Long-range charge transport is important for many applications like batteries, fuel cells, sensors, and catalysis. Obtaining microscopic insights into the atomistic mechanism is challenging, in particular if the underlying processes involve protons as the charge carriers. Here, large-scale reactive molecular dynamics simulations employing an efficient density-functional-theory-based neural network potential are used to unravel long-range proton transport mechanisms at solid-liquid interfaces, using the zinc oxide-water interface as a prototypical case. We find that the two most frequently occurring ZnO surface facets, (1010) and (1120), that typically dominate the morphologies of zinc oxide nanowires and nanoparticles, show markedly different proton conduction behaviors along the surface with respect to the number of possible proton transfer mechanisms, the role of the solvent for long-range proton migration, as well as the proton transport dimensionality. Understanding such surface-facet-specific mechanisms is crucial for an informed bottom-up approach for the functionalization and application of advanced oxide materials. © 2019 The Royal Society of Chemistry.view abstract doi: 10.1039/c8sc03033b 2019 • 228 OpenMolcas: From Source Code to Insight
Fdez. Galván, I. and Vacher, M. and Alavi, A. and Angeli, C. and Aquilante, F. and Autschbach, J. and Bao, J.J. and Bokarev, S.I. and Bogdanov, N.A. and Carlson, R.K. and Chibotaru, L.F. and Creutzberg, J. and Dattani, N. and Del...
Journal of Chemical Theory and Computation 15 5925-5964 (2019)In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets. Copyright © 2019 American Chemical Society.view abstract doi: 10.1021/acs.jctc.9b00532 2019 • 227 Priming effects in the crystallization of the phase change compound GeTe from atomistic simulations
Gabardi, S. and Sosso, G.G. and Behler, J. and Bernasconi, M.
Faraday Discussions 213 287-301 (2019)Strategies to reduce the incubation time for crystal nucleation and thus the stochasticity of the set process are of relevance for the operation of phase change memories in ultra-scaled geometries. With these premises, in this work we investigate the crystallization kinetics of the phase change compound GeTe. We have performed large scale molecular dynamics simulations using an interatomic potential, generated previously from a neural network fitting of a database of ab initio energies. We have addressed the crystallization of models of amorphous GeTe annealed at different temperatures above the glass transition. The results on the distribution of subcritical nuclei and on the crystal growth velocity of postcritical ones are compared with our previous simulations of the supercooled liquid quenched from the melt. We find that a large population of subcritical nuclei can form at the lower temperatures where the nucleation rate is large. This population partially survives upon fast annealing, which leads to a dramatic reduction of the incubation time at high temperatures where the crystal growth velocity is maximal. This priming effect could be exploited to enhance the speed of the set process in phase change memories. © 2019 The Royal Society of Chemistry.view abstract doi: 10.1039/c8fd00101d 2019 • 226 Probing the Degree of Heterogeneity within a Shear Band of a Model Glass
Hassani, M. and Lagogianni, A.E. and Varnik, F.
Physical Review Letters 123 (2019)Recent experiments provide evidence for density variations along shear bands in metallic glasses with a length scale of a few hundred nanometers. Via molecular dynamics simulations of a generic binary glass model, here we show that this is strongly correlated with variations of composition, coordination number, viscosity, and heat generation. Individual shear events along the shear band path show a mean distance of a few nanometers, comparable to recent experimental findings on medium range order. The aforementioned variations result from these localized perturbations, mediated by elasticity. © 2019 American Physical Society.view abstract doi: 10.1103/PhysRevLett.123.195502 2019 • 225 Semi-empirical force-field model for the Ti 1-x Al x N (0 ≤ x ≤ 1) system
Almyras, G.A. and Sangiovanni, D.G. and Sarakinos, K.
Materials 12 (2019)We present a modified embedded atom method (MEAM) semi-empirical force-field model for the Ti 1-x Al x N (0 ≤ x ≤ 1) alloy system. The MEAM parameters, determined via an adaptive simulated-annealing (ASA) minimization scheme, optimize the model's predictions with respect to 0 K equilibrium volumes, elastic constants, cohesive energies, enthalpies of mixing, and point-defect formation energies, for a set of ≈40 elemental, binary, and ternary Ti-Al-N structures and configurations. Subsequently, the reliability of the model is thoroughly verified against known finite-temperature thermodynamic and kinetic properties of key binary Ti-N and Al-N phases, as well as properties of Ti 1-x Al x N (0 < x < 1) alloys. The successful outcome of the validation underscores the transferability of our model, opening the way for large-scale molecular dynamics simulations of, e.g., phase evolution, interfacial processes, and mechanical response in Ti-Al-N-based alloys, superlattices, and nanostructures. © 2019 by the authors.view abstract doi: 10.3390/ma12020215 2019 • 224 Semi-empirical force-field model for the Ti1-xAlxN (0 ≤ x ≤ 1) system
Almyras, G.A. and Sangiovanni, D.G. and Sarakinos, K.
Materials 12 (2019)We present a modified embedded atom method (MEAM) semi-empirical force-field model for the Ti1-xAlxN (0 ≤ x ≤ 1) alloy system. The MEAM parameters, determined via an adaptive simulated-annealing (ASA) minimization scheme, optimize the model's predictions with respect to 0 K equilibrium volumes, elastic constants, cohesive energies, enthalpies of mixing, and point-defect formation energies, for a set of ≈40 elemental, binary, and ternary Ti-Al-N structures and configurations. Subsequently, the reliability of the model is thoroughly verified against known finite-temperature thermodynamic and kinetic properties of key binary Ti-N and Al-N phases, as well as properties of Ti1-xAlxN (0 < x < 1) alloys. The successful outcome of the validation underscores the transferability of our model, opening the way for large-scale molecular dynamics simulations of, e.g., phase evolution, interfacial processes, and mechanical response in Ti-Al-N-based alloys, superlattices, and nanostructures. © 2019 by the authors.view abstract doi: 10.3390/ma12020215 2019 • 223 Structure and Dynamics of the Liquid-Water/Zinc-Oxide Interface from Machine Learning Potential Simulations
Quaranta, V. and Behler, J. and Hellström, M.
Journal of Physical Chemistry C 123 1293-1304 (2019)Interfaces between water and metal oxides exhibit many interesting phenomena like dissociation and recombination of water molecules and water exchange between the interface and the bulk liquid. Moreover, a variety of structural motifs can be found, differing in hydrogen-bonding patterns and molecular orientations. Here, we report the structure and dynamics of liquid water interacting with the two most stable ZnO surfaces, (101Ì) and (112Ì), by means of reactive molecular dynamics simulations based on a machine learning high-dimensional neural network potential. For both surfaces, three distinct hydration layers can be observed within 10 Å from the surface with the first hydration layer (nearest to the surface) representing the most interesting region to investigate. There, water molecules dynamically dissociate and recombine, leading to a variety of chemical species at the interface. We characterized these species and their molecular environments by analyzing the properties of the hydrogen bonds and local geometries. At ZnO(112Ì0), some of the adsorbed hydroxide ions bridge two surface Zn ions, which is not observed at ZnO(101Ì0). For both surfaces, adsorbed water molecules always bind to a single Zn ion, and those located in proximity of the substrate are mostly "H-down" oriented for ZnO(101Ì0) and "flat-lying", i.e., parallel to the surface, for ZnO(112Ì0). The time scales for proton-transfer (PT) reactions are quite similar at the two surfaces, with the average lifetime of adsorbed hydroxide ions being around 41 ± 3 ps until recombination. However, water exchange events, in which adsorbed water molecules leave the surface and enter the bulk liquid, happen more frequently at ZnO(112Ì0) than at ZnO(101Ì0). © 2018 American Chemical Society.view abstract doi: 10.1021/acs.jpcc.8b10781 2019 • 222 Structure and thermodynamics of aqueous urea solutions from ambient to kilobar pressures: From thermodynamic modeling, experiments, and first principles simulations to an accurate force field description
Hölzl, C. and Kibies, P. and Imoto, S. and Noetzel, J. and Knierbein, M. and Salmen, P. and Paulus, M. and Nase, J. and Held, C. and Sadowski, G. and Marx, D. and Kast, S.M. and Horinek, D.
Biophysical Chemistry 254 (2019)Molecular simulations based on classical force fields are a powerful method for shedding light on the complex behavior of biomolecules in solution. When cosolutes are present in addition to water and biomolecules, subtle balances of weak intermolecular forces have to be accounted for. This imposes high demands on the quality of the underlying force fields, and therefore force field development for small cosolutes is still an active field. Here, we present the development of a new urea force field from studies of urea solutions at ambient and elevated hydrostatic pressures based on a combination of experimental and theoretical approaches. Experimental densities and solvation shell properties from ab initio molecular dynamics simulations at ambient conditions served as the target properties for the force field optimization. Since urea is present in many marine life forms, elevated hydrostatic pressure was rigorously addressed: densities at high pressure were measured by vibrating tube densitometry up to 500 bar and by X-ray absorption up to 5 kbar. Densities were determined by the perturbed-chain statistical associating fluid theory equation of state. Solvation properties were determined by embedded cluster integral equation theory and ab initio molecular dynamics. Our new force field is able to capture the properties of urea solutions at high pressures without further high-pressure adaption, unlike trimethylamine-N-oxide, for which a high-pressure adaption is necessary. © 2019view abstract doi: 10.1016/j.bpc.2019.106260 2019 • 221 Temperature dependence of the vibrational spectrum of porphycene: A qualitative failure of classical-nuclei molecular dynamics†
Litman, Y. and Behler, J. and Rossi, M.
Faraday Discussions 221 526-546 (2019)The temperature dependence of vibrational spectra can provide information about structural changes of a system and also serve as a probe to identify different vibrational mode couplings. Fully anharmonic temperature-dependent calculations of these quantities are challenging due to the cost associated with statistically converging trajectory-based methods, especially when accounting for nuclear quantum effects. Here, we train a high-dimensional neural network potential energy surface for the porphycene molecule based on data generated with DFT-B3LYP, including pairwise van der Waals interactions. In addition, we fit a kernel ridge regression model for the molecular dipole moment surface. The combination of this machinery with thermostatted path integral molecular dynamics (TRPMD) allows us to obtain well-converged, full-dimensional, fully-anharmonic vibrational spectra including nuclear quantum effects, without sacrificing the first-principles quality of the potential-energy surface or the dipole surface. Within this framework, we investigate the temperature and isotopologue dependence of the high-frequency vibrational fingerprints of porphycene. While classical-nuclei dynamics predicts a red shift of the vibrations encompassing the NH and CH stretches, TRPMD predicts a strong blue shift in the NH-stretch region and a smaller one in the CH-stretch region. We explain this behavior by analyzing the modulation of the effective potential with temperature, which arises from vibrational coupling between quasi-classical thermally activated modes and high-frequency quantized modes. © 2019 Royal Society of Chemistry. All rights reserved.view abstract doi: 10.1039/c9fd00056a 2019 • 220 The interaction between grain boundary and tool geometry in nanocutting of a bi-crystal copper
Wang, Z. and Sun, T. and Zhang, H. and Li, G. and Li, Z. and Zhang, J. and Yan, Y. and Hartmaier, A.
International Journal of Extreme Manufacturing 1 (2019)Anisotropy is one central influencing factor on achievable ultimate machined surface integrity of metallic materials. Specifically, grain boundary has a strong impact on the deformation behaviour of polycrystalline materials and correlated material removal at the microscale. In the present work, we perform molecular dynamics simulations and experiments to elucidate the underlying grain boundary-associated mechanisms and their correlations with machining results of a bi-crystal Cu under nanocutting using a Berkovich tool. Specifically, crystallographic orientations of simulated bi-crystal Cu with a misorientation angle of 44.1° are derived from electron backscatter diffraction characterization of utilized polycrystalline copper specimen. Simulation results reveal that blocking of dislocation motion at grain boundaries, absorption of dislocations by grain boundaries and dislocation nucleation from grain boundaries are operating deformation modes in nanocutting of the bi-crystal Cu. Furthermore, heterogeneous grain boundary-associated mechanisms in neighbouring grains lead to strong anisotropic machining behaviour in the vicinity of the grain boundary. Simulated machined surface morphology and machining force evolution in the vicinity of grain boundary qualitatively agree well with experimental results. It is also found that the geometry of Berkovich tool has a strong impact on grain boundary-associated mechanisms and resultant ploughing-induced surface pile-up phenomenon. © 2019 The Author(s). Published by IOP Publishing Ltd on behalf of the IMMTview abstract doi: 10.1088/2631-7990/ab4b68 2019 • 219 Thermodynamic Activity-Based Solvent Design for Bioreactions
Wangler, A. and Held, C. and Sadowski, G.
Trends in Biotechnology 37 1038-1041 (2019)To improve the kinetics of enzyme-catalyzed reactions, cosolvents are commonly added to reaction mixtures. The search for a good cosolvent is still empirical and experimentally based. We discuss a thermodynamic activity-based approach that improves biocatalytic processes by predicting cosolvent influences on Michaelis constants, ultimately reducing time and cost. © 2019 Elsevier Ltdview abstract doi: 10.1016/j.tibtech.2019.04.015 2019 • 218 Thermophysical properties of glyceline-water mixtures investigated by molecular modelling
Baz, J. and Held, C. and Pleiss, J. and Hansen, N.
Physical Chemistry Chemical Physics 21 6467-6476 (2019)The effect of water content on the static and dynamic properties of the deep eutectic solvent glyceline is studied using molecular dynamics (MD) simulations. Static properties are additionally calculated using the PC-SAFT equation of state. Force fields calibrated on water-free glyceline show predictive power for density and water activity over the entire composition range. In contrast, the PC-SAFT approach using pseudo one-component or two-component modelling strategies performed better for the density or the water activity, respectively. The MD simulations show that at low water content, the hydrogen-bond network between glycerol molecules as well as between glycerol and the cholinium cation is hardly affected by the water molecules while at higher water content, glycerol-glycerol hydrogen bonds are replaced by glycerol-water hydrogen bonds indicating the formation of an aqueous solution accompanied by a strong decrease of the shear viscosity. At the same time, the thermodynamic activity of water increases such that the MD simulations are able to guide the optimal composition with respect to requirements in biocatalytic applications such as low viscosity and low water activity. The combined application of PC-SAFT to efficiently predict static properties and molecular dynamics simulations to predict static and dynamic properties offers a powerful framework in solvent design applications. © 2019 the Owner Societies.view abstract doi: 10.1039/c9cp00036d 2019 • 217 Ti and its alloys as examples of cryogenic focused ion beam milling of environmentally-sensitive materials
Chang, Y. and Lu, W. and Guénolé, J. and Stephenson, L.T. and Szczpaniak, A. and Kontis, P. and Ackerman, A.K. and Dear, F.F. and Mouton, I. and Zhong, X. and Zhang, S. and Dye, D. and Liebscher, C.H. and Ponge, D. and Korte-Ker...
Nature Communications 10 (2019)Hydrogen pick-up leading to hydride formation is often observed in commercially pure Ti (CP-Ti) and Ti-based alloys prepared for microscopic observation by conventional methods, such as electro-polishing and room temperature focused ion beam (FIB) milling. Here, we demonstrate that cryogenic FIB milling can effectively prevent undesired hydrogen pick-up. Specimens of CP-Ti and a Ti dual-phase alloy (Ti-6Al-2Sn-4Zr-6Mo, Ti6246, in wt.%) were prepared using a xenon-plasma FIB microscope equipped with a cryogenic stage reaching −135 °C. Transmission electron microscopy (TEM), selected area electron diffraction, and scanning TEM indicated no hydride formation in cryo-milled CP-Ti lamellae. Atom probe tomography further demonstrated that cryo-FIB significantly reduces hydrogen levels within the Ti6246 matrix compared with conventional methods. Supported by molecular dynamics simulations, we show that significantly lowering the thermal activation for H diffusion inhibits undesired environmental hydrogen pick-up during preparation and prevents pre-charged hydrogen from diffusing out of the sample, allowing for hydrogen embrittlement mechanisms of Ti-based alloys to be investigated at the nanoscale. © 2019, The Author(s).view abstract doi: 10.1038/s41467-019-08752-7 2019 • 216 TiN film growth on misoriented TiN grains with simultaneous low-energy bombardment: Restructuring leading to epitaxy
Edström, D. and Sangiovanni, D.G. and Hultman, L. and Petrov, I. and Greene, J.E. and Chirita, V.
Thin Solid Films 688 (2019)We perform large-scale molecular dynamics simulations of TiN deposition at 1200 K on TiN substrates consisting of under-stoichiometric (N/Ti = 0.86) misoriented grains. The energy of incoming Ti atoms is 2 eV and that of incoming N atoms is 10 eV. The simulations show that misoriented grains are reoriented during the early stages of growth, after which the film grows 001 epitaxially and is nearly stoichiometric. The grain reorientation coincides with an increase in film N/Ti ratio. As the grains reorient, additional nitrogen can no longer be accommodated, and the film composition becomes stoichiometric as the overlayer grows epitaxially. © 2019 Elsevier B.V.view abstract doi: 10.1016/j.tsf.2019.06.030 2019 • 215 Tuning the Electric Field Response of MOFs by Rotatable Dipolar Linkers
Dürholt, J.P. and Jahromi, B.F. and Schmid, R.
ACS Central Science 5 1440-1448 (2019)Recently the possibility of using electric fields as a further stimulus to trigger structural changes in metal-organic frameworks (MOFs) has been investigated. In general, rotatable groups or other types of mechanical motion can be driven by electric fields. In this study we demonstrate how the electric response of MOFs can be tuned by adding rotatable dipolar linkers, generating a material that exhibits paraelectric behavior in two dimensions and dielectric behavior in one dimension. The suitability of four different methods to compute the relative permittivity κ by means of molecular dynamics simulations was validated. The dependency of the permittivity on temperature T and dipole strength μ was determined. It was found that the herein investigated systems exhibit a high degree of tunability and substantially larger dielectric constants as expected for MOFs in general. The temperature dependency of κ obeys the Curie-Weiss law. In addition, the influence of dipolar linkers on the electric field induced breathing behavior was investigated. With increasing dipole moment, lower field strengths are required to trigger the contraction. These investigations set the stage for an application of such systems as dielectric sensors, order-disorder ferroelectrics, or any scenario where movable dipolar fragments respond to external electric fields. Copyright © 2019 American Chemical Society.view abstract doi: 10.1021/acscentsci.9b00497 2018 • 214 A Multiperspective Approach to Solvent Regulation of Enzymatic Activity: HMG-CoA Reductase
Dirkmann, M. and Iglesias-Fernández, J. and Muñoz, V. and Sokkar, P. and Rumancev, C. and von Gundlach, A. and Krenczyk, O. and Vöpel, T. and Nowack, J. and Schroer, M.A. and Ebbinghaus, S. and Herrmann, C. and Rosenhahn, A. an...
ChemBioChem 19 153-158 (2018)3-Hydroxy-3-methylglutaryl–coenzyme A (HMG-CoA) reductase was investigated in different organic cosolvents by means of kinetic and calorimetric measurements, molecular dynamics simulations, and small-angle X-ray scattering. The combined experimental and theoretical techniques were essential to complement each other's limitations in the investigation of the complex interaction pattern between the enzyme, different solvent types, and concentrations. In this way, the underlying mechanisms for the loss of enzyme activity in different water-miscible solvents could be elucidated. These include direct inhibitory effects onto the active center and structural distortions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheimview abstract doi: 10.1002/cbic.201700596 2018 • 213 A set-up for simultaneous measurement of second harmonic generation and streaming potential and some test applications
Lützenkirchen, J. and Scharnweber, T. and Ho, T. and Striolo, A. and Sulpizi, M. and Abdelmonem, A.
Journal of Colloid and Interface Science 529 294-305 (2018)We present a measurement cell that allows simultaneous measurement of second harmonic generation (SHG) and streaming potential (SP) at mineral-water interfaces with flat specimen that are suitable for non-linear optical (NLO) studies. The set-up directly yields SHG data for the interface of interest and can also be used to obtain information concerning the influence of flow on NLO signals from that interface. The streaming potential is at present measured against a reference substrate (PTFE). The properties of this inert reference can be independently determined for the same conditions. With the new cell, for the first time the SHG signal and the SP for flat surfaces have been simultaneously measured on the same surface. This can in turn be used to unambiguously relate the two observations for identical solution composition. The SHG test of the cell with a fluorite sample confirmed previously observed differences in NLO signal under flow vs. no flow conditions in sum frequency generation (SFG) investigations. As a second test surface, an inert (“hydrophobic”) OTS covered sapphire-c electrolyte interface was studied to verify the zeta-potential measurements with the new cell. For this system we obtained combined zeta-potential/SHG data in the vicinity of the point of zero charge, which were found to be proportional to each other as expected. Furthermore, on the accessible time scales of the SHG measurements no effects of flow, flow velocity and stopped flow occurred on the interfacial water structure. This insensitivity to flow for the inert surface was corroborated by concomitant molecular dynamics simulations. Finally, the set-up was used for simultaneous measurements of the two properties as a function of pH in automated titrations with an oxidic surface. Different polarization combinations obtained in two separate titrations, yielded clearly different SHG data, while under identical conditions zeta-potentials were exactly reproduced. The polarization combination that is characteristic for dipoles perpendicular to the surface scaled with the zeta-potentials over the pH-range studied, while the other did not. The work provides an advanced approach for investigating liquid/surface interactions which play a major role in our environment. The set-up can be upgraded for SFG studies, which will allow more detailed studies on the chemistry and the water structure at a given interface, but also the combined study of specific adsorption including kinetics in combination with electrokinetics. Such investigations are crucial for the basic understanding of many environmental processes from aquatic to atmospheric systems. © 2018 Elsevier Inc.view abstract doi: 10.1016/j.jcis.2018.06.017 2018 • 212 Analysis of Energy Dissipation Channels in a Benchmark System of Activated Dissociation: N2 on Ru(0001)
Shakouri, K. and Behler, J. and Meyer, J. and Kroes, G.-J.
Journal of Physical Chemistry C 122 23470-23480 (2018)The excitation of electron-hole pairs in reactive scattering of molecules at metal surfaces often affects the physical and dynamical observables of interest, including the reaction probability. Here, we study the influence of electron-hole pair excitation on the dissociative chemisorption of N2 on Ru(0001) using the local density friction approximation method. The effect of surface atom motion has also been taken into account by a high-dimensional neural network potential. Our nonadiabatic molecular dynamics simulations with electronic friction show that the reaction of N2 is more strongly affected by the energy transfer to surface phonons than by the energy loss to electron-hole pairs. The discrepancy between the computed reaction probabilities and experimental results is within the experimental error both with and without friction; however, the incorporation of electron-hole pairs yields somewhat better agreement with experiments, especially at high collision energies. We also calculate the vibrational efficacy for the N2 + Ru(0001) reaction and demonstrate that the N2 reaction is more enhanced by exciting the molecular vibrations than by adding an equivalent amount of energy into translation. © 2018 American Chemical Society.view abstract doi: 10.1021/acs.jpcc.8b06729 2018 • 211 Anomalous Phonon Lifetime Shortening in Paramagnetic CrN Caused by Spin-Lattice Coupling: A Combined Spin and Ab Initio Molecular Dynamics Study
Stockem, I. and Bergman, A. and Glensk, A. and Hickel, T. and Körmann, F. and Grabowski, B. and Neugebauer, J. and Alling, B.
Physical Review Letters 121 (2018)We study the mutual coupling of spin fluctuations and lattice vibrations in paramagnetic CrN by combining atomistic spin dynamics and ab initio molecular dynamics. The two degrees of freedom are dynamically coupled, leading to nonadiabatic effects. Those effects suppress the phonon lifetimes at low temperature compared to an adiabatic approach. The dynamic coupling identified here provides an explanation for the experimentally observed unexpected temperature dependence of the thermal conductivity of magnetic semiconductors above the magnetic ordering temperature. © 2018 American Physical Society.view abstract doi: 10.1103/PhysRevLett.121.125902 2018 • 210 Atypical titration curves for GaAl12 Keggin-ions explained by a joint experimental and simulation approach
Sulpizi, M. and Lützenkirchen, J.
Journal of Chemical Physics 148 (2018)Although they have been widely used as models for oxide surfaces, the deprotonation behaviors of the Keggin-ions (MeAl127+) and typical oxide surfaces are very different. On Keggin-ions, the deprotonation occurs over a very narrow pH range at odds with the broad charging curve of larger oxide surfaces. Depending on the Me concentration, the deprotonation curve levels off sooner (high Me concentration) or later (for low Me concentration). The leveling off shows the onset of aggregation before which the Keggin-ions are present as individual units. We show that the atypical titration data previously observed for some GaAl12 solutions in comparison to the originally reported data can be explained by the presence of Ga2Al11 ions. The pKa value of aquo-groups bound to octahedral Ga was determined from ab initio molecular dynamics simulations relative to the pure GaAl12 ions. Using these results within a surface complexation model, the onset of deprotonation of the crude solution is surprisingly well predicted and the ratio between the different species is estimated to be in the proportion 20 (Ga2Al11): 20 (Al13): 60 (GaAl12). © 2018 Author(s).view abstract doi: 10.1063/1.5024201 2018 • 209 Coherent transfer of electron spin correlations assisted by dephasing noise
Nakajima, T. and Delbecq, M.R. and Otsuka, T. and Amaha, S. and Yoneda, J. and Noiri, A. and Takeda, K. and Allison, G. and Ludwig, Ar. and Wieck, A.D. and Hu, X. and Nori, F. and Tarucha, S.
Nature Communications 9 (2018)Quantum coherence of superposed states, especially of entangled states, is indispensable for many quantum technologies. However, it is vulnerable to environmental noises, posing a fundamental challenge in solid-state systems including spin qubits. Here we show a scheme of entanglement engineering where pure dephasing assists the generation of quantum entanglement at distant sites in a chain of electron spins confined in semiconductor quantum dots. One party of an entangled spin pair, prepared at a single site, is transferred to the next site and then adiabatically swapped with a third spin using a transition across a multi-level avoided crossing. This process is accelerated by the noise-induced dephasing through a variant of the quantum Zeno effect, without sacrificing the coherence of the entangled state. Our finding brings insight into the spin dynamics in open quantum systems coupled to noisy environments, opening an avenue to quantum state manipulation utilizing decoherence effects. © 2018 The Author(s).view abstract doi: 10.1038/s41467-018-04544-7 2018 • 208 Copper adatom, admolecule transport, and island nucleation on TiN(0 0 1) via ab initio molecular dynamics
Sangiovanni, D.G.
Applied Surface Science 450 180-189 (2018)Density-functional ab initio molecular dynamics (AIMD) simulations are carried out to determine Cu adatom and admolecule transport properties as a function of temperature, as well as atomistic processes leading to formation of Cu/TiN(0 0 1) islands at 350 K. At very low temperatures T ≤ 200 K, Cu adatoms (Cuad) migrate among favored fourfold-hollow surface sites by passing across atop-Ti metastable positions. For increasing temperatures, however, Cuad transport becomes progressively more isotropic, and switches continuously from normal- to super-diffusive with mean-square displacement dependencies on time that alternate between linear and exponential. Despite that, the Cuad diffusivity D can be expressed by a fairly Arrhenius-like behavior D(T) = 8.26(×2±1) × 10−4 cm2 s−1 exp[(−0.04 ± 0.01 eV)/(kBT)] over the entire investigated temperature range (100 ≤ T ≤ 1000 K). AIMD simulations also reveal that the condensation of Cu adatoms into Cux>1 adspecies is kinetically hindered by long-range (>5.5 Å) adatom/adatom repulsion. During Cu island nucleation, all Cu atoms occupy atop-N positions indicating favored Cu(0 0 1)/TiN(0 0 1) epitaxial growth. Nevertheless, Cu agglomerates formed by five, or more, atoms tend to arrange in 3D structures, which maximize intracluster bonds while minimizing film/substrate interactions. Results here presented provide insights for understanding the properties of weakly-interacting metal/substrate interface systems in general. © 2018 Elsevier B.V.view abstract doi: 10.1016/j.apsusc.2018.04.191 2018 • 207 Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases
Duan, J. and Senger, M. and Esselborn, J. and Engelbrecht, V. and Wittkamp, F. and Apfel, U.-P. and Hofmann, E. and Stripp, S.T. and Happe, T. and Winkler, M.
Nature Communications 9 (2018)The unmatched catalytic turnover rates of [FeFe]-hydrogenases require an exceptionally efficient proton-transfer (PT) pathway to shuttle protons as substrates or products between bulk water and catalytic center. For clostridial [FeFe]-hydrogenase CpI such a pathway has been proposed and analyzed, but mainly on a theoretical basis. Here, eleven enzyme variants of two different [FeFe]-hydrogenases (CpI and HydA1) with substitutions in the presumptive PT-pathway are examined kinetically, spectroscopically, and crystallographically to provide solid experimental proof for its role in hydrogen-turnover. Targeting key residues of the PT-pathway by site directed mutagenesis significantly alters the pH-activity profile of these variants and in presence of H2 their cofactor is trapped in an intermediate state indicative of precluded proton-transfer. Furthermore, crystal structures coherently explain the individual levels of residual activity, demonstrating e.g. how trapped H2O molecules rescue the interrupted PT-pathway. These features provide conclusive evidence that the targeted positions are indeed vital for catalytic proton-transfer. © 2018, The Author(s).view abstract doi: 10.1038/s41467-018-07140-x 2018 • 206 Density anomaly of water at negative pressures from first principles
Singraber, A. and Morawietz, T. and Behler, J. and Dellago, C.
Journal of Physics Condensed Matter 30 (2018)Using molecular dynamics simulations based on ab initio trained high-dimensional neural network potentials, we study the equation of state of liquid water at negative pressures. From density isobars computed for various pressures down to p = -230 MPa we determine the line of density maxima for two potentials based on the BLYP and the RPBE functionals, respectively. In both cases, dispersion corrections are included to account for non-local long-range correlations that give rise to van der Waals forces. We have followed the density maximum down to negative pressures close to the spinodal instability. For both functionals, the temperature of maximum density increases with decreasing pressure under moderate stretching, but changes slope at P ≈ -200 MPa and p ≈ -20 MPa for BLYP and RPBE, respectively. Our calculations confirm qualitatively the retracing shape of the line of density maxima found for empirical water models, indicating that the spinodal line maintains a positive slope even at strongly negative pressures. © 2018 IOP Publishing Ltd.view abstract doi: 10.1088/1361-648X/aac4f4 2018 • 205 Dynamical heterogeneities of rotational motion in room temperature ionic liquids evidenced by molecular dynamics simulations
Usui, K. and Hunger, J. and Bonn, M. and Sulpizi, M.
Journal of Chemical Physics 148 (2018)Room temperature ionic liquids (RTILs) have been shown to exhibit spatial heterogeneity or structural heterogeneity in the sense that they form hydrophobic and ionic domains. Yet studies of the relationship between this structural heterogeneity and the ∼picosecond motion of the molecular constituents remain limited. In order to obtain insight into the time scales relevant to this structural heterogeneity, we perform molecular dynamics simulations of a series of RTILs. To investigate the relationship between the structures, i.e., the presence of hydrophobic and ionic domains, and the dynamics, we gradually increase the size of the hydrophobic part of the cation from ethylammonium nitrate (EAN), via propylammonium nitrate (PAN), to butylammonium nitrate (BAN). The two ends of the organic cation, namely, the charged Nhead-H group and the hydrophobic Ctail-H group, exhibit rotational dynamics on different time scales, evidencing dynamical heterogeneity. The dynamics of the Nhead-H group is slower because of the strong coulombic interaction with the nitrate counter-ionic anions, while the dynamics of the Ctail-H group is faster because of the weaker van der Waals interaction with the surrounding atoms. In particular, the rotation of the Nhead-H group slows down with increasing cationic chain length, while the rotation of the Ctail-H group shows little dependence on the cationic chain length, manifesting that the dynamical heterogeneity is enhanced with a longer cationic chain. The slowdown of the Nhead-H group with increasing cationic chain length is associated with a lower number of nitrate anions near the Nhead-H group, which presumably results in the increase of the energy barrier for the rotation. The sensitivity of the Nhead-H rotation to the number of surrounding nitrate anions, in conjunction with the varying number of nitrate anions, gives rise to a broad distribution of Nhead-H reorientation times. Our results suggest that the asymmetry of the cations and the larger excluded volume for longer cationic chain are important for both the structural heterogeneity and the dynamical heterogeneities. The observed dynamical heterogeneities may affect the rates of chemical reactions depending on where the reactants are solvated in ionic liquids and provide an additional guideline for the design of RTILs as solvents. © 2018 Author(s).view abstract doi: 10.1063/1.5005143 2018 • 204 Generation of Frenkel defects above the Debye temperature by proliferation of phonons near the Brillouin zone edge
Jongmanns, M. and Raj, R. and Wolf, D.E.
New Journal of Physics 20 (2018)A novel, non-radiative mechanism is reported by which Frenkel pairs of vacancies and interstitials are generated in molar concentrations far above thermal equilibrium. This mechanism is demonstrated in molecular dynamics (MD) simulations of an aluminum single crystal with a free surface. They suggest that three conditions must be fulfilled: (i) lattice vibrations near the Brillouin zone edge are being excited, (ii) these vibrations proliferate at a sufficiently high rate, and (iii) the sample temperature is above the Debye temperature (but significantly below the melting point). The simulations employed an EAM potential for Al. We attempt to draw a confluence between our MD simulations and recent experiments on flash sintering of aluminum. The simulation results are also consistent with flash experiments on polycrystals and single crystals of zirconium and titanium oxides where the Debye temperature was discovered to be the lower limit for the onset of the flash. © 2018 The Author(s). Published by IOP Publishing Ltd on behalf of Deutsche Physikalische Gesellschaft.view abstract doi: 10.1088/1367-2630/aadd5a 2018 • 203 Increased Acid Dissociation at the Quartz/Water Interface
Parashar, S. and Lesnicki, D. and Sulpizi, M.
Journal of Physical Chemistry Letters 9 2186-2189 (2018)As shown by a quite significant amount of literature, acids at the water surface tend to be "less" acid, meaning that their associated form is favored over the conjugated base. What happens at the solid/liquid interface? In the case of the silica/water interface, we show how the acidity of adsorbed molecules can instead increase. Using a free energy perturbation approach in combination with electronic structure-based molecular dynamics simulations, we show how the acidity of pyruvic acid at the quartz/water interface is increased by almost two units. Such increased acidity is the result of the specific microsolvation at the interface and, in particular, of the stabilization of the deprotonated form by the silanols on the quartz surface and the special interfacial water layer. © 2018 American Chemical Society.view abstract doi: 10.1021/acs.jpclett.8b00686 2018 • 202 Influence of Chain Length and Branching on the Structure of Functionalized Gold Nanoparticles
Giri, A.K. and Spohr, E.
Journal of Physical Chemistry C 122 26739-26747 (2018)Functionalized gold nanoparticles (GNPs) in aqueous NaCl solutions have been studied using molecular dynamics simulations to assess the suitability of various functionalization chemistries to effectively shield the metallic core. Alkane thiol chains of various chain length (Cl) containing 6, 12, 18, and 24 carbon atoms are grafted onto the surface of the gold core. We compare the properties of GNPs functionalized with nonpolar CH3-terminated and polar COO-- and NH3 +-terminated chains, where the nanoparticle charge is compensated by appropriate numbers of excess Na+ or Cl- counterions. In addition to linear chains, we also investigate branched Y-shaped chains with the branching sites at the 4th, 8th, or 12th carbon atom from the sulfur atom that connects the chain to the gold core. The penetration depth of water and ions into the diffuse hydrocarbon shell region and its dependence on chain length, branching, and terminating group is found to increase with decreasing chain length irrespective of termination. Long linear chains, however, tend to form bundles independent of terminal group and can thus leave fractions of the nanoparticle surface exposed to small molecules, whereas shorter and branched chains do not form bundles and can cover the GNPs more homogeneously. © 2018 American Chemical Society.view abstract doi: 10.1021/acs.jpcc.8b08590 2018 • 201 Inherent toughness and fracture mechanisms of refractory transition-metal nitrides via density-functional molecular dynamics
Sangiovanni, D.G.
Acta Materialia 151 11-20 (2018)Hard refractory transition-metal nitrides possess unique combinations of outstanding mechanical and physical properties, but are typically brittle. Recent experimental results demonstrated that single-crystal NaCl-structure (B1) V0.5Mo0.5N pseudobinary solid solutions are both hard (∼20 GPa) and ductile; that is, they exhibit toughness, which is unusual for ceramics. However, key atomic-scale mechanisms underlying this inherent toughness are unknown. Here, I carry out density-functional ab initio molecular dynamics (AIMD) simulations at room temperature to identify atomistic processes and associated changes in the electronic structure which control strength, plasticity, and fracture in V0.5Mo0.5N, as well as reference B1 TiN, subject to <001> and <110> tensile deformation. AIMD simulations reveal that V0.5Mo0.5N is considerably tougher than TiN owing to its ability to (i) isotropically redistribute mechanical stresses within the elastic regime, (ii) dissipate the accumulated strain energy by activating local structural transformations beyond the yield point. In direct contrast, TiN breaks in brittle manner when applied stresses reach its tensile strength. Charge transfer maps show that the adaptive mechanical response of V0.5Mo0.5N originates from highly populated d-d metallic-states, which allow for counterbalancing the destabilization induced via tensile deformation by enabling formation of new chemical bonds. The high ionic character and electron-localization in TiN precludes the possibility of modifying bonding geometries to accommodate the accumulated stresses, thus suddenly causing material's fracture for relatively low strain values. © 2018 Acta Materialia Inc.view abstract doi: 10.1016/j.actamat.2018.03.038 2018 • 200 Locating Large, Flexible Ligands on Proteins
Grad, J.-N. and Gigante, A. and Wilms, C. and Dybowski, J.N. and Ohl, L. and Ottmann, C. and Schmuck, C. and Hoffmann, D.
Journal of Chemical Information and Modeling 58 315-327 (2018)Many biologically important ligands of proteins are large, flexible, and in many cases charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods such as docking or molecular dynamics (MD) simulation. The alternative approach proposed here is scanning of a spatial and angular grid around the protein with smaller fragments of the large ligand. Energy values for complete grids can be computed efficiently with a well-known fast Fourier transform-accelerated algorithm and a physically meaningful interaction model. We show that the approach can readily incorporate flexibility of the protein and ligand. The energy grids (EGs) resulting from the ligand fragment scans can be transformed into probability distributions and then directly compared to probability distributions estimated from MD simulations and experimental structural data. We test the approach on a diverse set of complexes between proteins and large, flexible ligands, including a complex of sonic hedgehog protein and heparin, three heparin sulfate substrates or nonsubstrates of an epimerase, a multibranched supramolecular ligand that stabilizes a protein-peptide complex, a flexible zwitterionic ligand that binds to a surface basin of a Kringle domain, and binding of ATP to a flexible site of an ion channel. In all cases, the EG approach gives results that are in good agreement with experimental data or MD simulations. © 2017 American Chemical Society.view abstract doi: 10.1021/acs.jcim.7b00413 2018 • 199 Maximally resolved anharmonic OH vibrational spectrum of the water/ZnO(10 1 0) interface from a high-dimensional neural network potential
Quaranta, V. and Hellström, M. and Behler, J. and Kullgren, J. and Mitev, P.D. and Hermansson, K.
Journal of Chemical Physics 148 (2018)Unraveling the atomistic details of solid/liquid interfaces, e.g., by means of vibrational spectroscopy, is of vital importance in numerous applications, from electrochemistry to heterogeneous catalysis. Water-oxide interfaces represent a formidable challenge because a large variety of molecular and dissociated water species are present at the surface. Here, we present a comprehensive theoretical analysis of the anharmonic OH stretching vibrations at the water/ZnO(1010) interface as a prototypical case. Molecular dynamics simulations employing a reactive high-dimensional neural network potential based on density functional theory calculations have been used to sample the interfacial structures. In the second step, one-dimensional potential energy curves have been generated for a large number of configurations to solve the nuclear Schrödinger equation. We find that (i) the ZnO surface gives rise to OH frequency shifts up to a distance of about 4 Å from the surface; (ii) the spectrum contains a number of overlapping signals arising from different chemical species, with the frequencies decreasing in the order ν(adsorbed hydroxide) > ν(non-adsorbed water) > ν(surface hydroxide) > ν(adsorbed water); (iii) stretching frequencies are strongly influenced by the hydrogen bond pattern of these interfacial species. Finally, we have been able to identify substantial correlations between the stretching frequencies and hydrogen bond lengths for all species. © 2018 Author(s).view abstract doi: 10.1063/1.5012980 2018 • 198 Molecular Dynamics Investigation of the Dielectric Decrement of Ion Solutions
Pache, D. and Schmid, R.
ChemElectroChem 5 1444-1450 (2018)Molecular dynamics simulations, using a classical force field model, have been used to determine the dependence of the static relative dielectric constant of ion solutions with respect to the nature and concentration of the ions and the field strength. The experimentally observed effect of a reduction of the dielectric permittivity due to solvated ions is known as dielectric decrement. We used both the polarization fluctuation at zero field and the constant dielectric displacement method for finite fields to determine the dielectric constant of the bulk solution. All the experimentally observed tendencies of the dielectric decrement could be qualitatively reproduced. The analysis of different solute solvent radial distribution functions indicate that the dielectric decrement arises from the competition between the macroscopic electric field and the local water-ion interaction. The results suggest that the electric field eventually manages to overcome the local molecular interactions, breaking up the structure of the solvation shell and thus lowering the ion's effect on the dielectric constant. This effect seems to correlate with the solvation energy of the individual ions as well as the type of counter ion, indicating that also long range interactions might play a role. The results can be used to improve especially continuum electrolyte models, used to study electrochemical interfaces, where currently the dielectric decrement is generally not included. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheimview abstract doi: 10.1002/celc.201800158 2018 • 197 Molecular dynamics simulation of silicon ion implantation into diamond and subsequent annealing
Fu, X. and Xu, Z. and He, Z. and Hartmaier, A. and Fang, F.
Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms (2018)Ion implantation is one of the best methods to manufacture silicon-vacancy (SiV) centers in diamond, which can be used as qubits. In this work, molecular dynamics (MD) simulation was conducted to analyze the damage evolution and distribution during the process of silicon ion implantation into bulk diamond and subsequent annealing. Tersoff-ZBL (Ziegler-Biersack-Littmark) potential was used to describe the atomic interaction. Identify Diamond Structure (IDS) and Wigner-Seitz defect analysis methods were used to calculate damages and vacancies. After 2393 K annealing, about 42.5% of ion induced IDS damages were recovered. During the temperature cooling down from 2393 K to 293 K, the movements of silicon atoms along the implantation direction were sensitive to the temperature variation, while vacancies were almost insensitive. MD simulation is helpful to illustrate the ion implant induced damages’ dynamic evolution and Si-V related defects, which can assist a deeper understanding of SiV center's manufacturing. © 2018 Elsevier B.V.view abstract doi: 10.1016/j.nimb.2018.04.027 2018 • 196 Molecular recognition of carboxylates in the protein leucine zipper by a multivalent supramolecular ligand: Residue-specific, sensitive and label-free probing by UV resonance Raman spectroscopy
Zakeri, B. and Niebling, S. and Martinéz, A.G. and Sokkar, P. and Sanchez-Garcia, E. and Schmuck, C. and Schlücker, S.
Physical Chemistry Chemical Physics 20 1817-1820 (2018)Ultraviolet resonance Raman (UVRR) spectroscopy is a selective, sensitive and label-free vibrational spectroscopic technique. Here, we demonstrate as proof of concept that UVRR can be used for probing the recognition between a multivalent supramolecular ligand and acidic residues in leucine zipper, an α-helical structural motif of many proteins. © 2017 Owner Societies.view abstract doi: 10.1039/c7cp04971d 2018 • 195 Norbornane-based cationic antimicrobial peptidomimetics targeting the bacterial membrane
Hickey, S.M. and Ashton, T.D. and Boer, G. and Bader, C.A. and Thomas, M. and Elliott, A.G. and Schmuck, C. and Yu, H.Y. and Li, J. and Nation, R.L. and Cooper, M.A. and Plush, S.E. and Brooks, D.A. and Pfeffer, F.M.
European Journal of Medicinal Chemistry 160 9-22 (2018)The design, synthesis and evaluation of a small series of potent amphiphilic norbornane antibacterial agents has been performed (compound 10 MIC = 0.25 μg/mL against MRSA). Molecular modelling indicates rapid aggregation of this class of antibacterial agent prior to membrane association and insertion. Two fluorescent analogues (compound 29 with 4-amino-naphthalimide and 34 with 4-nitrobenz-2-oxa-1,3-diazole fluorophores) with good activity (MIC = 0.5 μg/mL against MRSA) were also constructed and confocal microscopy studies indicate that the primary site of interaction for this family of compounds is the bacterial membrane. © 2018 Elsevier Masson SASview abstract doi: 10.1016/j.ejmech.2018.09.072 2018 • 194 Nuclear Quantum Effects in Sodium Hydroxide Solutions from Neural Network Molecular Dynamics Simulations
Hellström, M. and Ceriotti, M. and Behler, J.
Journal of Physical Chemistry B 122 10158-10171 (2018)Nuclear quantum effects (NQEs) cause the nuclei of light elements like hydrogen to delocalize, affecting numerous properties of water and aqueous solutions, such as hydrogen-bonding and proton transfer barriers. Here, we address the prototypical case of aqueous NaOH solutions by investigating the effects of quantum nuclear fluctuations on radial distribution functions, hydrogen-bonding geometries, power spectra, proton transfer barriers, proton transfer rates, water self-exchange rates around the Na+ cations, and diffusion coefficients, for the full room-temperature solubility range. These properties were calculated from classical and ring-polymer molecular dynamics simulations employing a reactive high-dimensional neural network potential based on dispersion-corrected density functional theory reference calculations. We find that NQEs have a very small impact on the solvation structure around Na+, slightly strengthen the water-water and water-hydroxide hydrogen bonds, and lower the peak positions in the power spectra for the HOH bending and OH stretching modes by about 50 and 100 cm-1, respectively. Moreover, NQEs significantly lower the proton transfer barriers, thus increasing the proton transfer rates, resulting in an increase of the diffusion coefficient in particular of OH-, as well as a decrease of the mean residence time of molecules in the first hydration shell around Na+ at high NaOH concentrations. © 2018 American Chemical Society.view abstract doi: 10.1021/acs.jpcb.8b06433 2018 • 193 Parallelization comparison and optimization of a scale-bridging framework to model Cottrell atmospheres
Ganesan, H. and Teijeiro, C. and Sutmann, G.
Computational Materials Science 155 439-449 (2018)Low carbon steels undergo strain aging when heat treated, which causes an increased yield strength that can be observed macroscopically. Such strengthening mechanism is driven by atomistic scale processes, i.e., solute segregation of carbon (C) or nitrogen interstitial atoms. Due to its low solubility, alloying elements can diffuse to defects (e.g., dislocations) and form the so-called Cottrell atmospheres. Consequently, the mobility of defects is strongly reduced because of the interaction with solutes, and higher stresses are needed to unpin them from the Cottrell atmosphere. As C segregation and atomistic motion take place at separate timescales, Classical Molecular Dynamics (MD) and Metropolis Monte Carlo (MC) are coupled in a unified framework to capture collective effects with underlying slow dynamics. The number of degrees of freedom and the need for large computational resources in this simulation requires the choice of an optimal parallelization technique for the MC part of such multi-scale simulations using an unbiased sampling of the configuration space. In the present work, two different parallel approaches for the MC routine applied to the simulation of Cottrell atmospheres are implemented and compared: (i) a manager-worker speculative scheme and (ii) a distributed manager-worker over a cell-based domain decomposition approach augmented by an efficient load balancing scheme. The parallel performance of different Fe-C containing defects with several millions of atoms is analyzed, and also the possible optimization of the efficiency of the MC solute segregation process is evaluated regarding energy minimization. © 2018 Elsevier B.V.view abstract doi: 10.1016/j.commatsci.2018.08.055 2018 • 192 Phase nucleation through confined spinodal fluctuations at crystal defects evidenced in Fe-Mn alloys
Kwiatkowski Da Silva, A. and Ponge, D. and Peng, Z. and Inden, G. and Lu, Y. and Breen, A. and Gault, B. and Raabe, D.
Nature Communications 9 (2018)Analysis and design of materials and fluids requires understanding of the fundamental relationships between structure, composition, and properties. Dislocations and grain boundaries influence microstructure evolution through the enhancement of diffusion and by facilitating heterogeneous nucleation, where atoms must overcome a potential barrier to enable the early stage of formation of a phase. Adsorption and spinodal decomposition are known precursor states to nucleation and phase transition; however, nucleation remains the less well-understood step in the complete thermodynamic sequence that shapes a microstructure. Here, we report near-atomic-scale observations of a phase transition mechanism that consists in solute adsorption to crystalline defects followed by linear and planar spinodal fluctuations in an Fe-Mn model alloy. These fluctuations provide a pathway for austenite nucleation due to the higher driving force for phase transition in the solute-rich regions. Our observations are supported by thermodynamic calculations, which predict the possibility of spinodal decomposition due to magnetic ordering. © 2018 The Author(s).view abstract doi: 10.1038/s41467-018-03591-4 2018 • 191 Precipitation hardening effects on extension twinning in magnesium alloys
Fan, H. and Zhu, Y. and El-Awady, J.A. and Raabe, D.
International Journal of Plasticity 106 186-202 (2018)Precipitation is an efficient method to strengthen metallic materials. While precipitation hardening effects on dislocation slip have been studied extensively in the past, the influence of precipitates on twinning mediated plasticity and the development of corresponding hardening models that account for twin-precipitate interactions have received less attention. Here, the interaction of {10-12} extension twin boundaries (TBs) in pure magnesium with precipitates of plate-, sphere- and rod-like shapes is studied using molecular dynamics (MD) simulations. We find that TBs that engulf precipitates are absorbed by the precipitate-matrix interfaces, and the precipitates are neither twinned nor sheared but deform elastically leading to their rotation. TBs can pass small precipitates (length? 20 nm) and remain intact. In contrast when TBs are interacting with large precipitates (length? 50 nm), basal dislocations or stacking faults nucleate from the interfaces, causing local plastic relaxation. The stress field around a plate-like precipitate as calculated in the MD simulations suggests that a strong back-stress is imposed on the TBs. We then coarse grain these mechanisms into an analytical mean field model of precipitation hardening on twinning in magnesium alloys, which is based on the energy conservation during the TB-precipitate interaction. The model is in good agreement with the current MD simulations and published experimental observations. The hardening model shows that spherical precipitates have the strongest hardening effect on twinning, basal and prismatic plate-like precipitates have a medium effect while rod-like precipitates exert the weakest influence. We also find that most types of precipitates show a stronger hardening effect on twinning mediated plasticity than on basal dislocation slip. Finally, prismatic plate-like precipitates are predicted to have reasonable hardening effects on both twinning and basal slip. These results can help guiding the development of magnesium alloys with enhanced strength and ductility. © 2018 Elsevier Ltd.view abstract doi: 10.1016/j.ijplas.2018.03.008 2018 • 190 Sum frequency generation spectra from velocity-velocity correlation functions: New developments and applications
Rémi, K. and Marialore, S.
High Performance Computing in Science and Engineering' 17: Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2017 141-156 (2018)At the interface, the properties of water can be rather different from those observed in the bulk. In this chapter we present an overview of our computational approach to understand water structure and dynamics at the interface including atomistic and electronic structure details. In particular we show how Density Functional Theory-based molecular dynamics simulations (DFT-MD) of water interfaces can provide a microscopic interpretation of recent experimental results from surface sensitive vibrational Sum Frequency Generation spectroscopy (SFG). In our recent work we developed an expression for the calculation of the SFG spectra of water interfaces which is based on the projection of the atomic velocities on the local normal modes. Our approach permits to obtain the SFG signal from suitable velocity-velocity correlation functions, reducing the computational cost to that of the accumulation of a molecular dynamics trajectory, and therefore cutting the overhead costs associated to the explicit calculation of the dipole moment and polarizability tensor. Our method permits to interpret the peaks in the spectrum in terms of local modes, also including the bending region. The results for the water-air interface, obtained using extensive ab initio molecular dynamics simulations over 400 ns, are discussed in connection to recent phase resolved experimental data. © Springer International Publishing AG 2018.view abstract doi: 10.1007/978-3-319-68394-2_8 2018 • 189 Unravelling the GLY-PRO-GLU tripeptide induced reconstruction of the Au(110) surface at the molecular scale
Geada, I.L. and Petit, I. and Sulpizi, M. and Tielens, F.
Surface Science 677 271-277 (2018)The adsorption of GLY-PRO-GLU tripeptide on Au(110) is investigated within the frame of all atom classical mechanics simulations and Density Functional Theory, focusing on the surface reconstruction. It is shown that the tripeptide adsorption reorganizes and restructures the Au(110) surface. A mechanism for the surface restructuration is proposed for both the neutral and zwitterionic form of the peptide at room temperature in Ultra High Vacuum. Diverse residues may be involved in the Au atoms displacement, and in particular glutamic acid, triggering a double proton transfer and the formation of a zwitter ionic state, is found to be responsible for the triggering of the surface reconstruction. © 2018 Elsevier B.V.view abstract doi: 10.1016/j.susc.2018.07.006 2018 • 188 Water Adsorption on Clean and Defective Anatase TiO 2 (001) Nanotube Surfaces: A Surface Science Approach
Kenmoe, S. and Lisovski, O. and Piskunov, S. and Bocharov, D. and Zhukovskii, Y.F. and Spohr, E.
Journal of Physical Chemistry B 122 5432-5440 (2018)We use ab initio molecular dynamics simulations to study the adsorption of thin water films with 1 and 2 ML coverage on anatase TiO 2 (001) nanotubes. The nanotubes are modeled as 2D slabs, which consist of partially constrained and partially relaxed structural motifs from nanotubes. The effect of anion doping on the adsorption is investigated by substituting O atoms with N and S impurities on the nanotube slab surface. Due to strain-induced curvature effects, water adsorbs molecularly on defect-free surfaces via weak bonds on Ti sites and H bonds to surface oxygens. While the introduction of an S atom weakens the interaction of the surface with water, which adsorbs molecularly, the presence of an N impurity renders the surface more reactive to water, with a proton transfer from the water film and the formation of an NH group at the N site. At 2 ML coverage, a further surface-assisted proton transfer takes place in the water film, resulting in the formation of an OH - group and an NH2 + cationic site on the surface. © 2018 American Chemical Society.view abstract doi: 10.1021/acs.jpcb.7b11697 2018 • 187 Water Adsorption on Clean and Defective Anatase TiO2 (001) Nanotube Surfaces: A Surface Science Approach
Kenmoe, S. and Lisovski, O. and Piskunov, S. and Bocharov, D. and Zhukovskii, Y.F. and Spohr, E.
Journal of Physical Chemistry B 122 5432-5440 (2018)We use ab initio molecular dynamics simulations to study the adsorption of thin water films with 1 and 2 ML coverage on anatase TiO2 (001) nanotubes. The nanotubes are modeled as 2D slabs, which consist of partially constrained and partially relaxed structural motifs from nanotubes. The effect of anion doping on the adsorption is investigated by substituting O atoms with N and S impurities on the nanotube slab surface. Due to strain-induced curvature effects, water adsorbs molecularly on defect-free surfaces via weak bonds on Ti sites and H bonds to surface oxygens. While the introduction of an S atom weakens the interaction of the surface with water, which adsorbs molecularly, the presence of an N impurity renders the surface more reactive to water, with a proton transfer from the water film and the formation of an NH group at the N site. At 2 ML coverage, a further surface-assisted proton transfer takes place in the water film, resulting in the formation of an OH- group and an NH2+ cationic site on the surface. © 2018 American Chemical Society.view abstract doi: 10.1021/acs.jpcb.7b11697 2017 • 186 Accurate Neural Network Description of Surface Phonons in Reactive Gas-Surface Dynamics: N2 + Ru(0001)
Shakouri, K. and Behler, J. and Meyer, J. and Kroes, G.-J.
Journal of Physical Chemistry Letters 8 2131-2136 (2017)Ab initio molecular dynamics (AIMD) simulations enable the accurate description of reactive molecule-surface scattering especially if energy transfer involving surface phonons is important. However, presently, the computational expense of AIMD rules out its application to systems where reaction probabilities are smaller than about 1%. Here we show that this problem can be overcome by a high-dimensional neural network fit of the molecule-surface interaction potential, which also incorporates the dependence on phonons by taking into account all degrees of freedom of the surface explicitly. As shown for N2 + Ru(0001), which is a prototypical case for highly activated dissociative chemisorption, the method allows an accurate description of the coupling of molecular and surface atom motion and accurately accounts for vibrational properties of the employed slab model of Ru(0001). The neural network potential allows reaction probabilities as low as 10-5 to be computed, showing good agreement with experimental results. © 2017 American Chemical Society.view abstract doi: 10.1021/acs.jpclett.7b00784 2017 • 185 Antibodies under pressure: A Small-Angle X-ray Scattering study of Immunoglobulin G under high hydrostatic pressure
König, N. and Paulus, M. and Julius, K. and Schulze, J. and Voetz, M. and Tolan, M.
Biophysical Chemistry 231 45-49 (2017)In the present work two subclasses of the human antibody Immunoglobulin G (IgG) have been investigated by Small-Angle X-ray Scattering under high hydrostatic pressures up to 5kbar. It is shown that IgG adopts a symmetric T-shape in solution which differs significantly from available crystal structures. Moreover, high-pressure experiments verify the high stability of the IgG molecule. It is not unfolded by hydrostatic pressures of up to 5kbar but a slight increase of the radius of gyration was observed at elevated pressures. © 2017 Elsevier B.V.view abstract doi: 10.1016/j.bpc.2017.05.016 2017 • 184 Cluster formation of NaCl in bulk solutions: Arithmetic vs. geometric combination rules
Giri, A.K. and Spohr, E.
Journal of Molecular Liquids 228 63-70 (2017)We have investigated the usability of three common ionic force fields, the AMBER-99, the OPLS-AA and the CHARMM-27 parameter sets for simulation of intermediate concentration NaCl solutions. We have found that the Amber and Opls force fields produce NaCl crystallites at concentrations between 1 and 2 m, when used with arithmetic combination rules to derive the Lennard-Jones σij,i≠j parameters. When switching to a geometric rule to derive these parameters, the NaCl solubility improves somewhat, but crystallisation still occurs at higher electrolyte concentrations. On the other hand, when using the Charmm force field, we observe no signs of crystallisation up to 2.0 m already for the arithmetic combination rules. In addition to the simulations with these ‘well-tempered’ parameter sets we have also performed simulations, in which the combination rules were applied individually for cation–anion, cation–(water) oxygen and anion–oxygen pairs. The altogether eight different parameter sets that can be obtained from combining three interactions with two combination rules have revealed that the Cl −–oxygen interactions are the most sensitive quantity. When switching from arithmetic to geometric combination rules, the value of the size parameter σij,i≠j is always smaller than the corresponding one for arithmetic averaging, which gives rise to larger Coulomb and thus larger total interaction energies. As a consequence, applying geometric combination rules to the Cl −–oxygen interactions improves solubility, applying it to the Cl −–Na + interactions reduces solubility and increases crystallisation; because the sodium cations are usually quite strongly solvated, the effect of combination rules is small for the cation–oxygen interactions. © 2016 Elsevier B.V.view abstract doi: 10.1016/j.molliq.2016.09.089 2017 • 183 Creating nanoporous graphene with swift heavy ions
Vázquez, H. and Åhlgren, E.H. and Ochedowski, O. and Leino, A.A. and Mirzayev, R. and Kozubek, R. and Lebius, H. and Karlušic, M. and Jakšic, M. and Krasheninnikov, A.V. and Kotakoski, J. and Schleberger, M. and Nordlund, K. a...
Carbon 114 511-518 (2017)We examine swift heavy ion-induced defect production in suspended single layer graphene using Raman spectroscopy and a two temperature molecular dynamics model that couples the ionic and electronic subsystems. We show that an increase in the electronic stopping power of the ion results in an increase in the size of the pore-type defects, with a defect formation threshold at 1.22–1.48 keV/layer. We also report calculations of the specific electronic heat capacity of graphene with different chemical potentials and discuss the electronic thermal conductivity of graphene at high electronic temperatures, suggesting a value in the range of 1 Wm−1 K−1. These results indicate that swift heavy ions can create nanopores in graphene, and that their size can be tuned between 1 and 4 nm diameter by choosing a suitable stopping power. © 2016 Elsevier Ltdview abstract doi: 10.1016/j.carbon.2016.12.015 2017 • 182 Effects of incident N atom kinetic energy on TiN/TiN(001) film growth dynamics: A molecular dynamics investigation
Edström, D. and Sangiovanni, D.G. and Hultman, L. and Petrov, I. and Greene, J.E. and Chirita, V.
Journal of Applied Physics 121 (2017)Large-scale classical molecular dynamics simulations of epitaxial TiN/TiN(001) thin film growth at 1200 K, a temperature within the optimal range for epitaxial TiN growth, with an incident N-to-Ti flux ratio of four, are carried out using incident N energies EN = 2 and 10 eV and incident Ti energy ETi = 2 eV. To further highlight the effect of EN, we grow a bilayer film with EN = 2 eV initially and then switch to EN = 10 eV. As-deposited layers are analyzed as a function of composition, island-size distribution, island-edge orientation, and vacancy formation. Results show that growth with EN = 2 eV results in films that are globally overstoichiometric with islands bounded by N-terminated polar 110 edges, whereas films grown with EN = 10 eV are flatter and closer to stoichiometric. However, EN = 10 eV layers exhibit local N deficiency leading to the formation of isolated 111-oriented islands. Films grown by changing the incident energy from 2 to 10 eV during growth are more compact than those grown entirely with EN = 2 eV and exhibit greatly reduced concentrations of upper-layer adatoms, admolecules, and small clusters. Islands with 110 edges formed during growth with EN = 2 eV transform to islands with 100 edges as EN is switched to 10 eV. © 2017 Author(s).view abstract doi: 10.1063/1.4972963 2017 • 181 Enrichment of Cross-Linked Peptides Using Charge-Based Fractional Diagonal Chromatography (ChaFRADIC)
Tinnefeld, V. and Venne, A.S. and Sickmann, A. and Zahedi, R.P.
Journal of Proteome Research 16 459-469 (2017)Chemical cross-linking of proteins is an emerging field with huge potential for the structural investigation of proteins and protein complexes. Owing to the often relatively low yield of cross-linking products, their identification in complex samples benefits from enrichment procedures prior to mass spectrometry analysis. So far, this is mainly accomplished by using biotin moieties in specific cross-linkers or by applying strong cation exchange chromatography (SCX) for a relatively crude enrichment. We present a novel workflow to enrich cross-linked peptides by utilizing charge-based fractional diagonal chromatography (ChaFRADIC). On the basis of two-dimensional diagonal SCX separation, we could increase the number of identified cross-linked peptides for samples of different complexity: pure cross-linked BSA, cross-linked BSA spiked into a simple protein mixture, and cross-linked BSA spiked into a HeLa lysate. We also compared XL-ChaFRADIC with size exclusion chromatography-based enrichment of cross-linked peptides. The XL-ChaFRADIC approach is straightforward, reproducible, and independent of the cross-linking chemistry and cross-linker properties. © 2016 American Chemical Society.view abstract doi: 10.1021/acs.jproteome.6b00587 2017 • 180 First Principles Neural Network Potentials for Reactive Simulations of Large Molecular and Condensed Systems
Behler, J.
Angewandte Chemie - International Edition 56 12828-12840 (2017)Modern simulation techniques have reached a level of maturity which allows a wide range of problems in chemistry and materials science to be addressed. Unfortunately, the application of first principles methods with predictive power is still limited to rather small systems, and despite the rapid evolution of computer hardware no fundamental change in this situation can be expected. Consequently, the development of more efficient but equally reliable atomistic potentials to reach an atomic level understanding of complex systems has received considerable attention in recent years. A promising new development has been the introduction of machine learning (ML) methods to describe the atomic interactions. Once trained with electronic structure data, ML potentials can accelerate computer simulations by several orders of magnitude, while preserving quantum mechanical accuracy. This Review considers the methodology of an important class of ML potentials that employs artificial neural networks. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheimview abstract doi: 10.1002/anie.201703114 2017 • 179 Identification of Intrahelical Bifurcated H-Bonds as a New Type of Gate in K+ Channels
Rauh, O. and Urban, M. and Henkes, L.M. and Winterstein, T. and Greiner, T. and Van Etten, J.L. and Moroni, A. and Kast, S.M. and Thiel, G. and Schroeder, I.
Journal of the American Chemical Society 139 7494-7503 (2017)Gating of ion channels is based on structural transitions between open and closed states. To uncover the chemical basis of individual gates, we performed a comparative experimental and computational analysis between two K+ channels, KcvS and KcvNTS. These small viral encoded K+ channel proteins, with a monomer size of only 82 amino acids, resemble the pore module of all complex K+ channels in terms of structure and function. Even though both proteins share about 90% amino acid sequence identity, they exhibit different open probabilities with ca. 90% in KcvNTS and 40% in KcvS. Single channel analysis, mutational studies and molecular dynamics simulations show that the difference in open probability is caused by one long closed state in KcvS. This state is structurally created in the tetrameric channel by a transient, Ser mediated, intrahelical hydrogen bond. The resulting kink in the inner transmembrane domain swings the aromatic rings from downstream Phes in the cavity of the channel, which blocks ion flux. The frequent occurrence of Ser or Thr based helical kinks in membrane proteins suggests that a similar mechanism could also occur in the gating of other ion channels. © 2017 American Chemical Society.view abstract doi: 10.1021/jacs.7b01158 2017 • 178 Interaction between phase transformations and dislocations at incipient plasticity of monocrystalline silicon under nanoindentation
Zhang, J. and Zhang, J. and Wang, Z. and Hartmaier, A. and Yan, Y. and Sun, T.
Computational Materials Science 131 55-61 (2017)Structural phase transformation and dislocation slip are two important deformation modes of monocrystalline silicon. In the present work, we elucidate mechanisms of inhomogeneous elastic-plastic transition in spherical nanoindentation of monocrystalline silicon by means of molecular dynamics simulations. The Stillinger-Weber potential is utilized to present simultaneous phase transformations and dislocation activities in the silicon nanoindentation. And a bond angle analysis-based method is proposed to quantitatively clarify silicon phases. The influence of crystallographic orientation on the silicon nanoindentation is further addressed. Our simulation results indicate that prior to the “Pop-In” event, Si(0 1 0) undergoes inelastic deformation accompanied by the phase transformation from the Si-I to the Si-III/Si-XII, which is not occurred in Si(1 1 0) and Si(1 1 1). While the phase transformation from the Si-I to the bct-5 is the dominant mechanism of incipient plasticity for each crystallographic orientation, dislocation nucleation is also an operating deformation mode in the elastic-plastic transition of Si(0 1 0). Furthermore, interactions between phase transformations and dislocations are more pronounced in Si(0 1 0) than the other two crystallographic orientations. © 2017 Elsevier B.V.view abstract doi: 10.1016/j.commatsci.2017.01.043 2017 • 177 Machine learning molecular dynamics for the simulation of infrared spectra
Gastegger, M. and Behler, J. and Marquetand, P.
Chemical Science 8 6924-6935 (2017)Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects-typically neglected by conventional quantum chemistry approaches-we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n-alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra. © 2017 The Royal Society of Chemistry.view abstract doi: 10.1039/c7sc02267k 2017 • 176 Molecular dynamics simulations of entangled polymers: The effect of small molecules on the glass transition temperature
Mahmoudinezhad, E. and Marquardt, A. and Eggeler, G. and Varnik, F.
Procedia Computer Science 108 265-271 (2017)Effect of small molecules, as they penetrate into a polymer system, is investigated via molecular dynamics simulations. It is found that small spherical particles reduce the glass transition temperature and thus introduce a softening of the material. Results are compared to experimental findings for the effect of different types of small molecules such as water, acetone and ethanol on the glass transition temperature of a polyurethane-based shape memory polymer. Despite the simplicity of the simulated model, MD results are found to be in good qualitative agreement with experimental data. © 2017 The Authors. Published by Elsevier B.V.view abstract doi: 10.1016/j.procs.2017.05.152 2017 • 175 Molecular dynamics study of stability and disintegration of long rod-like micelles: Dodecyltrimethylammonium chloride in solutions of hydroxybenzoates
Gujt, J. and Bešter-Rogač, M. and Spohr, E.
Journal of Molecular Liquids 228 150-159 (2017)Recently it was found out that different positions of the hydroxylic group on hydroxybenzoate anions (HB) crucially affect the thermodynamics of the self-organization of the cationic surfactant dodecyltrimethylammonium chloride (DTAC) and also the structure of resulting aggregates. In our previous work, the properties of stable long cylindrical DTAC micelles in the presence of NaHB at 1:1 DTAC/NaHB molar ratio in aqueous solutions were investigated by atomistic molecular dynamics simulations. In the present work, we first study the decay of cylindrical DTAC micelles in water without added salt and then extend our research to systems with low NaHB concentrations (DTAC/NaHB molar ratios of 4:1 and 2:1) in order to approach the real experimental conditions more closely. The geometry and structural properties of DTAC micelles in water are investigated, and also the decomposition of long cylindrical micelles and the solvent accessible surface area of micelles is discussed. We observe that the initial DTAC micelle without NaHB quickly disintegrates into smaller stable spherical micelles. At the 2:1 DTAC/NaHB molar ratio we find all initial DTAC micelles to remain stable; however, their geometry deviates significantly from initial cylindrical one. Furthermore, it is observed that o-HB induces a more ordered internal structure of the micelle, and is more strongly oriented than the other two isomers, which agrees well with the experiments and observations reported in our previous work. When the NaHB concentration is decreased to 4:1 DTAC/NaHB molar ratio, an initial DTAC micelle disintegrates forming smaller aggregates of spherical or elongated shapes regardless of the nature of the HB isomer present. The microscopic structure of the resultant micelles is very similar to the structure observed at higher NaHB concentration, however, the effect of HB ions is smaller. It was also observed that the micelle remains stable longer in the presence of o-HB than in the presence of the other two isomers. © 2016 Elsevier B.V.view abstract doi: 10.1016/j.molliq.2016.09.067 2017 • 174 Molecular Tweezers Inhibit PARP-1 by a New Mechanism
Wilch, C. and Talbiersky, P. and Berchner-Pfannschmidt, U. and Schaller, T. and Kirsch, M. and Klärner, F.-G. and Schrader, T.
European Journal of Organic Chemistry 2017 2223-2229 (2017)The inhibition of PARP-1 (poly[ADP-ribose]polymerase 1), a key enzyme for DNA quality control, has been achieved with synthetic molecular tweezers through a noncompetitive mechanism with an IC50 value of 3 µm. Displacement as well as electrophoretic mobility shift assays and molecular dynamics experiments point to a simultaneous inclusion of lysine side-chains in the cavity of the tweezers and the coordination of one phosphate arm to the central Zn2+ ion of the zinc finger; thereby, lesioned DNA is displaced. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheimview abstract doi: 10.1002/ejoc.201601596 2017 • 173 Nanophase Segregation of Self-Assembled Monolayers on Gold Nanoparticles
Meena, S.K. and Goldmann, C. and Nassoko, D. and Seydou, M. and Marchandier, T. and Moldovan, S. and Ersen, O. and Ribot, F. and Chanéac, C. and Sanchez, C. and Portehault, D. and Tielens, F. and Sulpizi, M.
ACS Nano 11 7371-7381 (2017)Nanophase segregation of a bicomponent thiol self-assembled monolayer is predicted using atomistic molecular dynamics simulations and experimentally confirmed. The simulations suggest the formation of domains rich in acid-terminated chains, on one hand, and of domains rich in amide-functionalized ethylene glycol oligomers, on the other hand. In particular, within the amide-ethylene glycol oligomers region, a key role is played by the formation of interchain hydrogen bonds. The predicted phase segregation is experimentally confirmed by the synthesis of 35 and 15 nm gold nanoparticles functionalized with several binary mixtures of ligands. An extensive study by transmission electron microscopy and electron tomography, using silica selective heterogeneous nucleation on acid-rich domains to provide electron contrast, supports simulations and highlights patchy nanoparticles with a trend toward Janus nano-objects depending on the nature of the ligands and the particle size. These results validate our computational platform as an effective tool to predict nanophase separation in organic mixtures on a surface and drive further exploration of advanced nanoparticle functionalization. © 2017 American Chemical Society.view abstract doi: 10.1021/acsnano.7b03616 2017 • 172 Polymer conformations in ionic microgels in the presence of salt: Theoretical and mesoscale simulation results
Kobayashi, H. and Halver, R. and Sutmann, G. and Winkler, R.G.
Polymers 9 (2017)We investigate the conformational properties of polymers in ionic microgels in the presence of salt ions by molecular dynamics simulations and analytical theory. A microgel particle consists of coarse-grained linear polymers, which are tetra-functionally crosslinked. Counterions and salt ions are taken into account explicitly, and charge-charge interactions are described by the Coulomb potential. By varying the charge interaction strength and salt concentration, we characterize the swelling of the polyelectrolytes and the charge distribution. In particular, we determine the amount of trapped mobile charges inside the microgel and the Debye screening length. Moreover, we analyze the polymer extension theoretically in terms of the tension blob model taking into account counterions and salt ions implicitly by the Debye-Hückel model. Our studies reveal a strong dependence of the amount of ions absorbed in the interior of the microgel on the electrostatic interaction strength, which is related to the degree of the gel swelling. This implies a dependence of the inverse Debye screening length k on the ion concentration; we find a power-law increase of k with the Coulomb interaction strength with the exponent 3/5 for a salt-free microgel and an exponent 1/2 for moderate salt concentrations. Additionally, the radial dependence of polymer conformations and ion distributions is addressed. © 2017 by the authors.view abstract doi: 10.3390/polym9010015 2017 • 171 Proton-Transfer Mechanisms at the Water-ZnO Interface: The Role of Presolvation
Quaranta, V. and Hellström, M. and Behler, J.
Journal of Physical Chemistry Letters 8 1476-1483 (2017)The dissociation of water is an important step in many chemical processes at solid surfaces. In particular, water often spontaneously dissociates near metal oxide surfaces, resulting in a mixture of H2O, H+, and OH- at the interface. Ubiquitous proton-transfer (PT) reactions cause these species to dynamically interconvert, but the underlying mechanisms are poorly understood. Here, we develop and use a reactive high-dimensional neural-network potential based on density functional theory data to elucidate the structural and dynamical properties of the interfacial species at the liquid-water-metal-oxide interface, using the nonpolar ZnO(101̅0) surface as a prototypical case. Molecular dynamics simulations reveal that water dissociation and recombination proceed via two types of PT reactions: (i) to and from surface oxide and hydroxide anions (“surface-PT”) and (ii) to and from neighboring adsorbed hydroxide ions and water molecules (“adlayer-PT”). We find that the adlayer-PT rate is significantly higher than the surface-PT rate. Water dissociation is, for both types of PT, governed by a predominant presolvation mechanism, i.e., thermal fluctuations that cause the adsorbed water molecules to occasionally accept a hydrogen bond, resulting in a decreased PT barrier and an increased dissociation rate as compared to when no hydrogen bond is present. Consequently, we are able to show that hydrogen bond fluctuations govern PT events at the water-metal-oxide interface in a way similar to that in acidic and basic aqueous bulk solutions. © 2017 American Chemical Society.view abstract doi: 10.1021/acs.jpclett.7b00358 2017 • 170 Proton-Transfer-Driven Water Exchange Mechanism in the Na+ Solvation Shell
Hellström, M. and Behler, J.
Journal of Physical Chemistry B 121 4184-4190 (2017)Ligand exchange plays an important role for organic and inorganic chemical reactions. We demonstrate the existence of a novel water exchange mechanism, the "proton transfer pathway" (PTP), around Na+(aq) in basic (high pH) solution, using reactive molecular dynamics simulations employing a high-dimensional neural network potential. An aqua ligand in the first solvation (hydration) shell around a sodium ion is only very weakly acidic, but if a hydroxide ion is present in the second solvation shell, thermal fluctuations can cause the aqua ligand to transfer a proton to the neighboring OH-, resulting in a transient direct-contact ion pair, Na+-OH-, which is only weakly bound and easily dissociates. The extent to which water exchange events follow the PTP is pH-dependent: in dilute NaOH(aq) solutions, only very few exchanges occur, whereas in saturated NaOH(aq) solutions up to a third of water self-exchange events are induced by proton transfer. The principles and results outlined here are expected to be relevant for chemical synthesis involving bases and alkali metal cations. © 2017 American Chemical Society.view abstract doi: 10.1021/acs.jpcb.7b01490 2017 • 169 Self-Diffusion of Surface Defects at Copper-Water Interfaces
Kondati Natarajan, S. and Behler, J.
Journal of Physical Chemistry C 121 4368-4383 (2017)Solid-liquid interfaces play an important role in many fields like electrochemistry, corrosion, and heterogeneous catalysis. For understanding the related processes, detailed insights into the elementary steps at the atomic level are mandatory. Here we unravel the properties of prototypical surface-defects like adatoms and vacancies at a number of copper-water interfaces including the low-index Cu(111), Cu(100), and Cu(110), as well as the stepped Cu(211) and Cu(311) surfaces. Using a first-principles quality neural network potential constructed from density functional theory reference data in combination with molecular dynamics and metadynamics simulations, we investigate the defect diffusion mechanisms and the associated free energy barriers. Further, the solvent structure and the mobility of the interfacial water molecules close to the defects are analyzed and compared to the defect-free surfaces. We find that, like at the copper-vacuum interface, hopping mechanisms are preferred compared to exchange mechanisms, while the associated barriers for hopping are reduced in the presence of liquid water. The water structure close to adatoms and vacancies exhibits pronounced local features and differs strongly from the structure at the ideal low-index surfaces. Moreover, in particular at Cu(111) the adatoms are very mobile and hopping events along the surface are more frequent than the exchange of coordinating water molecules in their local environment. Consequently, adatom self-diffusion processes at Cu(111) involve entities of adatoms and their associated solvation shells. © 2017 American Chemical Society.view abstract doi: 10.1021/acs.jpcc.6b12657 2017 • 168 Sum Frequency Generation Spectra from Velocity-Velocity Correlation Functions
Khatib, R. and Sulpizi, M.
Journal of Physical Chemistry Letters 8 1310-1314 (2017)We developed an expression for the calculation of the sum frequency generation spectra (SFG) of water interfaces that is based on the projection of the atomic velocities on the local normal modes. Our approach permits one to obtain the SFG signal from suitable velocity-velocity correlation functions, reducing the computational cost to that of the accumulation of a molecular dynamics trajectory, and therefore cutting the overhead costs associated with the explicit calculation of the dipole moment and polarizability tensor. Our method permits to interpret the peaks in the spectrum in terms of local modes, also including the bending region. The results for the water-air interface, obtained using ab initio molecular dynamics simulations, are discussed in connection to recent phase resolved experimental data. © 2017 American Chemical Society.view abstract doi: 10.1021/acs.jpclett.7b00207 2017 • 167 Tailored protein encapsulation into a DNA host using geometrically organized supramolecular interactions
Sprengel, A. and Lill, P. and Stegemann, P. and Bravo-Rodriguez, K. and Schöneweiß, E.-C. and Merdanovic, M. and Gudnason, D. and Aznauryan, M. and Gamrad, L. and Barcikowski, S. and Sanchez-Garcia, E. and Birkedal, V. and Gatso...
Nature Communications 8 (2017)The self-organizational properties of DNA have been used to realize synthetic hosts for protein encapsulation. However, current strategies of DNA-protein conjugation still limit true emulation of natural host-guest systems, whose formation relies on non-covalent bonds between geometrically matching interfaces. Here we report one of the largest DNA-protein complexes of semisynthetic origin held in place exclusively by spatially defined supramolecular interactions. Our approach is based on the decoration of the inner surface of a DNA origami hollow structure with multiple ligands converging to their corresponding binding sites on the protein surface with programmable symmetry and range-of-action. Our results demonstrate specific host-guest recognition in a 1:1 stoichiometry and selectivity for the guest whose size guarantees sufficient molecular diffusion preserving short intermolecular distances. DNA nanocontainers can be thus rationally designed to trap single guest molecules in their native form, mimicking natural strategies of molecular recognition and anticipating a new method of protein caging. © 2017 The Author(s).view abstract doi: 10.1038/ncomms14472 2017 • 166 The Hydrophobic Gap at High Hydrostatic Pressures
Wirkert, F.J. and Hölzl, C. and Paulus, M. and Salmen, P. and Tolan, M. and Horinek, D. and Nase, J.
Angewandte Chemie - International Edition 56 12958-12961 (2017)We have gained new insight into the so-called hydrophobic gap, a molecularly thin region of decreased electron density at the interface between water and a solid hydrophobic surface, by X-ray reflectivity experiments and molecular dynamics simulations at different hydrostatic pressures. Pressure variations show that the hydrophobic gap persists up to a pressure of 5 kbar. The electron depletion in the interfacial region strongly decreases with an increase in pressure, indicating that the interfacial region is compressed more strongly than bulk water. The decrease is most significant up to 2 kbar; beyond that, the pressure response of the depletion is less pronounced. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheimview abstract doi: 10.1002/anie.201706662 2017 • 165 The Molecular Tweezer CLR01 Stabilizes a Disordered Protein-Protein Interface
Bier, D. and Mittal, S. and Bravo-Rodriguez, K. and Sowislok, A. and Guillory, X. and Briels, J. and Heid, C. and Bartel, M. and Wettig, B. and Brunsveld, L. and Sanchez-Garcia, E. and Schrader, T. and Ottmann, C.
Journal of the American Chemical Society 139 16256-16263 (2017)Protein regions that are involved in protein-protein interactions (PPIs) very often display a high degree of intrinsic disorder, which is reduced during the recognition process. A prime example is binding of the rigid 14-3-3 adapter proteins to their numerous partner proteins, whose recognition motifs undergo an extensive disorder-to-order transition. In this context, it is highly desirable to control this entropy-costly process using tailored stabilizing agents. This study reveals how the molecular tweezer CLR01 tunes the 14-3-3/Cdc25CpS216 protein-protein interaction. Protein crystallography, biophysical affinity determination and biomolecular simulations unanimously deliver a remarkable finding: a supramolecular "Janus" ligand can bind simultaneously to a flexible peptidic PPI recognition motif and to a well-structured adapter protein. This binding fills a gap in the protein-protein interface, "freezes" one of the conformational states of the intrinsically disordered Cdc25C protein partner and enhances the apparent affinity of the interaction. This is the first structural and functional proof of a supramolecular ligand targeting a PPI interface and stabilizing the binding of an intrinsically disordered recognition motif to a rigid partner protein. © 2017 American Chemical Society.view abstract doi: 10.1021/jacs.7b07939 2017 • 164 The shear instability energy: A new parameter for materials design?
Kanani, M. and Hartmaier, A. and Janisch, R.
Modelling and Simulation in Materials Science and Engineering 25 (2017)Reliable and predictive relationships between fundamental microstructural material properties and observable macroscopic mechanical behaviour are needed for the successful design of new materials. In this study we establish a link between physical properties that are defined on the atomic level and the deformation mechanisms of slip planes and interfaces that govern the mechanical behaviour of a metallic material. To accomplish this, the shear instability energy Γ is introduced, which can be determined via quantum mechanical ab initio calculations or other atomistic methods. The concept is based on a multilayer generalised stacking fault energy calculation and can be applied to distinguish the different shear deformation mechanisms occurring at TiAl interfaces during finite-temperature molecular dynamics simulations. We use the new parameter Γ to construct a deformation mechanism map for different interfaces occurring in this intermetallic. Furthermore, Γ can be used to convert the results of ab initio density functional theory calculations into those obtained with an embedded atom method type potential for TiAl. We propose to include this new physical parameter into material databases to apply it for the design of materials and microstructures, which so far mainly relies on single-crystal values for the unstable and stable stacking fault energy. © 2017 IOP Publishing Ltd.view abstract doi: 10.1088/1361-651X/aa865a 2017 • 163 Thermal resistance of twist boundaries in silicon nanowires by nonequilibrium molecular dynamics
Bohrer, J.K. and Schröer, K. and Brendel, L. and Wolf, D.E.
AIP Advances 7 (2017)The thermal boundary resistance (Kapitza resistance) of (001) twist boundaries in silicon is investigated by nonequilibrium molecular dynamics simulations. In order to enable continuous adjustment of the mismatch angle, a cylindrical geometry with fixed atomic positions at the boundaries is devised. The influence of the boundary conditions on the Kapitza resistance is removed by means of a finite size analysis. Due to the diamond structure of silicon, twist boundaries with mismatch angles ϕ and 90°−ϕ are not equivalent, whereas those with ±ϕ or with 90°±ϕ are. The Kapitza resistance increases with mismatch angle up to 45°, where it reaches a plateau around 1.56±0.05Km2/GW. Between 80° and the 90°Σ1 grain boundary it drops by about 30%. Surprisingly, lattice coincidence at other angles (Σ5,Σ13,Σ27,Σ25) has no noticable effect on the Kapitza resistance. However, there is a clear correlation between the Kapitza resistance and the width of a non-crystalline layer at the twist boundaries. © 2017 Author(s).view abstract doi: 10.1063/1.4979982 2017 • 162 Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series
Güssregen, S. and Matter, H. and Hessler, G. and Lionta, E. and Heil, J. and Kast, S.M.
Journal of Chemical Information and Modeling 57 1652-1666 (2017)Water molecules play an essential role for mediating interactions between ligands and protein binding sites. Displacement of specific water molecules can favorably modulate the free energy of binding of protein-ligand complexes. Here, the nature of water interactions in protein binding sites is investigated by 3D RISM (three-dimensional reference interaction site model) integral equation theory to understand and exploit local thermodynamic features of water molecules by ranking their possible displacement in structure-based design. Unlike molecular dynamics-based approaches, 3D RISM theory allows for fast and noise-free calculations using the same detailed level of solute-solvent interaction description. Here we correlate molecular water entities instead of mere site density maxima with local contributions to the solvation free energy using novel algorithms. Distinct water molecules and hydration sites are investigated in multiple protein-ligand X-ray structures, namely streptavidin, factor Xa, and factor VIIa, based on 3D RISM-derived free energy density fields. Our approach allows the semiquantitative assessment of whether a given structural water molecule can potentially be targeted for replacement in structure-based design. Finally, PLS-based regression models from free energy density fields used within a 3D-QSAR approach (CARMa - comparative analysis of 3D RISM Maps) are shown to be able to extract relevant information for the interpretation of structure-activity relationship (SAR) trends, as demonstrated for a series of serine protease inhibitors. © 2017 American Chemical Society.view abstract doi: 10.1021/acs.jcim.6b00765 2017 • 161 Trimesic acid on Cu in ethanol: Potential-dependent transition from 2-D adsorbate to 3-D metal-organic framework
Schäfer, P. and Lalitha, A. and Sebastian, P. and Meena, S.K. and Feliu, J. and Sulpizi, M. and van der Veen, M.A. and Domke, K.F.
Journal of Electroanalytical Chemistry 793 226-234 (2017)We report the potential-dependent interactions of trimesic acid with Cu surfaces in EtOH. CV experiments and electrochemical surface-enhanced Raman spectroscopy show the presence of an adsorbed trimesic acid layer on Cu at potentials lower than 0 V vs Cu. The BTC coverage increases as the potential increases, reaching a maximum at 0 V. Based on molecular dynamics simulations, we report adsorption geometries and possible structures of the organic adlayer. We find that, depending on the crystal facet, trimesic acid adsorbs either flat or with one or two of the carboxyl groups facing the metal surface. At higher coverages, a multi-layer forms that is composed mostly of flat-lying trimesic acid molecules. Increasing the potential beyond 0 V activates the Cu-adsorbate interface in such a way that under oxidation of Cu to Cu2 +, a 3-D metal-organic framework forms directly on the electrode surface. © 2017 Elsevier B.V.view abstract doi: 10.1016/j.jelechem.2017.01.025 2017 • 160 Ultra-stiff metallic glasses through bond energy density design
Schnabel, V. and Köhler, M. and Music, D. and Bednarcik, J. and Clegg, W.J. and Raabe, D. and Schneider, J.M.
Journal of Physics Condensed Matter 29 (2017)The elastic properties of crystalline metals scale with their valence electron density. Similar observations have been made for metallic glasses. However, for metallic glasses where covalent bonding predominates, such as metalloid metallic glasses, this relationship appears to break down. At present, the reasons for this are not understood. Using high energy x-ray diffraction analysis of melt spun and thin film metallic glasses combined with density functional theory based molecular dynamics simulations, we show that the physical origin of the ultrahigh stiffness in both metalloid and non-metalloid metallic glasses is best understood in terms of the bond energy density. Using the bond energy density as novel materials design criterion for ultra-stiff metallic glasses, we are able to predict a Co33.0Ta3.5B63.5 short range ordered material by density functional theory based molecular dynamics simulations with a high bond energy density of 0.94 eV Å-3 and a bulk modulus of 263 GPa, which is 17% greater than the stiffest Co-B based metallic glasses reported in literature. © 2017 IOP Publishing Ltd.view abstract doi: 10.1088/1361-648X/aa72cb 2017 • 159 Verlet-like algorithms for Car-Parrinello molecular dynamics with unequal electronic occupations
Castañeda Medina, A. and Schmid, R.
Journal of Chemical Physics 147 (2017)The ab initio molecular dynamics simulations of metallic, charged, and electrochemical systems require, in principle, the inclusion of unequally occupied electronic states. In this contribution, the general approach to work with fixed but arbitrary occupations within the Car-Parrinello molecular dynamics scheme is revisited, focusing on the procedure which is required to maintain the orthonormality constraints in the commonly used position-Verlet integrator. Expressions to constrain also the orbital velocities, as it is demanded by a velocity-Verlet integrator, are then derived. The generalized unequal-occupation SHAKE algorithm is compared with the standard procedure for damped dynamics (energy optimization) of systems including fully unoccupied electronic states. In turn, the proposed unequal-occupation RATTLE algorithm is validated by the corresponding microcanonical ensemble simulations. It is shown that only with the proper orthogonalization method, a correct ordering of states and energy conserving dynamics can be achieved. © 2017 Author(s).view abstract doi: 10.1063/1.4987005 2016 • 158 A cascade screening approach for the identification of Bcr-Abl myristate pocket binders active against wild type and T315I mutant
Radi, M. and Schneider, R. and Fallacara, A.L. and Botta, L. and Crespan, E. and Tintori, C. and Maga, G. and Kissova, M. and Calgani, A. and Richters, A. and Musumeci, F. and Rauh, D. and Schenone, S.
Bioorganic and Medicinal Chemistry Letters 26 3436-3440 (2016)The major clinical challenge in drug-resistant chronic myelogenous leukemia (CML) is currently represented by the Bcr-Abl T315I mutant, which is unresponsive to treatment with common first and second generation ATP-competitive tyrosine kinase inhibitors (TKIs). Allosteric inhibition of Bcr-Abl represent a new frontier in the fight against resistant leukemia and few candidates have been identified in the last few years. Among these, myristate pocket (MP) binders discovered by Novartis (e.g. GNF2/5) showed promising results, although they proved to be active against the T315I mutant only in combination with first and second generation ATP-competitive inhibitors. Here we used a cascade screening approach based on sequential fluorescence polarization (FP) screening, in silico docking/dynamics studies and kinetic-enzymatic studies to identify novel MP binders. A pyrazolo[3,4-d]pyrimidine derivative (6) has been identified as a promising allosteric inhibitor active on 32D leukemia cell lines (expressing Bcr-Abl WT and T315I) with no need of combination with any ATP-competitive inhibitor. © 2016 Elsevier Ltdview abstract doi: 10.1016/j.bmcl.2016.06.051 2016 • 157 Ab Initio Molecular Dynamics Simulations of Nitrogen/VN(001) Surface Reactions: Vacancy-Catalyzed N2 Dissociative Chemisorption, N Adatom Migration, and N2 Desorption
Sangiovanni, D.G. and Mei, A.B. and Hultman, L. and Chirita, V. and Petrov, I. and Greene, J.E.
Journal of Physical Chemistry C 120 12503-12516 (2016)We use density-functional ab initio molecular dynamics to investigate the kinetics of N/VN(001) surface reactions at temperatures ranging from 1600 to 2300 K. N adatoms (Nad) on VN(001) favor epitaxial atop-V positions and diffuse among them by transiting through 4-fold hollow (FFH) sites, at which they are surrounded by two V and two N surface atoms. After several atop-V → FFH → atop-V jumps, isolated N adatoms bond strongly with an underlying N surface (Nsurf) atom. Frequent Nad/Nsurf pair exchange reactions lead to N2 desorption, which results in the formation of an anion surface vacancy. N vacancies rapidly migrate via in-plane 〈110〉 jumps and act as efficient catalysts for the dissociative chemisorption of incident N2 molecules. During exposure of VN(001) to incident atomic N gas atoms, Nad/Nad recombination and desorption is never observed, despite a continuously high N monomer surface coverage. Instead, N2 desorption is always initiated by a N adatom removing a N surface atom or by energetic N gas atoms colliding with Nad or Nsurf atoms. Similarities and differences between N/VN(001) vs. previous N/TiN(001) results, discussed on the basis of temperature-dependent ab initio electronic structures and chemical bonding, provide insights for controlling the reactivity of NaCl-structure transition-metal nitride (001) surfaces via electron-concentration tuning. © 2016 American Chemical Society.view abstract doi: 10.1021/acs.jpcc.6b02652 2016 • 156 Atomic mobility in the overheated amorphous GeTe compound for phase change memories
Sosso, G.C. and Behler, J. and Bernasconi, M.
Physica Status Solidi (A) Applications and Materials Science 213 329-334 (2016)Phase change memories rest on the ability of some chalcogenide alloys to undergo a fast and reversible transition between the crystalline and amorphous phases upon Joule heating. The fast crystallization is due to a high nucleation rate and a large crystal growth velocity which are actually possible thanks to the fragility of the supercooled liquid that allows for the persistence of a high atomic mobility at high supercooling where the thermodynamical driving force for crystallization is also high. Since crystallization in the devices occurs by rapidly heating the amorphous phase, hysteretic effects might arise with a different diffusion coefficient and viscosity on heating than on cooling. In this work, we have quantified these hysteretic effects in the phase change compound GeTe by means of molecular dynamics simulations. The atomic mobility in the overheated amorphous phase is lower than in supercooled liquid at the same temperature and the viscosity is consequently higher. Still, the simulations of the overheated amorphous phase reveal a breakdown of the Stokes-Einstein relation between the diffusion coefficient and the viscosity, similarly to what we found previously in the supercooled liquid. Evidences are provided that the breakdown is due to the emergence of dynamical heterogeneities at high supercooling. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.view abstract doi: 10.1002/pssa.201532378 2016 • 155 Concentration-Dependent Proton Transfer Mechanisms in Aqueous NaOH Solutions: From Acceptor-Driven to Donor-Driven and Back
Hellström, M. and Behler, J.
Journal of Physical Chemistry Letters 7 3302-3306 (2016)Proton transfer processes play an important role in many fields of chemistry. In dilute basic aqueous solutions, proton transfer from water molecules to hydroxide ions is aided by "presolvation", i.e., thermal fluctuations that modify the hydrogen-bonding environment around the proton-receiving OH- ion to become more similar to that of a neutral H2O molecule. In particular at high concentrations, however, the underlying mechanisms and especially the role of the counterions are little understood. As a prototypical case, we investigate aqueous NaOH solutions using molecular dynamics simulations employing a reactive high-dimensional neural-network potential constructed from density functional theory reference data. We find that with increasing concentration the predominant proton transfer mechanism changes from being "acceptor-driven", i.e., governed by the presolvation of OH-, to "donor-driven", i.e., governed by the presolvation of H2O, and back to acceptor-driven near the room-temperature solubility limit of 19 mol/L, which corresponds to an extremely solvent-deficient system containing only about one H2O molecule per ion. Specifically, we identify concentration ranges where the proton transfer rate is mostly affected by OH- losing an accepted hydrogen bond, OH- forming a donated hydrogen bond, H2O forming an accepted hydrogen bond, or H2O losing a coordinated Na+. Presolvation also manifests itself in the shortening of the Na+-OH2 distances, in that the Na+ "pushes" one of the H2O protons away. © 2016 American Chemical Society.view abstract doi: 10.1021/acs.jpclett.6b01448 2016 • 154 Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy
Klocke, M. and Wolf, D.E.
Beilstein Journal of Nanotechnology 7 708-720 (2016)A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM cantilever. It gives new insight into the correlation between the experimentally monitored frequency shift and cantilever damping due to the interaction between tip atoms and scanned surface. Applying the model to ionic crystals with rock salt structure two damping mechanisms are investigated, which occur separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism. When the long range ionic interaction is switched off, the two damping mechanisms occur with a completely different pattern, which is explained by the energy landscape for the apex atom of the tip. In this case the adhesion hysteresis is always associated with a distinct lateral displacement of the tip. It is shown how this may lead to a systematic shift between the periodic patterns obtained from the frequency and from the damping signal, respectively. © 2016 Klocke and Wolf.view abstract doi: 10.3762/bjnano.7.63 2016 • 153 Design principles for high-pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures
Hölzl, C. and Kibies, P. and Imoto, S. and Frach, R. and Suladze, S. and Winter, R. and Marx, D. and Horinek, D. and Kast, S.M.
Journal of Chemical Physics 144 (2016)Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures - while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute's response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields. © 2016 AIP Publishing LLC.view abstract doi: 10.1063/1.4944991 2016 • 152 Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory
Mrugalla, F. and Kast, S.M.
Journal of Physics Condensed Matter 28 (2016)Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems. © 2016 IOP Publishing Ltd.view abstract doi: 10.1088/0953-8984/28/34/344004 2016 • 151 Estimation of energy of cubic iron-carbon nanoclusters by molecular mechanic method: Berechnung der Energie von kubischen Eisen-Kohlenstoff-Nanoclustern durch molekularmechanische Methoden
Epple, M. and Prylutskyy, Y. and Nedolya, A.V. and Shapar, D.Y.
Materialwissenschaft und Werkstofftechnik 47 128-132 (2016)The energy of cubic iron-carbon nanoclusters was evaluated using the method of molecular mechanics. The focus was on two types of interstitial sites: octahedral and tetrahedral, in which the carbon atoms can be located. The calculation results showed that in the surface layer of the face-centered cubic nanocluster, all of the tetrahedral interstitial sites were energetically equivalent. If a carbon atom changes position between two tetrahedral interstices in the direction of the 111, it can occupy an energetically preferable position in octahedral interstitial space. The comparison of the nanoclusters energy between the cases of surface and subsurface location of the carbon atoms in the octahedral interstice showed that the system has lower energy in the former case. For body-centered cubic nanocluster, octahedral interstitial sites are more energetically favorable for carbon atoms than the tetrahedral interstice, excluding the surface. However, the octahedral interstitial sites on the surface are more preferable than tetrahedral interstice. Based on the calculations it was found that body-centered cubic and face-centered cubic nanoclusters could be unstable by the volumetric concentration of carbon. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.view abstract doi: 10.1002/mawe.201600481 2016 • 150 From Gold Nanoseeds to Nanorods: The Microscopic Origin of the Anisotropic Growth
Meena, S.K. and Sulpizi, M.
Angewandte Chemie - International Edition 55 11960-11964 (2016)Directly manipulating and controlling the size and shape of metal nanoparticles is a key step for their tailored applications. In this work, molecular dynamics simulations were applied to understand the microscopic origin of the asymmetric growth mechanism in gold nanorods. Different factors influencing the growth were selectively included in the models to unravel the role of the surfactants and ions. In the early stage of the growth, when the seed is only a few nanometers large, a dramatic symmetry breaking occurs as the surfactant layer preferentially covers the (100) and (110) facets, leaving the (111) facets unprotected. This anisotropic surfactant layer in turn promotes anisotropic growth with the less protected tips growing faster. When silver salt is added to the growth solution, the asymmetry of the facets is preserved, but the Br−concentration at the interface increases, resulting in increased surface passivation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheimview abstract doi: 10.1002/anie.201604594 2016 • 149 Guanidiniocarbonyl-pyrrole-aryl conjugates as inhibitors of human dipeptidyl peptidase III: Combined experimental and computational study
Matić, J. and Šupljika, F. and Tir, N. and Piotrowski, P. and Schmuck, C. and Abramić, M. and Piantanida, I. and Tomić, S.
RSC Advances 6 83044-83052 (2016)Dipeptidyl peptidase III (DPP III) is a zinc dependant peptidase which catalyses hydrolysis of the second peptide bond from the N-termini of its substrates. DPP III is an enzyme of broad substrate specificity and it has been found in many organisms. It has been recognised in several processes of interest for drug development like pain modulation and defence against oxidative stress. However, its fundamental physiological role is unknown and specific inhibitors would be of significant help in identifying this role. In this work we combined experimental (UV/Vis, fluorimetry and microcalorimetry experiments) with molecular dynamic simulations to study the binding of several newly designed and synthesised guanidiniocarbonyl-pyrrole-aryl conjugates to human DPP III. We found that new compounds bind with micromolar affinity to the enzyme and with varied efficiency inhibit hydrolysis of Arg-Arg-2-naphthylamide, the standard synthetic substrate of DPP III. The molecular modelling study revealed multiple binding modes of the guanidiniocarbonyl-pyrrole-aryl conjugates into the active site of human DPP III. In order to elucidate which one is the most favourable we studied the molecular determinants for their binding to DPP III as well as their influence on protein structure. It seems that the main requirement for a good DPP III inhibitor is a bulky aryl-substituent and a linker of suitable length and flexibility between it and the guanidiniocarbonyl-pyrrole. The obtained results gave directions for future development and improvement of DPP III inhibitors. © 2016 The Royal Society of Chemistry.view abstract doi: 10.1039/c6ra16966j 2016 • 148 High order path integrals made easy
Kapil, V. and Behler, J. and Ceriotti, M.
Journal of Chemical Physics 145 (2016)The precise description of quantum nuclear fluctuations in atomistic modelling is possible by employing path integral techniques, which involve a considerable computational overhead due to the need of simulating multiple replicas of the system. Many approaches have been suggested to reduce the required number of replicas. Among these, high-order factorizations of the Boltzmann operator are particularly attractive for high-precision and low-temperature scenarios. Unfortunately, to date, several technical challenges have prevented a widespread use of these approaches to study the nuclear quantum effects in condensed-phase systems. Here we introduce an inexpensive molecular dynamics scheme that overcomes these limitations, thus making it possible to exploit the improved convergence of high-order path integrals without having to sacrifice the stability, convenience, and flexibility of conventional second-order techniques. The capabilities of the method are demonstrated by simulations of liquid water and ice, as described by a neural-network potential fitted to the dispersion-corrected hybrid density functional theory calculations. © 2016 Author(s).view abstract doi: 10.1063/1.4971438 2016 • 147 How van der waals interactions determine the unique properties of water
Morawietz, T. and Singraber, A. and Dellago, C. and Behler, J.
Proceedings of the National Academy of Sciences of the United States of America 113 8368-8373 (2016)Whereas the interactions between water molecules are dominated by strongly directional hydrogen bonds (HBs), it was recently proposed that relatively weak, isotropic van der Waals (vdW) forces are essential for understanding the properties of liquid water and ice. This insight was derived from ab initio computer simulations, which provide an unbiased description of water at the atomic level and yield information on the underlying molecular forces. However, the high computational cost of such simulations prevents the systematic investigation of the influence of vdW forces on the thermodynamic anomalies of water. Here, we develop efficient ab initio-quality neural network potentials and use them to demonstrate that vdW interactions are crucial for the formation of water's density maximum and its negative volume of melting. Both phenomena can be explained by the flexibility of the HB network, which is the result of a delicate balance of weak vdW forces, causing, e.g., a pronounced expansion of the second solvation shell upon cooling that induces the density maximum.view abstract doi: 10.1073/pnas.1602375113 2016 • 146 Hydrodynamics in adaptive resolution particle simulations: Multiparticle collision dynamics
Alekseeva, U. and Winkler, R.G. and Sutmann, G.
Journal of Computational Physics 314 14-34 (2016)A new adaptive resolution technique for particle-based multi-level simulations of fluids is presented. In the approach, the representation of fluid and solvent particles is changed on the fly between an atomistic and a coarse-grained description. The present approach is based on a hybrid coupling of the multiparticle collision dynamics (MPC) method and molecular dynamics (MD), thereby coupling stochastic and deterministic particle-based methods. Hydrodynamics is examined by calculating velocity and current correlation functions for various mixed and coupled systems. We demonstrate that hydrodynamic properties of the mixed fluid are conserved by a suitable coupling of the two particle methods, and that the simulation results agree well with theoretical expectations. © 2016 Elsevier Inc.view abstract doi: 10.1016/j.jcp.2016.02.065 2016 • 145 Inclusion of mPRISM potential for polymer-induced protein interactions enables modeling of second osmotic virial coefficients in aqueous polymer-salt solutions
Herhut, M. and Brandenbusch, C. and Sadowski, G.
Biotechnology Journal 11 146-154 (2016)The downstream processing of therapeutic proteins is a challenging task. Key information needed to estimate applicable workup strategies (e.g. crystallization) are the interactions of the proteins with other components in solution. This information can be deduced from the second osmotic virial coefficient B22, measurable by static light scattering. Thermodynamic models are very valuable for predicting B22 data for different process conditions and thus decrease the experimental effort. Available B22 models consider aqueous salt solutions but fail for the prediction of B22 if an additional polymer is present in solution. This is due to the fact that depending on the polymer concentration protein-protein interactions are not rectified as assumed within these models. In this work, we developed an extension of the xDLVO model to predict B22 data of proteins in aqueous polymer-salt solutions. To show the broad applicability of the model, lysozyme, γ-globulin and D-xylose ketol isomerase in aqueous salt solution containing polyethylene glycol were considered. For all proteins considered, the modified xDLVO model was able to predict the experimentally observed non-monotonical course in B22 data with high accuracy. When used in an early stage in process development, the model will contribute to an efficient and cost effective downstream processing development. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.view abstract doi: 10.1002/biot.201500086 2016 • 144 Influence of pore dimension on the host-guest interaction in metal-organic frameworks
Amirjalayer, S. and Schmid, R.
Journal of Physical Chemistry C 120 27319-27327 (2016)Atomistic simulations were performed in order to investigated the effect of pore dimension on the interaction of guest molecules with the inner surface of metal-organic frameworks (MOFs). In these systems, which only differ in the metric of their open structure, the chemical nature is conserved, and less impact on the host-guest interaction is expected compared to chemically funcionalized MOFs. However, by performing molecular dynamics simulations of benzene loaded MOF-5 derivatives (IRMOFs), which differ just in the length of the organic linker, it can be shown that impacts are present. The influence of the soft-modification can be explained only by a detailed analysis of the free energy topology and the diffusion mechanism. Note that the calculated self-diffusivity of benzene Dself shows no change with respect to the elongation of the linkers. The apparent contradiction between the macroscopic observable Dself and the microscopic free energy landscape could be resolved by introducing a hopping model for the diffusion process and subsequent Monte Carlo simulations. This study demonstrates the importance of atomistic simulations and the need to understand the host-guest interaction in MOFs in a multiscale fashion. © 2016 American Chemical Society.view abstract doi: 10.1021/acs.jpcc.6b08609 2016 • 143 Large-scale molecular dynamics simulations of TiN/TiN(001) epitaxial film growth
Edström, D. and Sangiovanni, D.G. and Hultman, L. and Petrov, I. and Greene, J.E. and Chirita, V.
Journal of Vacuum Science and Technology A: Vacuum, Surfaces and Films 34 (2016)Large-scale classical molecular dynamics simulations of epitaxial TiN/TiN(001) thin film growth at 1200 K are carried out using incident flux ratios N/Ti = 1, 2, and 4. The films are analyzed as a function of composition, island size distribution, island edge orientation, and vacancy formation. Results show that N/Ti = 1 films are globally understoichiometric with dispersed Ti-rich surface regions which serve as traps to nucleate 111-oriented islands, leading to local epitaxial breakdown. Films grown with N/Ti = 2 are approximately stoichiometric and the growth mode is closer to layer-by-layer, while N/Ti = 4 films are stoichiometric with N-rich surfaces. As N/Ti is increased from 1 to 4, island edges are increasingly polar, i.e., 110-oriented, and N-terminated to accommodate the excess N flux, some of which is lost by reflection of incident N atoms. N vacancies are produced in the surface layer during film deposition with N/Ti = 1 due to the formation and subsequent desorption of N2 molecules composed of a N adatom and a N surface atom, as well as itinerant Ti adatoms pulling up N surface atoms. The N vacancy concentration is significantly reduced as N/Ti is increased to 2; with N/Ti = 4, Ti vacancies dominate. Overall, our results show that an insufficient N/Ti ratio leads to surface roughening via nucleation of small dispersed 111 islands, whereas high N/Ti ratios result in surface roughening due to more rapid upper-layer nucleation and mound formation. The growth mode of N/Ti = 2 films, which have smoother surfaces, is closer to layer-by-layer. © 2016 American Vacuum Society.view abstract doi: 10.1116/1.4953404 2016 • 142 Model Study of Thermoresponsive Behavior of Metal-Organic Frameworks Modulated by Linker Functionalization
Alaghemandi, M. and Schmid, R.
Journal of Physical Chemistry C 120 6835-6841 (2016)The temperature-responsive behavior of functionalized metal-organic frameworks (fu-MOF) with the general formula [Zn2(fu-L)2dabco]n has been investigated using molecular dynamics simulations (fu-L = alkoxy-functionalized 1,4-benzenedicarboxylate, dabco = 1,4-diazabicyclo[2.2.2]octane). The studied frameworks show a narrow pore (np) form at low temperatures, while at higher temperatures, large pore (lp) structures can be observed. The transition temperature is controlled by the chemical nature of the linker's side chains as well as their length. In general, enhancing the side chain length decreases the transition temperature. On the other hand, more polar linkers shift the transition temperature to higher values. The so-called opening process of the narrow pores is caused by the thermally induced motion of the alkoxy side chains of the functionalized linkers. For qualitative comparison, the difference in internal energy as well as entropy between two forms (np and lp) was calculated for all studied linker types. (Figure Presented). © 2016 American Chemical Society.view abstract doi: 10.1021/acs.jpcc.5b12331 2016 • 141 Molecular Dynamics Simulations of SFG Librational Modes Spectra of Water at the Water-Air Interface
Khatib, R. and Hasegawa, T. and Sulpizi, M. and Backus, E.H.G. and Bonn, M. and Nagata, Y.
Journal of Physical Chemistry C 120 18665-18673 (2016)At the water-air interface, the hydrogen-bond network of water molecules is interrupted, and accordingly, the structure and dynamics of the interfacial water molecules are altered considerably compared with the bulk. Such interfacial water molecules have been studied by surface-specific vibrational sum-frequency generation (SFG) spectroscopy probing high-frequency O-H stretch and H-O-H bending modes. In contrast, the low-frequency librational mode has been much less studied with SFG. Because this mode is sensitive to the hydrogen-bond connectivity, understanding the librational mode of the interfacial water is crucial for unveiling a microscopic view of the interfacial water. Here, we compute the SFG librational mode spectra at the water-air interface by using molecular dynamics simulation. We show that the modeling of the polarizability has a drastic effect on the simulated librational mode spectra, whereas the spectra are less sensitive to the force field models and the modeling of the dipole moment. The simulated librational spectra display a peak centered at ∼700 cm-1, which is close to the infrared peak frequency of the liquid water librational mode of 670 cm-1. This indicates that the librational mode of the interfacial water at the water-air interface closely resembles that of bulk liquid water. © 2016 American Chemical Society.view abstract doi: 10.1021/acs.jpcc.6b06371 2016 • 140 Molecular dynamics simulations of thermal transport in isotopically modulated semiconductor nanostructures
Frieling, R. and Eon, S. and Wolf, D. and Bracht, H.
Physica Status Solidi (A) Applications and Materials Science 213 549-556 (2016)In this paper, we investigate the effect of isotopic modulation on the thermal conductivity of semiconductor nanostructures. The isotope doping is of particular interest for the application of semiconductors as thermoelectric materials as it leaves the electronic properties practically unaffected while the phononic transport is retarded. This approach could increase the figure of merit of thermoelectric generators by decreasing the thermal conductivity of semiconductors. We use non-equilibrium molecular dynamics simulations to examine thermal transport in isotopically engineered semiconductors. The temperature profiles along the sample region deduced from the simulations allow the extraction of thermal conductivities. The reliability of the MD-predicted thermal conductivities is studied by analyzing the influence of the input parameters on the results. The first set of samples are isotopically modified silicon samples. The influence of temperature, isotopic composition, and ordering of isotopic defects on the thermal conductivity of silicon is studied. The second material system under investigation is silicon germanium alloys. The influence of isotopic modulation on the thermal conductivity of Si-Ge alloys is examined for varying chemical composition. The thermal conductivities predicted by MD are compared to results derived from the solution of the Boltzmann transport equation in the relaxation time approach. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.view abstract doi: 10.1002/pssa.201532469 2016 • 139 Molecular Mechanism of Crystal Growth Inhibition at the Calcium Oxalate/Water Interfaces
Parvaneh, L.S. and Donadio, D. and Sulpizi, M.
Journal of Physical Chemistry C 120 4410-4417 (2016)Understanding the molecular mechanisms which nature uses to control biomineral growth is a fundamental science goal with profound medical implication. In the case of calcium oxalate, a microscopic understanding of the interactions which regulate the growth and stabilization of metastable phases would permit to inhibit the growth of the crystals which are the main components of kidney stones. Here we use ab initio molecular dynamics simulations to unravel how specific molecular interactions occurring on calcium oxalate dihydrate surface can promote an anisotropic crystal growth. We find that the calcium oxalate dihydrate (100) and (101) surfaces are both hydrophilic and solvated by a strongly bound layer of water; however, they exhibit important differences in their ability to bind water and small molecules such as acetate. In particular, on the (100) surface, the more exposed Ca2+ ions can more strongly bind to negatively charged groups, exerting a protecting action on the surface and preventing its further growth. This mechanism in turn would favor an anisotropic growth of the calcium oxalate dihydrate crystals in the [100] direction, as observed in experiments. © 2016 American Chemical Society.view abstract doi: 10.1021/acs.jpcc.5b12474 2016 • 138 Multiscale description of carbon-supersaturated ferrite in severely drawn pearlitic wires
Nematollahi, Gh.A. and Grabowski, B. and Raabe, D. and Neugebauer, J.
Acta Materialia 111 321-334 (2016)A multiscale simulation approach based on atomistic calculations and a discrete diffusion model is developed and applied to carbon-supersaturated ferrite, as experimentally observed in severely deformed pearlitic steel. We employ the embedded atom method and the nudged elastic band technique to determine the energetic profile of a carbon atom around a screw dislocation in bcc iron. The results clearly indicate a special region in the proximity of the dislocation core where C atoms are strongly bound, but where they can nevertheless diffuse easily due to low barriers. Our analysis suggests that the previously proposed pipe mechanism for the case of a screw dislocation is unlikely. Instead, our atomistic as well as the diffusion model results support the so-called drag mechanism, by which a mobile screw dislocation is able to transport C atoms along its glide plane. Combining the C-dislocation interaction energies with density-functional-theory calculations of the strain dependent C formation energy allows us to investigate the C supersaturation of the ferrite phase under wire drawing conditions. Corresponding results for local and total C concentrations agree well with previous atom probe tomography measurements indicating that a significant contribution to the supersaturation during wire drawing is due to dislocations. © 2016 Acta Materialia Inc.view abstract doi: 10.1016/j.actamat.2016.03.052 2016 • 137 N and Ti adatom dynamics on stoichiometric polar TiN(111) surfaces
Sangiovanni, D.G. and Tasnádi, F. and Hultman, L. and Petrov, I. and Greene, J.E. and Chirita, V.
Surface Science 649 72-79 (2016)We use molecular dynamics (MD) based on the modified embedded atom method (MEAM) to determine diffusion coefficients and migration pathways for Ti and N adatoms (Tiad and Nad) on TiN(111). The reliability of the classical model-potential is verified by comparison with density functional theory (DFT) results at 0 K. MD simulations carried out at temperatures between 600 and 1800 K show that both Tiad and Nad favor fcc surface sites and migrate among them by passing through metastable hcp positions. We find that Nad species are considerably more mobile than Tiad on TiN(111); contrary to our previous results on TiN(001). In addition, we show that lattice vibrations at finite temperatures strongly modify the potential energy landscape and result in smaller adatom migration energies, Ea = 1.03 for Tiad and 0.61 eV for Nad, compared to 0 K values Ea0K = 1.55 (Tiad) and 0.79 eV (Nad). We also demonstrate that the inclusion of dipole corrections, neglected in previous DFT calculations, is necessary in order to obtain the correct formation energies for polar surfaces such as TiN(111). © 2016 Elsevier B.V. All rights reserve.view abstract doi: 10.1016/j.susc.2016.01.031 2016 • 136 Nuclear Quantum Effects in Water at the Triple Point: Using Theory as a Link between Experiments
Cheng, B. and Behler, J. and Ceriotti, M.
Journal of Physical Chemistry Letters 7 2210-2215 (2016)One of the most prominent consequences of the quantum nature of light atomic nuclei is that their kinetic energy does not follow a Maxwell-Boltzmann distribution. Deep inelastic neutron scattering (DINS) experiments can measure this effect. Thus, the nuclear quantum kinetic energy can be probed directly in both ordered and disordered samples. However, the relation between the quantum kinetic energy and the atomic environment is a very indirect one, and cross-validation with theoretical modeling is therefore urgently needed. Here, we use state of the art path integral molecular dynamics techniques to compute the kinetic energy of hydrogen and oxygen nuclei in liquid, solid, and gas-phase water close to the triple point, comparing three different interatomic potentials and validating our results against equilibrium isotope fractionation measurements. We will then show how accurate simulations can draw a link between extremely precise fractionation experiments and DINS, therefore establishing a reliable benchmark for future measurements and providing key insights to increase further the accuracy of interatomic potentials for water. © 2016 American Chemical Society.view abstract doi: 10.1021/acs.jpclett.6b00729 2016 • 135 Stacking fault based analysis of shear mechanisms at interfaces in lamellar TiAl alloys
Kanani, M. and Hartmaier, A. and Janisch, R.
Acta Materialia 106 208-218 (2016)The interfaces in lamellar TiAl alloys have a strong influence on the strength and deformability of the microstructure. It is widely accepted that their number and spacing can be used to tune these properties. However, the results of molecular dynamics simulations of sliding at γ/γ interfaces in lamellar TiAl alloys presented here suggest that important factors, namely the sequence of different interface types as well as the orientation of in-plane directions with respect to the loading axis, have to be included into meso-scale models. Simulations of bicrystal shear show significant differences in the deformation behavior of the different interfaces, as well as pronounced in-plane anisotropy of the shear strength of the individual interfaces. The critical stresses derived from bicrystal shear simulations are of the same order of magnitude as the one for nucleation and motion of twins in a γ-single crystal, showing that these mechanisms are competitive. In total four different deformation mechanisms, interface migration, twin nucleation and migration, dislocation nucleation, and rigid grain boundary sliding are observed. Their occurrence can be understood based on a multilayer generalized stacking fault energy analysis. This link between physical properties, geometry and deformation mechanism can provide guidelines for future alloy development. © 2016 Published by Elsevier Ltd on behalf of Acta Materialia Inc.view abstract doi: 10.1016/j.actamat.2015.11.047 2016 • 134 Structure and Stability of Long Rod-like Dodecyltrimethylammonium Chloride Micelles in Solutions of Hydroxybenzoates: A Molecular Dynamics Simulation Study
Gujt, J. and Bešter-Rogač, M. and Spohr, E.
Langmuir 32 8275-8286 (2016)The relative position of the hydroxylic and carboxylic groups in the isomeric hydroxybenzoate (HB) anions is experimentally known to have a large impact on the thermodynamics of micellization of cationic surfactants, such as dodecyltrimethylammonium chloride (DTAC), and on the structure of the resulting micelles. To understand the effect of the different isomers on the molecular level, we employed atomistic molecular dynamics simulations to study systems containing infinitely long cylindrical DTAC micelles in aqueous solutions of the sodium salts of all three isomers of HB at a temperature and a pressure of 298.15 K and 1 atm. In all studied systems, the number of DTAC unimers is identical to the number of HB anions. At this concentration, the initially cylindrical micelles remain stable, irrespective of the nature of the isomer, whereas micelles rapidly disintegrated in the absence of HB anions. The HB isomers decrease the line density of unimers along the micellar axis and its concomitant thickness in the order o-HB > m-HB > p-HB. It is further observed that o-HB anions penetrate more deeply into the micellar core, induce a more ordered internal structure of the micelle, and are oriented more strongly than the other two isomers. In addition, the ortho isomer shows two different preferential orientations with respect to the radial direction of the cylindrical micelle; it can either be incorporated almost completely into the micelle or it can be attached through hydrogen bonding to one of those o-HB anions that are already incorporated into the micelle, and thus stick out of the micellar surface. © 2016 American Chemical Society.view abstract doi: 10.1021/acs.langmuir.6b02076 2016 • 133 Structure and thermodynamics of nondipolar molecular liquids and solutions from integral equation theory
Frach, R. and Heil, J. and Kast, S.M.
Molecular Physics 114 2461-2476 (2016)Solvent-induced solute polarisation of nondipolar solvents originates mainly from specific directional interactions and higher electrostatic multipole moments. Popular continuum solvation models such as the polarisable continuum models ignore such interactions and, therefore, cannot adequately model solvation effects on electronic structure in these environments. Important examples of nondipolar solvents that are indistinguishable by continuum methods are benzene and hexafluorobenzene. Both substances have very similar macroscopic properties, while solutes dissolved in either benzene or hexafluorobenzene behave differently due to their inverted electrostatic quadrupole moments and slightly different size. As a first step towards a proper and computationally feasible description of nondipolar molecular solvents, we present here integral equation theory results based on various forms of the reference interaction site model coupled to quantum-chemical calculations for benzene and hexafluorobenzene solutions of small molecules. We analyse solvation structures, also in comparison with molecular dynamics simulations, and show that predictions of transfer Gibbs energies, which define partition constants, benefit substantially from considering the exact, wave function-derived electrostatic field distribution beyond a simple point charge solute model in comparison with experimental data. Moreover, by constructing artificial uncharged and charge-inverted toy models of the solvents, it is possible to dissect the relative importance of dispersion and quadrupolar electrostatic effects on the partitioning equilibria. Such insight can help to design specifically optimised solvents to control solubility and selectivity for a wide range of applications. © 2016 Informa UK Limited, trading as Taylor & Francis Groupview abstract doi: 10.1080/00268976.2016.1167266 2015 • 132 Ab Initio Liquid Water Dynamics in Aqueous TMAO Solution
Usui, K. and Hunger, J. and Sulpizi, M. and Ohto, T. and Bonn, M. and Nagata, Y.
Journal of Physical Chemistry B 119 10597-10606 (2015)Ab initio molecular dynamics (AIMD) simulations in trimethylamine N-oxide (TMAO)-D2O solution are employed to elucidate the effects of TMAO on the reorientational dynamics of D2O molecules. By decomposing the O-D groups of the D2O molecules into specific subensembles, we reveal that water reorientational dynamics are retarded considerably in the vicinity of the hydrophilic TMAO oxygen (OTMAO) atom, due to the O-D···OTMAO hydrogen-bond. We find that this reorientational motion is governed by two distinct mechanisms: The O-D group rotates (1) after breaking the O-D···OTMAO hydrogen-bond, or (2) together with the TMAO molecule while keeping this hydrogen-bond intact. While the orientational slow-down is prominent in the AIMD simulation, simulations based on force field models exhibit much faster dynamics. The simulated angle-resolved radial distribution functions illustrate that the O-D···OTMAO hydrogen-bond has a strong directionality through the sp3 orbital configuration in the AIMD simulation, and this directionality is not properly accounted for in the force field simulation. These results imply that care must be taken when modeling negatively charged oxygen atoms as single point charges; force field models may not adequately describe the hydration configuration and dynamics. © 2015 American Chemical Society.view abstract doi: 10.1021/acs.jpcb.5b02579 2015 • 131 Adaptive dynamic load-balancing with irregular domain decomposition for particle simulations
Begau, C. and Sutmann, G.
Computer Physics Communications 190 51-61 (2015)We present a flexible and fully adaptive dynamic load-balancing scheme, which is designed for particle simulations of three-dimensional systems with short ranged interactions. The method is based on domain decomposition with non-orthogonal non-convex domains, which are constructed based on a local repartitioning of computational work between neighbouring processors. Domains are dynamically adjusted in a flexible way under the condition that the original topology is not changed, i.e. neighbour relations between domains are retained, which guarantees a fixed communication pattern for each domain during a simulation. Extensions of this scheme are discussed and illustrated with examples, which generalise the communication patterns and do not fully restrict data exchange to direct neighbours. The proposed method relies on a linked cell algorithm, which makes it compatible with existing implementations in particle codes and does not modify the underlying algorithm for calculating the forces between particles. The method has been implemented into the molecular dynamics community code IMD and performance has been measured for various molecular dynamics simulations of systems representing realistic problems from materials science. It is found that the method proves to balance the work between processors in simulations with strongly inhomogeneous and dynamically changing particle distributions, which results in a significant increase of the efficiency of the parallel code compared both to unbalanced simulations and conventional load-balancing strategies. © 2015 Elsevier B.V. All rights reserved.view abstract doi: 10.1016/j.cpc.2015.01.009 2015 • 130 Atom probe informed simulations of dislocation-precipitate interactions reveal the importance of local interface curvature
Prakash, A. and Guénolé, J. and Wang, J. and Müller, J. and Spiecker, E. and Mills, M.J. and Povstugar, I. and Choi, P. and Raabe, D. and Bitzek, E.
Acta Materialia 92 33-45 (2015)The interaction of dislocations with precipitates is an essential strengthening mechanism in metals, as exemplified by the superior high-temperature strength of Ni-base superalloys. Here we use atomistic simulation samples generated from atom probe tomography data of a single crystal superalloy to study the interactions of matrix dislocations with a γ′ precipitate in molecular dynamics simulations. It is shown that the precipitate morphology, in particular its local curvature, and the local chemical composition significantly alter both, the misfit dislocation network which forms at the precipitate interface, and the core structure of the misfit dislocations. Simulated tensile tests reveal the atomic scale details of many experimentally observed dislocation-precipitate interaction mechanisms, which cannot be reproduced by idealized simulation setups with planar interfaces. We thus demonstrate the need to include interface curvature in the study of semicoherent precipitates and introduce as an enabling method atom probe tomography-informed atomistic simulations. © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.view abstract doi: 10.1016/j.actamat.2015.03.050 2015 • 129 Atomistic investigation of wear mechanisms of a copper bi-crystal
Zhang, J. and Begau, C. and Geng, L. and Hartmaier, A.
Wear 332-333 941-948 (2015)In the present work, we investigate the wear mechanisms of a Cu bi-crystal containing a random high angle grain boundary by means of molecular dynamics simulations. The underlying deformation behavior of the material is analyzed and further related to the observed characteristics of mechanical response and resulting morphology of the worn surface. In particular, the grain boundary-associated mechanisms are characterized by advanced analysis techniques for lattice defects. Our simulation results indicate that in addition to dislocation slip and dislocation-grain boundary interactions, grain boundary migration plays an important role in the plastic deformation of Cu bi-crystal. It is found that the wear behavior of Cu depends on the crystallographic orientation of the worn surface and can be altered quite significantly by the presence of a grain boundary. © 2015 Elsevier B.V.view abstract doi: 10.1016/j.wear.2015.02.023 2015 • 128 Characteristics of flexibility in metal-organic framework solid solutions of composition [Zn2(BME-bdc)x(DB-bdc)2-xdabco]n: In situ powder X-ray diffraction, in situ NMR spectroscopy, and molecular dynamics simulations
Bon, V. and Pallmann, J. and Eisbein, E. and Hoffmann, H.C. and Senkovska, I. and Schwedler, I. and Schneemann, A. and Henke, S. and Wallacher, D. and Fischer, R.A. and Seifert, G. and Brunner, E. and Kaskel, S.
Microporous and Mesoporous Materials 216 64-74 (2015)Porosity switching in the crystalline solid state is a unique phenomenon observed only in a limited number of materials. The switching behavior of two metal-organic frameworks as well as their respective solid solutions of composition [Zn2(BME-bdc)x(DB-bdc)2-xdabco]n (x = 2; 1.5; 1.0; 0.5; 0) is studied in situ during the adsorption of CO2 and Xe using X-ray diffraction and NMR techniques. The diffraction data, measured during the adsorption suggest a direct one-step phase transition (switching) from the narrow pore phase to the large pore phase beyond the transition pressure. An intermediate phase was found only in one compound within a narrow pressure range around the phase transition pressure region. In situ high-pressure 13C NMR spectroscopy of adsorbed CO2 also allowed following the gating behavior of the studied materials by monitoring the signal of adsorbed CO2. The 13C NMR spectra exhibit a pronounced broadening indicating a certain degree of order for the adsorbed molecules inside the pores. This ordering effect and the resulting line broadening depend on the linker functionalization as could be confirmed by corresponding molecular dynamics (MD) simulations. © 2015 Elsevier Inc.view abstract doi: 10.1016/j.micromeso.2015.02.042 2015 • 127 Conformational Equilibria of Organic Adsorbates on Nanostructures in Aqueous Solution: MD Simulations
Giri, A.K. and Spohr, E.
Journal of Physical Chemistry C 119 25566-25575 (2015)We have performed atomistic molecular dynamics (MD) simulations of gold nanoparticles (GNPs) in aqueous NaCl solution. Alkanethiol chain-covered GNPs at grafting densities between approximately one-third and full coverage were studied with nonpolar CH3 and charged COO- and NH3 terminations. Special attention was given to the penetration depth of water and ions into the diffuse shell of the functionalized alkanethiol chains and its dependence on grafting density and functionalization. Solutions with polar terminations were neutralized by an excess of Na+ and Cl- ions. The penetration of water and ions into the hydration shell increases with decreasing grafting density irrespective of termination. High grafting densities lead to more extended hydrocarbon chains. Charged functionalized GNPs produce nonmonotonous counter charge distributions with reduced ion mobility. Partial replacement of first shell solvation water by the charged groups leads to a drastic increase in torsional relaxation times of the chain termini. Due to the large curvature of the GNPs with a diameter of 2 nm, gold cores remain accessible to both ions and water even at the highest studied grafting densities of about 5 chains/nm2. © 2015 American Chemical Society.view abstract doi: 10.1021/acs.jpcc.5b06249 2015 • 126 Constructing high-dimensional neural network potentials: A tutorial review
Behler, J.
International Journal of Quantum Chemistry 115 1032-1050 (2015)A lot of progress has been made in recent years in the development of atomistic potentials using machine learning (ML) techniques. In contrast to most conventional potentials, which are based on physical approximations and simplifications to derive an analytic functional relation between the atomic configuration and the potential-energy, ML potentials rely on simple but very flexible mathematical terms without a direct physical meaning. Instead, in case of ML potentials the topology of the potential-energy surface is "learned" by adjusting a number of parameters with the aim to reproduce a set of reference electronic structure data as accurately as possible. Due to this bias-free construction, they are applicable to a wide range of systems without changes in their functional form, and a very high accuracy close to the underlying first-principles data can be obtained. Neural network potentials (NNPs), which have first been proposed about two decades ago, are an important class of ML potentials. Although the first NNPs have been restricted to small molecules with only a few degrees of freedom, they are now applicable to high-dimensional systems containing thousands of atoms, which enables addressing a variety of problems in chemistry, physics, and materials science. In this tutorial review, the basic ideas of NNPs are presented with a special focus on developing NNPs for high-dimensional condensed systems. A recipe for the construction of these potentials is given and remaining limitations of the method are discussed. © 2015 Wiley Periodicals, Inc.view abstract doi: 10.1002/qua.24890 2015 • 125 Dynamics enhanced by HCl doping triggers full Pauling entropy release at the ice XII-XIV transition
Köster, K.W. and Fuentes-Landete, V. and Raidt, A. and Seidl, M. and Gainaru, C. and Loerting, T. and Böhmer, R.
Nature Communications 6 (2015)The pressure-temperature phase diagram of ice displays a perplexing variety of structurally distinct phases. In the century-long history of scientific research on ice, the proton-ordered ice phases numbered XIII through XV were discovered only recently. Despite considerable effort, none of the transitions leading from the low-temperature ordered ices VIII, IX, XI, XIII, XIV and XV to their high-temperature disordered counterparts were experimentally found to display the full Pauling entropy. Here we report calorimetric measurements on suitably high-pressure-treated, hydrogen chloride-doped ice XIV that demonstrate just this at the transition to ice XII. Dielectric spectroscopy on undoped and on variously doped ice XII crystals reveals that addition of hydrogen chloride, the agent triggering complete proton order in ice XIV, enhances the precursor dynamics strongest. These discoveries provide new insights into the puzzling observation that different dopants trigger the formation of different proton-ordered ice phases. © 2015 Macmillan Publishers Limited.view abstract doi: 10.1038/ncomms8349 2015 • 124 Electrolyte effects in a model of proton discharge on charged electrodes
Wiebe, J. and Kravchenko, K. and Spohr, E.
Surface Science 631 35-41 (2015)We report results on the influence of NaCl electrolyte dissolved in water on proton discharge reactions from aqueous solution to charged platinum electrodes. We have extended a recently developed combined proton transfer/proton discharge model on the basis of empirical valence bond theory to include NaCl solutions with several different concentrations of cations and anions, both stoichiometric (1:1) compositions and non-stoichiometric ones with an excess of cations. The latter solutions partially screen the electrostatic potential from the surface charge of the negatively charged electrode. 500-1000 trajectories of a discharging proton were integrated by molecular dynamics simulations until discharge occurred, or for at most 1.5 ns. The results show a strong dependence on ionic strength, but only a weak dependence on the screening behavior, when comparing stoichiometric and non-stoichiometric solutions. Overall, the Na+ cations exert a more dominant effect on the discharge reaction, which we argue is likely due to the very rigid arrangements of the cations on the negatively polarized electrode surface. Thus, our model predicts, for the given and very high negative surface charge densities, the fastest discharge reaction for pure water, but obviously cannot take into account the fact that such high charge densities are even more out of reach experimentally than for higher electrolyte concentrations. © 2014 Elsevier Ltd. All rights reserved.view abstract doi: 10.1016/j.susc.2014.06.016 2015 • 123 Electron-phonon interaction and thermal boundary resistance at the crystal-amorphous interface of the phase change compound GeTe
Campi, D. and Donadio, D. and Sosso, G.C. and Behler, J. and Bernasconi, M.
Journal of Applied Physics 117 (2015)Phonon dispersion relations and electron-phonon coupling of hole-doped trigonal GeTe have been computed by density functional perturbation theory. This compound is a prototypical phase change material of interest for applications in phase change non-volatile memories. The calculations allowed us to estimate the electron-phonon contribution to the thermal boundary resistance at the interface between the crystalline and amorphous phases present in the device. The lattice contribution to the thermal boundary resistance has been computed by non-equilibrium molecular dynamics simulations with an interatomic potential based on a neural network scheme. We find that the electron-phonon term contributes to the thermal boundary resistance to an extent which is strongly dependent on the concentration and mobility of the holes. Further, for measured values of the holes concentration and electrical conductivity, the electron-phonon term is larger than the contribution from the lattice. It is also shown that the presence of Ge vacancies, responsible for the p-type degenerate character of the semiconductor, strongly affects the lattice thermal conductivity of the crystal. © 2015 AIP Publishing LLC.view abstract doi: 10.1063/1.4904910 2015 • 122 Formation of dislocation networks in a coherent Cu Σ3(1 1 1) twin boundary
Jeon, J.B. and Dehm, G.
Scripta Materialia 102 71-74 (2015)Molecular dynamics simulations were performed to investigate dislocation network formations in a coherent twin boundary in Cu. Depending on the activated glide system, the initial flawless twin boundary can be heavily or sparsely decorated by a dislocation network. The dislocation mechanism leading to a heavy dislocation network at the twin boundary and its consequence on mechanical properties will be discussed. © 2015 Acta Materialia Inc.view abstract doi: 10.1016/j.scriptamat.2015.02.016 2015 • 121 Heterogeneous crystallization of the phase change material GeTe via atomistic simulations
Sosso, G.C. and Salvalaglio, M. and Behler, J. and Bernasconi, M. and Parrinello, M.
Journal of Physical Chemistry C 119 6428-6434 (2015)Phase change materials are the active compounds in optical disks and in nonvolatile phase change memory devices. These applications rest on the fast and reversible switching between the amorphous and the crystalline phases, which takes place in the nano domain in both the time and the length scales. The fast crystallization is a key feature for the applications of phase change materials. In this work, we have investigated by means of large scale molecular dynamics simulations the crystal growth of the prototypical phase change compound GeTe at the interface between the crystalline and the supercooled liquid reached in the device upon heating the amorphous phase. A neural network interatomic potential, markedly faster with respect to first-principles methods, allowed us to consider high-symmetry crystalline surfaces as well as polycrystalline models that are very close to the actual geometry of the memory devices. We have found that the crystal growth from the interface is dominant at high temperatures while it is competing with homogeneous crystallization in the melt at lower temperatures. The crystal growth velocity markedly depends on the crystallographic plane exposed at the interface, the (100) surface being kinetically dominant with respect to the (111) surface. Polycrystalline interfaces, representative of realistic conditions in phase change memory devices, grow at significantly slower pace because of the presence of grain boundaries. © 2015 American Chemical Society.view abstract doi: 10.1021/acs.jpcc.5b00296 2015 • 120 How Atomic Steps Modify Diffusion and Inter-adsorbate Forces: Empirical Evidence from Hopping Dynamics in Na/Cu(115)
Godsi, O. and Corem, G. and Kravchuk, T. and Bertram, C. and Morgenstern, K. and Hedgeland, H. and Jardine, A.P. and Allison, W. and Ellis, J. and Alexandrowicz, G.
Journal of Physical Chemistry Letters 6 4165-4170 (2015)We followed the collective atomic-scale motion of Na atoms on a vicinal Cu(115) surface within a time scale of pico- to nanoseconds using helium spin echo spectroscopy. The well-defined stepped structure of Cu(115) allows us to study the effect that atomic steps have on the adsorption properties, the rate for motion parallel and perpendicular to the step edge, and the interaction between the Na atoms. With the support of a molecular dynamics simulation we show that the Na atoms perform strongly anisotropic 1D hopping motion parallel to the step edges. Furthermore, we observe that the spatial and temporal correlations between the Na atoms that lead to collective motion are also anisotropic, suggesting the steps efficiently screen the lateral interaction between Na atoms residing on different terraces. © 2015 American Chemical Society.view abstract doi: 10.1021/acs.jpclett.5b01939 2015 • 119 Hydrogen diffusion and segregation in α iron ∑ 3 (111) grain boundaries
Hamza, M. and Hatem, T.M. and Raabe, D. and El-Awady, J.A.
ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE) 9-2015 (2015)Polycrystalline material generally exhibits degradation in its mechanical properties and shows more tendency for intergranular fracture due to segregation and diffusion of hydrogen on the grain boundaries (GBs). Understanding the parameters affecting the diffusion and binding of hydrogen within GBs will allow enhancing the mechanical properties of the commercial engineering materials and developing interface dominant materials. In practice during forming processes, the coincidence site lattice (CSL) GBs are experiencing deviations from their ideal configurations. Consequently, this will change the atomic structural integrity by superposition of sub-boundary dislocation networks on the ideal CSL interfaces. For this study, the ideal ∑ 3 111 [11 0] GB structure and its angular deviations in BCC iron within the range of Brandon criterion will be studied comprehensively using molecular statics (MS) simulations. The clean GB energy will be quantified, followed by the GB and free surface segregation energies calculations for hydrogen atoms. Rice-Wang model will be used to assess the embrittlement impact variation over the deviation angles. The results showed that the ideal GB structure is having the greatest resistance to embrittlement prior GB hydrogen saturation, while the 3° deviated GB is showing the highest susceptibility to embrittlement. Upon saturation, the 5° deviated GB appears to have the highest resistance instead due to the lowest stability of hydrogen atoms observed in the free surfaces of its simulation cell. Molecular dynamics (MD) simulations are then applied to calculate hydrogen diffusivity within the ideal and deviated GB structure. It is shown that hydrogen diffusivity decreases significantly in the deviated GB models. In addition, the 5° deviated GB is representing the local minimum for diffusivity results suggesting the existence of the highest atomic disorder and excessive secondary dislocation accommodation within this interface. Copyright © 2015 by ASME.view abstract doi: 10.1115/IMECE2015-53118 2015 • 118 Impact of bacterial endotoxin on the structure of DMPC membranes
Nagel, M. and Brauckmann, S. and Moegle-Hofacker, F. and Effenberger-Neidnicht, K. and Hartmann, M. and De Groot, H. and Mayer, C.
Biochimica et Biophysica Acta - Biomembranes 1848 2271-2276 (2015)Abstract Bacterial lipopolysaccharides are believed to have a toxic effect on human cell membranes. In this study, the influence of a lipopolysaccharide (LPS) from Escherichia coli on the structure, the dynamics and the mechanical strength of phospholipid membranes are monitored by nuclear magnetic resonance spectroscopy (NMR) and by atomic force microscopy (AFM). Model membranes are formed from 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and are either prepared as multilamellar bulk samples or multilamellar vesicles. Field gradient NMR data directly prove the rapid integration of LPS into DMPC membranes. Solid state NMR experiments primarily detect decreasing molecular order parameters with increasing LPS content. This is accompanied by a mechanical softening of the membrane bilayers as is shown by AFM indentation measurements. Altogether, the data prove that lipopolysaccharide molecules quickly insert into phospholipid bilayers, increase membrane fluctuation amplitudes and significantly weaken their mechanical stiffness. © 2015 Published by Elsevier B.V.view abstract doi: 10.1016/j.bbamem.2015.06.008 2015 • 117 Large scale Molecular Dynamics simulation of microstructure formation during thermal spraying of pure copper
Wang, T. and Begau, C. and Sutmann, G. and Hartmaier, A.
Surface and Coatings Technology 280 72-80 (2015)Thermal spray processes are widely used for the manufacture of advanced coating systems, e.g. metallic coatings for wear and corrosion protection. The desired coating properties are closely related to the microstructure, which is highly influenced by the processing parameters, such as temperature, size and velocity of the sprayed particles. In this paper, large scale Molecular Dynamics simulations are conducted to investigate the microstructure formation mechanisms during the spraying process of hot nano-particles onto a substrate at room temperature using pure copper as a benchmark material representing for a wider class of face-centered-cubic metals. To evaluate the influence of processing parameters on the coating morphology, a number of simulations are performed in which the initial temperature, size and velocity of copper particles are systematically varied in order to investigate the thermal and microstructural evolution during impaction. Two distinct types of microstructural formation mechanisms, resulting in different coating morphologies, are observed in the present investigation, which are either governed by plastic deformation or by the process of melting and subsequent solidification. Furthermore, a thermodynamically motivated model as a function of the particle temperature and velocity is developed, which predicts the microstructural mechanisms observed in the simulations. The results provide an elementary insight into the microstructure formation mechanisms on an atomistic scale, which can serve as basic input for continuum modeling of thermal spray process. © 2015 Published by Elsevier B.V.view abstract doi: 10.1016/j.surfcoat.2015.08.034 2015 • 116 Lipid Carbonyl Groups Terminate the Hydrogen Bond Network of Membrane-Bound Water
Ohto, T. and Backus, E.H.G. and Hsieh, C.-S. and Sulpizi, M. and Bonn, M. and Nagata, Y.
Journal of Physical Chemistry Letters 6 4499-4503 (2015)We present a combined experimental sum-frequency generation (SFG) spectroscopy and ab initio molecular dynamics simulations study to clarify the structure and orientation of water at zwitterionic phosphatidylcholine (PC) lipid and amine N-oxide (AO) surfactant monolayers. Simulated O-H stretch SFG spectra of water show good agreement with the experimental data. The SFG response at the PC interface exhibits positive peaks, whereas both negative and positive bands are present for the similar zwitterionic AO interface. The positive peaks at the water/PC interface are attributed to water interacting with the lipid carbonyl groups, which act as efficient hydrogen bond acceptors. This allows the water hydrogen bond network to reach, with its (up-oriented) O-H groups, into the headgroup of the lipid, a mechanism not available for water underneath the AO surfactant. This highlights the role of the lipid carbonyl group in the interfacial water structure at the membrane interface, namely, stabilizing the water hydrogen bond network. © 2015 American Chemical Society.view abstract doi: 10.1021/acs.jpclett.5b02141 2015 • 115 Mesoscopic simulation of phospholipid membranes, peptides, and proteins with molecular fragment dynamics
Truszkowski, A. and Van Den Broek, K. and Kuhn, H. and Zielesny, A. and Epple, M.
Journal of Chemical Information and Modeling 55 983-997 (2015)Molecular fragment dynamics (MFD) is a variant of dissipative particle dynamics (DPD), a coarse-grained mesoscopic simulation technique for isothermal complex fuids and soft matter systems with particles that are chosen to be adequate fluid elements. MFD choses its particles to be small molecules which may be connected by harmonic springs to represent larger molecular entities in order to maintain a comparatively accurate representation of covalent bonding and molecular characteristics. For this study the MFD approach is extended to accomplish long-term simulations (up to the microsecond scale) of large molecular ensembles (representing millions of atoms) containing phospholipid membranes, peptides, and proteins. For peptides and proteins a generally applicable fragmentation scheme is introduced in combination with specific backbone forces that keep native spatial shapes with adequate levels of flexibility or rigidity. The new approach is demonstrated by MFD simulations of the formation and characteristics of phospholipid membranes and vesicles, vesicle-membrane fusion, the backbone force dependency of the overall structural flexibility of dumbbell-shaped Calmodulin, the stability of subunit-aggregation of tetrameric hemoglobin, and the collaborative interaction of Kalata B1 cyclotides with a phospholipid membrane. All findings are in reasonable agreement with experimental as well as alternative simulation results. Thus, the extended MFD approach may become a new tool for biomolecular system studies to allow for comparatively fast simulative investigations in combination with a comparatively high chemical granularity. © 2015 American Chemical Society.view abstract doi: 10.1021/ci5006096 2015 • 114 Monte Carlo simulation of dense polymer melts using event chain algorithms
Kampmann, T.A. and Boltz, H.-H. and Kierfeld, J.
Journal of Chemical Physics 143 (2015)We propose an efficient Monte Carlo algorithm for the off-lattice simulation of dense hard sphere polymer melts using cluster moves, called event chains, which allow for a rejection-free treatment of the excluded volume. Event chains also allow for an efficient preparation of initial configurations in polymer melts. We parallelize the event chain Monte Carlo algorithm to further increase simulation speeds and suggest additional local topology-changing moves ("swap" moves) to accelerate equilibration. By comparison with other Monte Carlo and molecular dynamics simulations, we verify that the event chain algorithm reproduces the correct equilibrium behavior of polymer chains in the melt. By comparing intrapolymer diffusion time scales, we show that event chain Monte Carlo algorithms can achieve simulation speeds comparable to optimized molecular dynamics simulations. The event chain Monte Carlo algorithm exhibits Rouse dynamics on short time scales. In the absence of swap moves, we find reptation dynamics on intermediate time scales for long chains. © 2015 AIP Publishing LLC.view abstract doi: 10.1063/1.4927084 2015 • 113 Representing the potential-energy surface of protonated water clusters by high-dimensional neural network potentials
Kondati Natarajan, S. and Morawietz, T. and Behler, J.
Physical Chemistry Chemical Physics 17 8356-8371 (2015)Investigating the properties of protons in water is essential for understanding many chemical processes in aqueous solution. While important insights can in principle be gained by accurate and well-established methods like ab initio molecular dynamics simulations, the computational costs of these techniques are often very high. This prevents studying large systems on long time scales, which is severely limiting the applicability of computer simulations to address a wide range of interesting phenomena. Developing more efficient potentials enabling the simulation of water including dissociation and recombination events with first-principles accuracy is a very challenging task. In particular protonated water clusters have become important model systems to assess the reliability of such potentials, as the presence of the excess proton induces substantial changes in the local hydrogen bond patterns and many energetically similar isomers exist, which are extremely difficult to describe. In recent years it has been demonstrated for a number of systems including neutral water clusters of varying size that neural networks (NNs) can be used to construct potentials with close to first-principles accuracy. Based on density-functional theory (DFT) calculations, here we present a reactive full-dimensional NN potential for protonated water clusters up to the octamer. A detailed investigation of this potential shows that the energetic, structural, and vibrational properties are in excellent agreement with DFT results making the NN approach a very promising candidate for developing a high-quality potential for water. This finding is further supported by first preliminary but very encouraging NN-based simulations of the bulk liquid. This journal is © the Owner Societies 2015.view abstract doi: 10.1039/c4cp04751f 2015 • 112 Rotational and translational dynamics of CO2 adsorbed in MOF Zn2(bdc)2(dabco)
Peksa, M. and Burrekaew, S. and Schmid, R. and Lang, J. and Stallmach, F.
Microporous and Mesoporous Materials 216 75-81 (2015)The dynamics of adsorbed CO2 in the metal-organic framework Zn2(bdc)2 dabco (DMOF-1) was investigated using molecular dynamics (MD) simulations and 13C NMR spectroscopy. The statistical analysis of the MD trajectories suggest a preferred localization of the CO2 molecules in the Zn2(bdc)4 corners of the DMOF-1 lattice. The adsorbed molecules retain a high but anisotropic rotational and translational mobility in the channel system. Based on these MD-results, the residual chemical shift anisotropy 〈Δδ〉MD = -114 ppm and the diffusion anisotropy (D∥D⊥)MD = 9.8 ± 0.5 were calculated. They are found to be in reasonable agreement with the experimental NMR data of 〈Δδ〉NMR=-(55 ± 2) ppm and (D∥D⊥)NMR = 3 respectively. © 2015 Elsevier Inc. All rights reserved.view abstract doi: 10.1016/j.micromeso.2015.02.043 2015 • 111 Special issue focused on two areas pertinent to chemical biology: Post-translational modifications and new frontiers on kinases
Rauh, D.
ACS Chemical Biology 10 1-2 (2015)doi: 10.1021/acschembio.5b00010 2015 • 110 Spin-torque-induced dynamics at fine-split frequencies in nano-oscillators with two stacked vortices
Sluka, V. and Kákay, A. and Deac, A.M. and Bürgler, D.E. and Schneider, C.M. and Hertel, R.
Nature Communications 6 (2015)The gyrotropic rotation around the equilibrium position constitutes the fundamental excitation of magnetic vortices in nanostructures. The frequency of this mode varies with material and sample geometry, but is independent of the vortex handedness and its core direction. Here, we demonstrate that this degeneracy is lifted in a spin-torque oscillator containing two vortices stacked on top of each other. When driven by spin-polarized currents, such devices exhibit a set of dynamic modes with discretely split frequencies, each corresponding to a specific combination of vorticities and relative core polarities. The fine splitting occurs even in the absence of external fields, demonstrating that such devices can function as zero-field, multi-channel, nano-oscillators for communication technologies. It also facilitates the detection of the relative core polarization and allows for the eight non-degenerate configurations to be distinguished electrically, which may enable the design of multi-state memory devices based on double-vortex nanopillars. © 2015 Macmillan Publishers Limited. All rights reserved.view abstract doi: 10.1038/ncomms7409 2015 • 109 Tectonics of a K+ channel: The importance of the N-terminus for channel gating
Hoffgaard, F. and Kast, S.M. and Moroni, A. and Thiel, G. and Hamacher, K.
Biochimica et Biophysica Acta - Biomembranes 1848 3197-3204 (2015)The small K+ channel Kcv represents the pore module of complex potassium channels. It was found that its gating can be modified by sensor domains, which are N-terminally coupled to the pore. This implies that the short N-terminus of the channel can transmit conformational changes from upstream sensors to the channel gates. To understand the functional role of the N-terminus in the context of the entire channel protein, we apply combinatorial screening of the mechanical coupling and long-range interactions in the Kcv potassium channel by reduced molecular models. The dynamics and mechanical connections in the channel complex show that the N-terminus is indeed mechanically connected to the pore domain. This includes a long rang coupling to the pore and the inner and outer transmembrane domains. Since the latter domains host the two gates of the channel, the data support the hypothesis that mechanical perturbation of the N-terminus can be transmitted to the channel gates. This effect is solely determined by the topology of the channel; sequence details only have an implicit effect on the coarse-grained dynamics via the fold and not through biochemical details at a smaller scale. This observation has important implications for engineering of synthetic channels on the basis of a K+ channel pore. © 2015 Elsevier B.V.All rights reserved.view abstract doi: 10.1016/j.bbamem.2015.09.015 2015 • 108 The dynamic influence of cells on the formation of stable emulsions in organic–aqueous biotransformations
Collins, J. and Grund, M. and Brandenbusch, C. and Sadowski, G. and Schmid, A. and Bühler, B.
Journal of Industrial Microbiology and Biotechnology 42 1011-1026 (2015)Emulsion stability plays a crucial role for mass transfer and downstream processing in organic–aqueous bioprocesses based on whole microbial cells. In this study, emulsion stability dynamics and the factors determining them during two-liquid phase biotransformation were investigated for stereoselective styrene epoxidation catalyzed by recombinant Escherichia coli. Upon organic phase addition, emulsion stability rapidly increased correlating with a loss of solubilized protein from the aqueous cultivation broth and the emergence of a hydrophobic cell fraction associated with the organic–aqueous interface. A novel phase inversion-based method was developed to isolate and analyze cellular material from the interface. In cell-free experiments, a similar loss of aqueous protein did not correlate with high emulsion stability, indicating that the observed particle-based emulsions arise from a convergence of factors related to cell density, protein adsorption, and bioreactor conditions. During styrene epoxidation, emulsion destabilization occurred correlating with product-induced cell toxification. For biphasic whole-cell biotransformations, this study indicates that control of aqueous protein concentrations and selective toxification of cells enables emulsion destabilization and emphasizes that biological factors and related dynamics must be considered in the design and modeling of respective upstream and especially downstream processes. © 2015, Society for Industrial Microbiology and Biotechnology.view abstract doi: 10.1007/s10295-015-1621-x 2015 • 107 The dynamics of TiN x (x = 1-3) admolecule interlayer and intralayer transport on TiN/TiN(001) islands
Edström, D. and Sangiovanni, D.G. and Hultman, L. and Petrov, I. and Greene, J.E. and Chirita, V.
Thin Solid Films 589 133-144 (2015)It has been shown both experimentally and by density functional theory calculations that the primary diffusing species during the epitaxial growth of TiN/TiN(001) are Ti and N adatoms together with TiN<inf>x</inf> complexes (x = 1, 2, 3), in which the dominant N-containing admolecule species depends upon the incident N/Ti flux ratio. Here, we employ classical molecular dynamics (CMD) simulations to probe the dynamics of TiN<inf>x</inf> (x = 1-3) admolecules on 8 × 8 atom square, single-atom-high TiN islands on TiN(001), as well as pathways for descent over island edges. The simulations are carried out at 1000 K, a reasonable epitaxial growth temperature. We find that despite their lower mobility on infinite TiN(001) terraces, both TiN and TiN<inf>2</inf> admolecules funnel toward descending steps and are incorporated into island edges more rapidly than Ti adatoms. On islands, TiN diffuses primarily via concerted translations, but rotation is the preferred diffusion mechanism on infinite terraces. TiN<inf>2</inf> migration is initiated primarily by rotation about one of the N admolecule atoms anchored at an epitaxial site. TiN admolecules descend from islands by direct hopping over edges and by edge exchange reactions, while TiN<inf>2</inf> trimers descend exclusively by hopping. In contrast, TiN<inf>3</inf> admolecules are essentially stationary and serve as initiators for local island growth. Ti adatoms are the fastest diffusing species on infinite TiN(001) terraces, but on small TiN/TiN(001) islands, TiN dimers provide more efficient mass transport. The overall results reveal the effect of the N/Ti precursor flux ratio on TiN(001) surface morphological evolution and growth modes. © 2015 Elsevier B.V.view abstract doi: 10.1016/j.tsf.2015.05.013 2015 • 106 Visualization of nanocrystal breathing modes at extreme strains
Szilagyi, E. and Wittenberg, J.S. and Miller, T.A. and Lutker, K. and Quirin, F. and Lemke, H. and Zhu, D. and Chollet, M. and Robinson, J. and Wen, H. and Sokolowski-Tinten, K. and Lindenberg, A.M.
Nature Communications 6 (2015)Nanoscale dimensions in materials lead to unique electronic and structural properties with applications ranging from site-specific drug delivery to anodes for lithium-ion batteries. These functional properties often involve large-amplitude strains and structural modifications, and thus require an understanding of the dynamics of these processes. Here we use femtosecond X-ray scattering techniques to visualize, in real time and with atomic-scale resolution, light-induced anisotropic strains in nanocrystal spheres and rods. Strains at the percent level are observed in CdS and CdSe samples, associated with a rapid expansion followed by contraction along the nanosphere or nanorod radial direction driven by a transient carrier-induced stress. These morphological changes occur simultaneously with the first steps in the melting transition on hundreds of femtosecond timescales. This work represents the first direct real-time probe of the dynamics of these large-amplitude strains and shape changes in few-nanometre-scale particles. © 2015 Macmillan Publishers Limited. All rights reserved.view abstract doi: 10.1038/ncomms7577 2014 • 105 Ab initio and classical molecular dynamics simulations of N2 desorption from TiN(001) surfaces
Sangiovanni, D.G. and Edström, D. and Hultman, L. and Petrov, I. and Greene, J.E. and Chirita, V.
Surface Science 624 25-31 (2014)Ab initio molecular dynamics simulations based on density functional theory show that N adatoms are chemisorbed in threefold sites close to a N surface atom and between the two diagonally opposed neighboring Ti surface atoms on TiN(001). The most probable N adatom reaction pathway, even in the presence of nearby N adatoms, is for the N adatom and N surface atom pair to first undergo several exchange reactions and then desorb as a N2 molecule, resulting in a surface anion vacancy, with an activation barrier Edes of 1.37 eV and an attempt frequency Ades = 3.4 × 10 13 s- 1. Edes is essentially equal to the N adatom surface diffusion barrier, Es = 1.39 eV, while As is only three to four times larger than Ades, indicating that isolated N adatoms migrate for only short distances prior to N2 desorption. The probability of N2 desorption via recombination of N adatoms on TiN(001) is much lower due to repulsive adatom/adatom interactions at separations less than ~ 3 Å which rapidly increase to ~ 2 eV at a separation of 1.5 Å. We obtain good qualitative and quantitative agreement with the above results using the modified embedded atom method potential to perform classical molecular dynamics simulations. © 2014 Elsevier B.V.view abstract doi: 10.1016/j.susc.2014.01.007 2014 • 104 Anharmonicity, mechanical instability, and thermodynamic properties of the Cr-Re σ-phase
Palumbo, M. and Fries, S.G. and Pasturel, A. and Alfè, D.
Journal of Chemical Physics 140 (2014)Using density-functional theory in combination with the direct force method and molecular dynamics we investigate the vibrational properties of a binary Cr-Re σ-phase. In the harmonic approximation, we have computed phonon dispersion curves and density of states, evidencing structural and chemical effects. We found that the σ-phase is mechanically unstable in some configurations, for example, when all crystallographic sites are occupied by Re atoms. By using a molecular-dynamics-based method, we have analysed the anharmonicity in the system and found negligible effects (∼0.5 kJ/mol) on the Helmholtz energy of the binary Cr-Re σ-phase up to 2000 K (∼0.8Tm). Finally, we show that the vibrational contribution has significant consequences on the disordering of the σ-phase at high temperature. © 2014 AIP Publishing LLC.view abstract doi: 10.1063/1.4869800 2014 • 103 Anomalously large isotope effect in the glass transition of water
Gainaru, C. and Agapov, A.L. and Fuentes-Landete, V. and Amann-Winkel, K. and Nelson, H. and Köster, K.W. and Kolesnikov, A.I. and Novikov, V.N. and Richert, R. and Böhmer, R. and Loerting, T. and Sokolov, A.
Proceedings of the National Academy of Sciences of the United States of America 111 17402-17407 (2014)We present the discovery of an unusually large isotope effect in the structural relaxation and the glass transition temperature Tg of water. Dielectric relaxation spectroscopy of low-density as well as of vapor-deposited amorphous water reveal Tg differences of 10 ± 2 K between H2O and D2O, sharply contrasting with other hydrogen- bonded liquids for which H/D exchange increases Tg by typically less than 1 K. We show that the large isotope effect and the unusual variation of relaxation times in water at low temperatures can be explained in terms of quantum effects. Thus, our findings shed new light on water's peculiar low-temperature dynamics and the possible role of quantum effects in its structural relaxation, and possibly in dynamics of other low-molecularweight liquids.view abstract doi: 10.1073/pnas.1411620111 2014 • 102 Atomistic simulation of the a0 〈1 0 0〉 binary junction formation and its unzipping in body-centered cubic iron
Hafez Haghighat, S.M. and Schäublin, R. and Raabe, D.
Acta Materialia 64 24-32 (2014)Molecular dynamics simulation is used to study the formation of the a 0 〈1 0 0〉 binary dislocation junction in body-centered cubic Fe. Results show that under an applied strain two intersecting 1/2 a 0 〈1 1 1〉 dislocations, one mobile edge and one immobile screw, form an a0 〈1 0 0〉 binary junction of mixed character in the glide plane of the mobile edge dislocation. It appears, however, that the binary junction does not necessarily lay in one of the three possible {1 1 0} glide planes of the screw dislocation. The binary junction starts to unzip as the impinging edge dislocation bows around and moves away, which results in the formation of a screw dipole along its Burgers vector. The dipole eventually annihilates, completing the unzipping process of the junction, which liberates the edge dislocation. The effects of temperature and strain rate on the unzipping of the junction are quantified by the critical release stress needed to detach the edge dislocation from the screw one. The critical stress decreases when the temperature increases from 10 to 300 K, whereas it increases with increasing applied strain rate, or dislocation speed. The interaction mechanism and strength of the a0 〈1 0 0〉 binary junction as an obstacle to the edge dislocation are compared to that of other types of defect, namely nanosized voids, Cu and Cr precipitates, and dislocation loops in Fe. It appears that the binary junction strength is in the lowest range, comparable to that of a coherent Cr precipitate. © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.view abstract doi: 10.1016/j.actamat.2013.11.037 2014 • 101 Atomistic study of the influence of lattice defects on the thermal conductivity of silicon
Wang, T. and Madsen, G.K.H. and Hartmaier, A.
Modelling and Simulation in Materials Science and Engineering 22 (2014)Lattice defects such as vacancies, voids and dislocations are inevitably present in any material of technological interest. In this work, non-equilibrium molecular dynamics simulations are conducted to investigate how the monatomic vacancies and nanovoids influence the lattice thermal conductivity of silicon. The results show a clear non-linear decrease of the thermal conductivity with increasing defect volume fraction. Furthermore, it is found that for a given volume fraction of defects, a random distribution shows a lower lattice thermal conductivity. To develop a fundamental understanding of these observations, the spectral energy densities for all phonon branches obtained from 2D Fourier transformations of the atomic trajectories are analyzed. This yields the mean phonon group velocities and relaxation times, which are the main physical quantities contributing to the lattice thermal conductivity. Our analysis reveals that the phonon relaxation time is the most important parameter for describing the degrading of the thermal transport behavior in the defected structures. © 2014 IOP Publishing Ltd.view abstract doi: 10.1088/0965-0393/22/3/035011 2014 • 100 Bridge function of the repulsive Weeks-Chandler-Andersen (WCA) fluid
Tomazic, D. and Hoffgaard, F. and Kast, S.M.
Chemical Physics Letters 591 237-242 (2014)The bridge function of a simple liquid is calculated for the repulsive part of the Weeks-Chandler-Andersen (WCA) separation of the Lennard-Jones potential. We employ explicit molecular dynamics simulations of the potential of mean force between constrained dimers in order to extract bridge data near zero separation and illustrate the difference to full Lennard-Jones results. We compare direct, reciprocal space and iterative, real space inversions of the Ornstein-Zernike equation. Bridge functions for various thermodynamic states are analyzed as to their parametric dependence on the renormalized indirect correlation function, which has consequences for the analytic representation of the free energy functional. © 2013 Elsevier B.V. All rights reserved.view abstract doi: 10.1016/j.cplett.2013.11.025 2014 • 99 Convergence of an analytic bond-order potential for collinear magnetism in Fe
Ford, M.E. and Drautz, R. and Hammerschmidt, T. and Pettifor, D.G.
Modelling and Simulation in Materials Science and Engineering 22 (2014)Analytic bond-order potentials (BOPs) for magnetic transition metals are applied for pure iron as described by an orthogonal d-valent tight-binding (TB) model. Explicit analytic equations for the gradients of the binding energy with respect to the Hamiltonian on-site levels are presented, and are then used to minimize the energy with respect to the magnetic moments, which is equivalent to a TB self-consistency scheme. These gradients are also used to calculate the exact forces, consistent with the energy, necessary for efficient relaxations and molecular dynamics. The Jackson kernel is used to remove unphysical negative densities of states, and approximations for the asymptotic recursion coefficients are examined. BOP, TB and density functional theory results are compared for a range of bulk and defect magnetic structures. The BOP energies and magnetic moments for bulk structures are shown to converge with increasing numbers of moments, with nine moments sufficient for a quantitative comparison of structural energy differences. The formation energies of simple defects such as the monovacancies and divacancies also converge rapidly. Other physical quantities, such as the position of the high-spin to low-spin transition in ferromagnetic fcc (face centred cubic) iron, surface peaks in the local density of states, the elastic constants and the formation energies of the self-interstitial atom defects, require higher moments for convergence. © 2014 IOP Publishing Ltd.view abstract doi: 10.1088/0965-0393/22/3/034005 2014 • 98 Double layer effects in a model of proton discharge on charged electrodes
Wiebe, J. and Spohr, E.
Beilstein Journal of Nanotechnology 5 973-982 (2014)We report first results on double layer effects on proton discharge reactions from aqueous solutions to charged platinum electrodes. We have extended a recently developed combined proton transfer/proton discharge model on the basis of empirical valence bond theory to include specifically adsorbed sodium cations and chloride anions. For each of four studied systems 800-1000 trajectories of a discharging proton were integrated by molecular dynamics simulations until discharge occurred. The results show significant influences of ion presence on the average behavior of protons prior to the discharge event. Rationalization of the observed behavior cannot be based solely on the electrochemical potential (or surface charge) but needs to resort to the molecular details of the double layer structure. © 2014 Wiebe and Spohr; licensee Beilstein-Institut.view abstract doi: 10.3762/bjnano.5.111 2014 • 97 Ferrocene in the metal-organic framework MOF-5 studied by homo- and heteronuclear correlation NMR and MD simulation
Wehring, M. and Magusin, P.C.M.M. and Amirjalayer, S. and Schmid, R. and Stallmach, F.
Microporous and Mesoporous Materials 186 130-136 (2014)Advanced solid-state 2D NMR spectroscopy and molecular dynamics computation are employed to investigate the interaction between adsorbed ferrocene molecules and the MOF-5 lattice. Relayed 13C-1H heteronuclear correlation (HETCOR) 2D NMR spectra clearly indicate short-distance contacts between the ferrocene guests and the benzene-1,4-dicarboxylic-acid linkers, mediated via intermolecular 1 H spin diffusion. By use of 2D 1H-1H correlation spectroscopy the distances between 1H nuclei in the guests and the linkers are estimated to be shorter than 0.5 nm. MD computer simulations support the interpretation of the 2D solid state NMR studies. Moreover, they suggest a wide distribution of intermolecular distances in this host-guest system with the shortest intermolecular hydrogen-hydrogen distances of 0.15 nm. © 2013 Elsevier Inc. All rights reserved.view abstract doi: 10.1016/j.micromeso.2013.11.045 2014 • 96 In situ nanoparticle size measurements of gas-borne silicon nanoparticles by time-resolved laser-induced incandescence
Sipkens, T.A. and Mansmann, R. and Daun, K.J. and Petermann, N. and Titantah, J.T. and Karttunen, M. and Wiggers, H. and Dreier, T. and Schulz, C.
Applied Physics B: Lasers and Optics 116 623-636 (2014)This paper describes the application of time-resolved laser-induced incandescence (TiRe-LII), a combustion diagnostic used mainly for measuring soot primary particles, to size silicon nanoparticles formed within a plasma reactor. Inferring nanoparticle sizes from TiRe-LII data requires knowledge of the heat transfer through which the laser-heated nanoparticles equilibrate with their surroundings. Models of the free molecular conduction and evaporation are derived, including a thermal accommodation coefficient found through molecular dynamics. The model is used to analyze TiRe-LII measurements made on silicon nanoparticles synthesized in a low-pressure plasma reactor containing argon and hydrogen. Nanoparticle sizes inferred from the TiRe-LII data agree with the results of a Brunauer-Emmett-Teller analysis. © 2013 Springer-Verlag Berlin Heidelberg.view abstract doi: 10.1007/s00340-013-5745-2 2014 • 95 In Situ Particle Size Measurements of Gas-borne Silicon Nanoparticles by Time-resolved Laser-induced Incandescence
Sipkens, T. A. and Petermann, N. and Daun, K. J. and Titantah, J. and Karttunen, M. and Wiggers, H. and Dreier, T. and Schulz, C.
Proceedings of the Asme Summer Heat Transfer Conference - 2013, Vol 1 V001T03A001 (2014)The functionality of silicon nanoparticles is strongly size-dependent, so there is a pressing need for laser diagnostics that can characterize aerosolized silicon nanoparticles. The present work is the first attempt to extend time-resolved laser-induced incandescence (TiRe-LII), a combustion diagnostic used for sizing soot, to size silicon nanoparticles. TiRe-LII measurements are made on silicon nanoparticles synthesized in a low-pressure plasma reactor containing argon. Molecular dynamics (MD) is used to predict the accommodation coefficient between silicon nanoparticles and argon and helium, which is needed to interpret the TiRe-LII data. The MD-derived thermal accommodation coefficients will be validated by comparing them to experimentally-derived values found using transmission electron microscopy (TEM) and Brunauer-Emmett-Teller (BET) analysis.view abstract doi: 10.1115/HT2013-17246 2014 • 94 Influence of the dislocation core on the glide of the 〈1 1 〉{1 1 0} edge dislocation in bcc-iron: An embedded atom method study
Hafez Haghighat, S.M. and Von Pezold, J. and Race, C.P. and Körmann, F. and Friák, M. and Neugebauer, J. and Raabe, D.
Computational Materials Science 87 274-282 (2014)Four commonly used embedded atom method potentials for bcc-Fe by Ackland et al. (1997), Mendelev et al. (2003), Chiesa et al. (2009) and Malerba et al. (2010) are critically evaluated with respect to their description of the edge dislocation core structure and its dynamic behavior. Our results allow us to quantify the transferability of the various empirical potentials in the study of the 〈1 1 〉{1 1 0} edge dislocation core structure and kinetics. Specifically, we show that the equilibrium dislocation core structure is a direct consequence of the shape of the extended gamma surface. We further find that there is a strong correlation between the structure of the edge dislocation core and its glide stress. An in depth analysis of the dislocation migration results reveals that the dominant migration mechanism is via progressing straight line segments of the dislocation. This is further confirmed by the excellent qualitative agreement of nudged elastic band calculations of the Peierls barrier with the dynamically determined critical shear stresses. © 2014 Elsevier B.V. All rights reserved.view abstract doi: 10.1016/j.commatsci.2014.02.031 2014 • 93 Interaction of charged amino-acid side chains with ions: An optimization strategy for classical force fields
Kahlen, J. and Salimi, L. and Sulpizi, M. and Peter, C. and Donadio, D.
Journal of Physical Chemistry B 118 3960-3972 (2014)Many well-established classical biomolecular force fields, fitted on the solvation properties of single ions, do not necessarily describe all the details of ion pairing accurately, especially for complex polyatomic ions. Depending on the target application, it might not be sufficient to reproduce the thermodynamics of ion pairing, but it may also be necessary to correctly capture structural details, such as the coordination mode. In this work, we analyzed how classical force fields can be optimized to yield a realistic description of these different aspects of ion pairing. Given the prominent role of the interactions of negatively charged amino-acid side chains and divalent cations in many biomolecular systems, we chose calcium acetate as a benchmark system to devise a general optimization strategy that we applied to two popular force fields, namely, GROMOS and OPLS-AA. Using experimental association constants and first-principles molecular dynamics simulations as a reference, we found that small modifications of the van der Waals ion-ion interaction parameters allow a systematic improvement of the essential thermodynamic and structural properties of ion pairing. © 2014 American Chemical Society.view abstract doi: 10.1021/jp412490c 2014 • 92 Intrinsic acidity of surface sites in calcium silicate hydrates and its implication to their electrokinetic properties
Churakov, S.V. and Labbez, C. and Pegado, L. and Sulpizi, M.
Journal of Physical Chemistry C 118 11752-11762 (2014)Calcium Silicate Hydrates (C-S-H) are the major hydration products of portland cement paste. The accurate description of acid-base reactions at the surface of C-S-H particles is essential for both understanding the ion sorption equilibrium in cement and prediction of mechanical properties of the hardened cement paste. Ab initio molecular dynamics simulations at the density functional level of theory were applied to calculate intrinsic acidity constants (pK a's) of the relevant -SiOH and -CaOH2 groups on the C-S-H surfaces using a thermodynamic integration technique. Ion sorption equilibrium in C-S-H was modeled applying ab initio calculated pKa's in titrating Grand Canonical Monte Carlo simulations using a coarse-grained model for C-S-H/solution interface in the framework of the Primitive Model for electrolytes. The modeling results were compared with available data from electrophoretic measurements. The model predictions were found to satisfactorily reproduce available experimental data. © 2014 American Chemical Society.view abstract doi: 10.1021/jp502514a 2014 • 91 Liquid-solid interfaces: Structure and dynamics from spectroscopy and simulations
Gaigeot, M.-P. and Sulpizi, M.
Journal of Physics Condensed Matter 26 (2014)doi: 10.1088/0953-8984/26/24/240301 2014 • 90 Molecular dynamics studies of poly(N-isopropylacrylamide) endgrafted on the surfaces of model slab pores
Lorbeer, L. and Alaghemandi, M. and Spohr, E.
Journal of Molecular Liquids 189 57-62 (2014)We report first results of a systematic study of the properties of thermo-responsive polymer chains of poly(N-isopropylacrylamide) (PNIPAM), which are endgrafted onto the inner surfaces of a slab pore of approximately 9 nm width. We have systematically varied the strength of the PNIPAM-surface interaction energy to estimate the variation of the extent of the thermo-responsive effect on different surfaces. For weak to intermediate PNIPAM-surface interactions, the MD simulations show thermo-responsive behavior as characteristic changes of the radius of gyration and other measures of the polymer structure and polymer-water interactions, when comparing simulations below (at 280 K) and above (at 320 K) the lower critical solution temperature of PNIPAM, which is at 305 K. When the PNIPAM-surface interactions become stronger, the polymer loses its thermo-responsive behavior and is adsorbed flatly on the pore walls at both investigated temperatures. © 2013 Elsevier B.V. All rights reserved.view abstract doi: 10.1016/j.molliq.2013.05.022 2014 • 89 Multiple reentrant glass transitions in confined hard-sphere glasses
Mandal, S. and Lang, S. and Gross, M. and Oettel, M. and Raabe, D. and Franosch, T. and Varnik, F.
Nature Communications 5 (2014)Glass-forming liquids exhibit a rich phenomenology upon confinement. This is often related to the effects arising from wall-fluid interactions. Here we focus on the interesting limit where the separation of the confining walls becomes of the order of a few particle diameters. For a moderately polydisperse, densely packed hard-sphere fluid confined between two smooth hard walls, we show via event-driven molecular dynamics simulations the emergence of a multiple reentrant glass transition scenario upon a variation of the wall separation. Using thermodynamic relations, this reentrant phenomenon is shown to persist also under constant chemical potential. This allows straightforward experimental investigation and opens the way to a variety of applications in micro-and nanotechnology, where channel dimensions are comparable to the size of the contained particles. The results are in line with theoretical predictions obtained by a combination of density functional theory and the mode-coupling theory of the glass transition. © 2014 Macmillan Publishers Limited.view abstract doi: 10.1038/ncomms5435 2014 • 88 Representing potential energy surfaces by high-dimensional neural network potentials
Behler, J.
Journal of Physics Condensed Matter 26 (2014)The development of interatomic potentials employing artificial neural networks has seen tremendous progress in recent years. While until recently the applicability of neural network potentials (NNPs) has been restricted to low-dimensional systems, this limitation has now been overcome and high-dimensional NNPs can be used in large-scale molecular dynamics simulations of thousands of atoms. NNPs are constructed by adjusting a set of parameters using data from electronic structure calculations, and in many cases energies and forces can be obtained with very high accuracy. Therefore, NNP-based simulation results are often very close to those gained by a direct application of first-principles methods. In this review, the basic methodology of high-dimensional NNPs will be presented with a special focus on the scope and the remaining limitations of this approach. The development of NNPs requires substantial computational effort as typically thousands of reference calculations are required. Still, if the problem to be studied involves very large systems or long simulation times this overhead is regained quickly. Further, the method is still limited to systems containing about three or four chemical elements due to the rapidly increasing complexity of the configuration space, although many atoms of each species can be present. Due to the ability of NNPs to describe even extremely complex atomic configurations with excellent accuracy irrespective of the nature of the atomic interactions, they represent a general and therefore widely applicable technique, e.g. for addressing problems in materials science, for investigating properties of interfaces, and for studying solvation processes. © 2014 IOP Publishing Ltd.view abstract doi: 10.1088/0953-8984/26/18/183001 2014 • 87 Scale bridging between atomistic and mesoscale modelling: Applications of amplitude equation descriptions
Hüter, C. and Nguyen, C.-D. and Spatschek, R. and Neugebauer, J.
Modelling and Simulation in Materials Science and Engineering 22 (2014)Amplitude equations are discussed as an extension of phase field models, which contain atomic resolution and allow one to describe polycrystalline structures, lattice deformations and defects. The interaction of adjacent grains, which are separated by a thin melt layer, leads to structural interactions if the grains are slightly misplaced, similar to the concept of γ-surfaces. We are able to predict these interactions essentially analytically, leading to a superposition of short-ranged interaction terms related to the individual density waves. Deviations from the analytical predictions are found only at short distances between the grains and are most pronounced in situations with different ranges of the contributions. Furthermore, we demonstrate the ability of the amplitude equation model to predict dislocation pairing transitions at high temperatures, which supports earlier findings using molecular dynamics and phase field crystal simulations. To effectively perform the numerical simulations, we present a way to implement the model on graphics cards. An enormous acceleration of the code in comparison to a single CPU code by up to two orders of magnitude is reached. © 2014 IOP Publishing Ltd.view abstract doi: 10.1088/0965-0393/22/3/034001 2014 • 86 The amorphous silica-liquid water interface studied by ab initio molecular dynamics (AIMD): Local organization in global disorder
Cimas, Á. and Tielens, F. and Sulpizi, M. and Gaigeot, M.-P. and Costa, D.
Journal of Physics Condensed Matter 26 (2014)The structural organization of water at a model of amorphous silica-liquid water interface is investigated by ab initio molecular dynamics (AIMD) simulations at room temperature. The amorphous surface is constructed with isolated, H-bonded vicinal and geminal silanols. In the absence of water, the silanols have orientations that depend on the local surface topology (i.e. presence of concave and convex zones). However, in the presence of liquid water, only the strong inter-silanol H-bonds are maintained, whereas the weaker ones are replaced by H-bonds formed with interfacial water molecules. All silanols are found to act as H-bond donors to water. The vicinal silanols are simultaneously found to be H-bond acceptors from water. The geminal pairs are also characterized by the formation of water H-bonded rings, which could provide special pathways for proton transfer(s) at the interface. The first water layer above the surface is overall rather disordered, with three main domains of orientations of the water molecules. We discuss the similarities and differences in the structural organization of the interfacial water layer at the surface of the amorphous silica and at the surface of the crystalline (0 0 0 1) quartz surface. © 2014 IOP Publishing Ltd.view abstract doi: 10.1088/0953-8984/26/24/244106 2014 • 85 Thermal conductivity of isotopically controlled silicon nanostructures
Bracht, H. and Eon, S. and Frieling, R. and Plech, A. and Issenmann, D. and Wolf, D. and Lundsgaard Hansen, J. and Nylandsted Larsen, A. and Ager Iii, J.W. and Haller, E.E.
New Journal of Physics 16 (2014)Nanostructured semiconductors open the opportunity to independently tailor electric and thermal conductivity by manipulation of the phonon transport. Nanostructuring of materials is a highly promising strategy for engineering thermoelectric devices with improved efficiency. The concept of reducing the thermal conductivity without degrading the electrical conductivity is most ideally realized by controlled isotope doping. This work reports on experimental and theoretical investigations on the thermal conductivity of isotopically modulated silicon nanostructures. State-of-the-art pump-and-probe experiments are conducted to determine the thermal conductivity of the different nanostructures of isotopically enriched silicon layers epitaxially grown on natural silicon substrates. Concomitant molecular dynamics calculations are performed to study the impact of the silicon isotope mass, isotope interfaces, and of the isotope layer ordering and thickness on the thermal conductivity. Engineering the isotope distribution is a striking concept to reduce the thermal conductivity of silicon without affecting its electronic properties. This approach, using isotopically engineered silicon, might pave the way for future commercial thermoelectric devices. © 2014 IOP Publishing and Deutsche Physikalische Gesellschaft.view abstract doi: 10.1088/1367-2630/16/1/015021 2014 • 84 Ti and N adatom descent pathways to the terrace from atop two-dimensional TiN/TiN(001) islands
Edström, D. and Sangiovanni, D.G. and Hultman, L. and Chirita, V. and Petrov, I. and Greene, J.E.
Thin Solid Films 558 37-46 (2014)We use classical molecular dynamics and the modified embedded atom method to determine residence times and descent pathways of Ti and N adatoms on square, single-atom-high, TiN islands on TiN(001). Simulations are carried out at 1000 K, which is within the optimal range for TiN(001) epitaxial growth. Results show that the frequency of descent events, and overall adatom residence times, depend strongly on both the TiN(001) diffusion barrier for each species as well as the adatom island-edge location immediately prior to descent. Ti adatoms, with a low diffusion barrier, rapidly move toward the island periphery, via funneling, where they diffuse along upper island edges. The primary descent mechanism for Ti adatoms is via push-out/exchange with Ti island-edge atoms, a process in which the adatom replaces an island edge atom by moving down while pushing the edge atom out onto the terrace to occupy an epitaxial position along the island edge. Double push-out events are also observed for Ti adatoms descending at N corner positions. N adatoms, with a considerably higher diffusion barrier on TiN(001), require much longer times to reach island edges and, consequently, have significantly longer residence times. N adatoms are found to descend onto the terrace by direct hopping over island edges and corner atoms, as well as by concerted push-out/exchange with N atoms adjacent to Ti corners. For both adspecies, we also observe several complex adatom/island interactions, before and after descent onto the terrace, including two instances of Ti island-atom ascent onto the island surface. © 2014 Elsevier B.V. All rights reserved.view abstract doi: 10.1016/j.tsf.2014.02.053 2014 • 83 Tribenzotriquinacene receptors for C60 fullerene rotors: Towards C3 symmetrical chiral stators for unidirectionally operating nanoratchets
Bredenkötter, B. and Grzywa, M. and Alaghemandi, M. and Schmid, R. and Herrebout, W. and Bultinck, P. and Volkmer, D.
Chemistry - A European Journal 20 9100-9110 (2014)The synthesis of a stereochemically pure concave tribenzotriquinacene receptor (7) for C60 fullerene, possessing C3 point group symmetry, by threefold condensation of C2-symmetric 1,2-diketone synthons (5) and a hexaaminotribenzotriquinacene core (6) is described. The chiral diketone was synthesized in a five-step reaction sequence starting from C2h-symmetric 2,6-di-tert-butylanthracene. The highly diastereo-discriminating Diels-Alder reaction of 2,6-di-tert-butylanthracene with fumaric acid di(-)menthyl ester, catalyzed by aluminium chloride, is the relevant stereochemistry introducing step. The structure of the fullerene receptor was verified by 1H and 13C NMR spectroscopy, mass spectrometry and single crystal X-ray diffraction. VCD and ECD spectra were recorded, which were corroborated by ab initio DFT calculations, establishing the chiral nature of 7 with about 99.7 % ee, based on the ee (99.9 %) of the chiral synthon (1). The absolute configuration of 7 could thus be established as all-S [(2S,7S,16S,21S,30S,35S)-(7)]. Spectroscopic titration experiments reveal that the host forms 1:1 complexes with either pure fullerene (C60) or fullerene derivatives, such as rotor 1'-(4-nitrophenyl)-3'-(4-N,N- dimethylaminophenyl)-pyrazolino[4',5':1,2][60]fullerene (R). The complex stability constants of the complexes dissolved in CHCl3/CS 2 (1:1 vol. %) are K([C60-7])=319(±156) M -1 and K([R-7])=110(±50) M-1. With molecular dynamics simulations using a first-principles parameterized force field the asymmetry of the rotational potential for [R-7] was shown, demonstrating the potential suitability of receptor 7 to act as a stator in a unidirectionally operating nanoratchet. Going through the motions: The synthesis of a stereochemically pure concave tribenzotriquinacene receptor (1) for C 60 fullerenes is described. Spectroscopic titration experiments reveal that the host forms 1:1 complexes with fullerenes. Molecular dynamics simulations show the asymmetry of the rotational potential for [R-1], demonstrating the potential suitability of receptor 1 to act as a stator in a unidirectionally operating nanoratchet (see figure). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.view abstract doi: 10.1002/chem.201304980 2013 • 82 A density-functional theory-based neural network potential for water clusters including van der waals corrections
Morawietz, T. and Behler, J.
Journal of Physical Chemistry A 117 7356-7366 (2013)The fundamental importance of water for many chemical processes has motivated the development of countless efficient but approximate water potentials for large-scale molecular dynamics simulations, from simple empirical force fields to very sophisticated flexible water models. Accurate and generally applicable water potentials should fulfill a number of requirements. They should have a quality close to quantum chemical methods, they should explicitly depend on all degrees of freedom including all relevant many-body interactions, and they should be able to describe molecular dissociation and recombination. In this work, we present a high-dimensional neural network (NN) potential for water clusters based on density-functional theory (DFT) calculations, which is constructed using clusters containing up to 10 monomers and is in principle able to meet all these requirements. We investigate the reliability of specific parametrizations employing two frequently used generalized gradient approximation (GGA) exchange-correlation functionals, PBE and RPBE, as reference methods. We find that the binding energy errors of the NN potentials with respect to DFT are significantly lower than the typical uncertainties of DFT calculations arising from the choice of the exchange-correlation functional. Further, we examine the role of van der Waals interactions, which are not properly described by GGA functionals. Specifically, we incorporate the D3 scheme suggested by Grimme (J. Chem. Phys. 2010, 132, 154104) in our potentials and demonstrate that it can be applied to GGA-based NN potentials in the same way as to DFT calculations without modification. Our results show that the description of small water clusters provided by the RPBE functional is significantly improved if van der Waals interactions are included, while in case of the PBE functional, which is well-known to yield stronger binding than RPBE, van der Waals corrections lead to overestimated binding energies. © 2013 American Chemical Society.view abstract doi: 10.1021/jp401225b 2013 • 81 A full-dimensional neural network potential-energy surface for water clusters up to the hexamer
Morawietz, T. and Behler, J.
Zeitschrift fur Physikalische Chemie 227 1559-1581 (2013)Water clusters have attracted a lot of attention as prototype systems to study hydrogen bonded molecular aggregates but also to gain deeper insights into the properties of liquid water, the solvent of life. All these studies depend on an accurate description of the atomic interactions and countless potentials have been proposed in the literature in the past decades to represent the potential-energy surface (PES) of water. Many of these potentials employ drastic approximations like rigid water monomers and fixed point charges, while on the other hand also several attempts have been made to derive very accurate PESs by fitting data obtained in high-level electronic structure calculations. In recent years artificial neural networks (NNs) have been established as a powerful tool to construct high-dimensional PESs of a variety of systems, but to date no full-dimensional NN PES for water has been reported. Here, we present NN potentials for water clusters containing two to six water molecules trained to density functional theory (DFT) data employing two different exchange-correlation functionals, PBE and RPBE. In contrast to other potentials fitted to first principles data, these NN potentials are not based on a truncated many-body expansion of the energy but consider the interactions between all water molecules explicitly. For both functionals an excellent agreement with the underlying DFT calculations has been found with binding energy errors of only about 1%.© by Oldenbourg Wissenschaftsverlag, München.view abstract doi: 10.1524/zpch.2013.0384 2013 • 80 A molecular dynamics study of poly(N-isopropylacrylamide) endgrafted on a model cylindrical pore surface
Alaghemandi, M. and Spohr, E.
RSC Advances 3 3638-3647 (2013)Structure and dynamic behavior of the thermo-responsive polymer poly(N-isopropylacrylamide) (PNIPAM) endgrafted onto the inner surface of a simple cylindrical pore model that resembles a carbon nanotube (CNT) with a diameter of 8.4 nm is studied as a function of temperature, of surface-polymer interaction strength, and of pore water content. A free PNIPAM chain in water shows thermo-responsive behavior with a lower critical solution temperature (LCST) of about 305 K. We have investigated two different strengths of PNIPAM-pore interactions. In the strong interaction case, which corresponds to force-field parameters taken without change from the AMBER force field, the endgrafted PNIPAM chain collapses onto the surface at all temperatures studied and hence does not adopt a brush structure. In the weak interaction case the PNIPAM-pore interaction strengths were scaled by a factor of 10, and the temperature-responsive behavior of the PNIPAM chain re-emerges. End-to-end distances, radii of gyration, density profiles, number of hydrogen bonds, and radial distribution functions demonstrate the temperature-dependent structural changes of endgrafted PNIPAM in the pore. Analysis of the translational motion of water molecules in the pore shows that the ratio of the water self diffusion coefficient in a pore with a free pore surface relative to the self diffusion coefficient in a pore containing an end-grafted PNIPAM molecule is less strongly reduced above the LCST than below the LCST, where the chain is in a more extended state. © 2013 The Royal Society of Chemistry.view abstract doi: 10.1039/c3ra22266g 2013 • 79 A new class of nanoengines based on thermoresponsive polymers: Conceptual design and behavior study
Alaghemandi, M. and Spohr, E.
Chemical Physics Letters 581 80-84 (2013)A model nanoengine based on endgrafted Poly(N-isopropylacrylamide) (PNIPAM) on graphene-like sheets is proposed. The nanoengine consists of a water-filled slab and four PNIPAM chains, which are at one end grafted to one of the slab walls and on the other end to a mobile square graphene 'piston'. The basis of the reciprocating motion of the piston is the reversible coil-to-globule transition of polymer chains when changing the temperature of the aqueous environment. Molecular dynamics simulations have been used to investigate the behavior of the proposed system at the full atomistic level. At temperatures below the lower critical solution temperature (LCST) PNIPAM chains are swollen and the nanopiston is in an expanded open state. Above the LCST, the PNIPAM chains are shrunken and the piston is retracted. The studied nanopiston exhibits an amplitude of approximately 10 Å when the temperature is reduced from 310 to 300 K or increased from 300 to 310 K with a frequency of about 10 9 rotations per minute; however the efficiency is very low. © 2013 Elsevier B.V. All rights reserved.view abstract doi: 10.1016/j.cplett.2013.07.017 2013 • 78 Ab Initio Based conformational study of the crystalline α-chitin
Petrov, M. and Lymperakis, L. and Friák, M. and Neugebauer, J.
Biopolymers 99 22-34 (2013)The equilibrium structure including the network of hydrogen bonds of an α-chitin crystal is determined combining density-functional theory (DFT), self-consistent DFT-based tight-binding (SCC-DFTB), and empirical forcefield molecular dynamics (MD) simulations. Based on the equilibrium geometry several possible crystal conformations (local energy minima) have been identified and related to hydrogen bond patterns. Our results provide new insight and allow to resolve the contradicting α-chitin structural models proposed by various experiments. © 2012 Wiley Periodicals, Inc. Copyright © 2012 Wiley Periodicals, Inc.view abstract doi: 10.1002/bip.22131 2013 • 77 Bifurcation of velocity distributions in cooperative transport of filaments by fast and slow motors
Li, X. and Lipowsky, R. and Kierfeld, J.
Biophysical Journal 104 666-676 (2013)Several intracellular processes are governed by two different species of molecular motors, fast and slow ones, that both move in the same direction along the filaments but with different velocities. The transport of filaments arising from the cooperative action of these motors has been recently studied by three in vitro experiments, in which the filament velocity was measured for varying fraction of the fast motors adsorbed onto substrate surfaces in a gliding assay. As the fast motor fraction was increased, two experiments found a smooth change whereas the third one observed an abrupt increase of the filament velocity. Here, we show that all of these experimental results reflect the competition between fast and slow motors and can be understood in terms of an underlying saddle-node bifurcation. The comparison between theory and experiment leads to predictions for the detachment forces of the two motor species. Our theoretical study shows the existence of three different motility regimes: 1), fast transport with a single velocity; 2), slow transport with a single velocity; and 3), bistable transport, where the filament velocity stochastically switches between fast and slow transport. We determine the parameter regions for these regimes in terms of motility diagrams as a function of the surface fraction of fast motors and microscopic single-motor parameters. An abrupt increase of the filament velocity for an increasing fraction of fast motors is associated with the occurrence of bistable transport. © 2013 Biophysical Society.view abstract doi: 10.1016/j.bpj.2012.11.3834 2013 • 76 Breakdown of Stokes-Einstein relation in the supercooled liquid state of phase change materials [Phys. Status Solidi B 249, No. 10, 1880-1885 (2012)]
Sosso, G.C. and Behler, J. and Bernasconi, M.
Physica Status Solidi (B) Basic Research 250 1453-1453 (2013)Values of the melting temperature at normal pressure $T_m$, of the slope of the melting line, and of the activation energies for the diffusion coefficient and viscosity are corrected. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.view abstract doi: 10.1002/pssb.201349218 2013 • 75 Broadband dynamics in neat 4-methyl-3-heptanol and in mixtures with 2-ethyl-1-hexanol
Bauer, S. and Wittkamp, H. and Schildmann, S. and Frey, M. and Hiller, W. and Hecksher, T. and Olsen, N.B. and Gainaru, C. and Böhmer, R.
Journal of Chemical Physics 139 (2013)The relatively small dielectric Debye-like process of the monohydroxy alcohol 4-methyl-3-heptanol (4M3H) was found to depend slightly on the intramolecular conformation. Proton and deuteron nuclear magnetic resonance demonstrate that the hydroxyl dynamics and the overall molecular dynamics take place on similar time scales in contrast to the situation for the structural isomer 2-ethyl-1-hexanol (2E1H) [S. Schildmann, J. Chem. Phys. 135, 174511 (2011)]. This indicates a very weak decoupling of Debye-like and structural relaxation which was further probed using volume expansivity experiments. Shear viscosity as well as diffusometry measurements were performed and the data were analyzed in terms of the Debye-Stokes-Einstein equations. In mixtures of 4M3H with 2E1H the Debye-like process becomes much stronger and for 2E1H mole fraction of more than 25% the behavior of this alcohol is rapidly approached. This finding is interpreted to indicate that the ring-like supramolecular structures in 4M3H become energetically unfavorable when adding 2E1H, an alcohol that tends to form chain-like molecular aggregates. The concentration dependence of the Kirkwood factor in these mixtures displays a high degree of similarity with experimental results on monohydroxy alcohols in which the pressure or the location of the OH group within the molecular structure is varied. © 2013 AIP Publishing LLC.view abstract doi: 10.1063/1.4821229 2013 • 74 Experimental and numerical atomistic investigation of the third body formation process in dry tungsten/tungsten-carbide tribo couples
Stoyanov, P. and Romero, P.A. and Järvi, T.T. and Pastewka, L. and Scherge, M. and Stemmer, P. and Fischer, A. and Dienwiebel, M. and Moseler, M.
Tribology Letters 50 67-80 (2013)The third body in tungsten/tungsten-carbide sliding systems is studied using a combination of experiments and atomistic simulations. Ex situ X-ray photoelectron spectroscopy and focused ion beam analysis of the structural and chemical changes near the surfaces reveals that sliding of tungsten against tungsten-carbide results in plastic deformation of the W surface, leading to grain refinement, and the formation of a mechanically mixed amorphous layer on the WC counter body. Molecular dynamics simulations of W/WC sliding couples exhibit the formation of a nanoscale amorphous W/WC interface. The infrequent occurrence of atomic jamming events in the interface resulted in the emission of dislocations into the W bulk and the generation of amorphous shear bands in the WC counter body in agreement with the different third bodies observed in W and WC after the experiments. © 2012 Springer Science+Business Media New York.view abstract doi: 10.1007/s11249-012-0085-7 2013 • 73 Friction and wear mechanisms of tungsten-carbon systems: A comparison of dry and lubricated conditions
Stoyanov, P. and Stemmer, P. and Järvi, T.T. and Merz, R. and Romero, P.A. and Scherge, M. and Kopnarski, M. and Moseler, M. and Fischer, A. and Dienwiebel, M.
ACS Applied Materials and Interfaces 5 6123-6135 (2013)The unfolding of a sheared mechanically mixed third-body (TB) in tungsten/tungsten carbide sliding systems is studied using a combination of experiments and simulations. Experimentally, the topographical evolution and the friction response, for both dry and lubricated sliding, are investigated using an online tribometer. Ex situ X-ray photoelectron spectroscopy, transmission electron microscopy, and cross-sectional focused ion beam analysis of the structural and chemical changes near the surfaces show that dry sliding of tungsten against tungsten carbide results in plastic deformation of the tungsten surface, leading to grain refinement, and the formation of a mechanically mixed layer on the WC counterface. Sliding with hexadecane as a lubricant results in a less pronounced third-body formation due to much lower dissipated frictional power. Molecular dynamics simulations of the sliding couples predict chemical changes near the surface in agreement with the interfacial processes observed experimentally. Finally, online topography measurements demonstrate an excellent correlation between the evolution of the roughness and the frictional resistance during sliding. © 2013 American Chemical Society.view abstract doi: 10.1021/am4010094 2013 • 72 Guided hierarchical co-assembly of soft patchy nanoparticles
Gröschel, A.H. and Walther, A. and Löbling, T.I. and Schacher, F.H. and Schmalz, H. and Müller, A.H.E.
Nature 503 247-251 (2013)The concept of hierarchical bottom-up structuring commonly encountered in natural materials provides inspiration for the design of complex artificial materials with advanced functionalities. Natural processes have achieved the orchestration of multicomponent systems across many length scales with very high precision, but man-made self-assemblies still face obstacles in realizing well-defined hierarchical structures. In particle-based self-assembly, the challenge is to program symmetries and periodicities of superstructures by providing monodisperse building blocks with suitable shape anisotropy or anisotropic interaction patterns ('patches'). Irregularities in particle architecture are intolerable because they generate defects that amplify throughout the hierarchical levels. For patchy microscopic hard colloids, this challenge has been approached by using top-down methods (such as metal shading or microcontact printing), enabling molecule-like directionality during aggregation. However, both top-down procedures and particulate systems based on molecular assembly struggle to fabricate patchy particles controllably in the desired size regime (10-100 nm). Here we introduce the co-assembly of dynamic patchy nanoparticles-that is, soft patchy nanoparticles that are intrinsically self-assembled and monodisperse-as a modular approach for producing well-ordered binary and ternary supracolloidal hierarchical assemblies. We bridge up to three hierarchical levels by guiding triblock terpolymers (length scale ∼10 nm) to form soft patchy nanoparticles (20-50 nm) of different symmetries that, in combination, co-assemble into substructured, compartmentalized materials (>10 μm) with predictable and tunable nanoscale periodicities. We establish how molecular control over polymer composition programs the building block symmetries and regulates particle positioning, offering a route to well-ordered mixed mesostructures of high complexity. © 2013 Macmillan Publishers Limited. All rights reserved.view abstract doi: 10.1038/nature12610 2013 • 71 Maintaining the equipartition theorem in small heterogeneous molecular dynamics ensembles
Siboni, N.H. and Raabe, D. and Varnik, F.
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 87 (2013)It has been reported recently that the equipartition theorem is violated in molecular dynamics simulations with periodic boundary condition. This effect is associated with the conservation of the total momentum. Here, we propose a fluctuating center of mass molecular dynamics approach to solve this problem. Using the analogy to a system exchanging momentum with its surroundings, we work out - and validate via simulations - an expression for the rate at which fluctuations shall be added to the system. It is shown that the proposed method maintains equipartition both at equilibrium and beyond equilibrium in the linear response regime. © 2013 American Physical Society.view abstract doi: 10.1103/PhysRevE.87.030101 2013 • 70 Mechanisms of anisotropic friction in nanotwinned Cu revealed by atomistic simulations
Zhang, J.J. and Hartmaier, A. and Wei, Y.J. and Yan, Y.D. and Sun, T.
Modelling and Simulation in Materials Science and Engineering 21 (2013)The nature of nanocrystalline materials determines that their deformation at the grain level relies on the orientation of individual grains. In this work, we investigate the anisotropic response of nanotwinned Cu to frictional contacts during nanoscratching by means of molecular dynamics simulations. Nanotwinned Cu samples containing embedded twin boundaries parallel, inclined and perpendicular to scratching surfaces are adopted to address the effects of crystallographic orientation and inclination angle of aligned twin boundaries cutting the scratching surface. The transition in deformation mechanisms, the evolution of friction coefficients and the friction-induced microstructural changes are analyzed in detail and are related to the loading conditions and the twinned microstructures of the materials. Furthermore, the effect of twin spacing on the frictional behavior of Cu samples is studied. Our simulation results show that the crystallographic orientation strongly influences the frictional response in different ways for samples with different twin spacing, because the dominant deformation mode varies upon scratching regions of different orientations. A critical inclination angle of 26.6° gives the lowest yield strength and the highest friction coefficient, at which the plasticity is dominated by twin boundary migration and detwinning. It is demonstrated that the anisotropic frictional response of nanotwinned Cu originates from the heterogeneous localized deformation, which is strongly influenced by crystallographic orientation, twin boundary orientation and loading condition. © 2013 IOP Publishing Ltd.view abstract doi: 10.1088/0965-0393/21/6/065001 2013 • 69 Microscopic structure of water at elevated pressures and temperatures
Sahle, C.J. and Sternemann, C. and Schmidt, C. and Lehtola, S. and Jahn, S. and Simonelli, L. and Huotari, S. and Hakala, M. and Pylkkänen, T. and Nyrow, A. and Mende, K. and Tolan, M. and Hämäläinen, K. and Wilke, M.
Proceedings of the National Academy of Sciences of the United States of America 110 6301-6306 (2013)We report on the microscopic structure of water at sub- and supercritical conditions studied using X-ray Raman spectroscopy, ab initio molecular dynamics simulations, and density functional theory. Systematic changes in the X-ray Raman spectra with increasing pressure and temperature are observed. Throughout the studied thermodynamic range, the experimental spectra can be interpreted with a structural model obtained from the molecular dynamics simulations. A spatial statistical analysis using Ripley's K-function shows that this model is homogeneous on the nanometer length scale. According to the simulations, distortions of the hydrogen-bond network increase dramatically when temperature and pressure increase to the supercritical regime. In particular, the average number of hydrogen bonds per molecule decreases to ≈0.6at600 °C and p = 134 MPa.view abstract doi: 10.1073/pnas.1220301110 2013 • 68 Molecular fragment dynamics study on the water-air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants
Truszkowski, A. and Epple, M. and Fiethen, A. and Zielesny, A. and Kuhn, H.
Journal of Colloid and Interface Science 410 140-145 (2013)Molecular fragment dynamics (MFD) is a mesoscopic simulation technique based on dissipative particle dynamics (DPD). MFD simulations of the self-aggregation of the polyoxyethylene alkyl ether surfactants C6E6, C10E6, C12E6 and C16E6 at the water-air surface lead to equilibrium nanoscale structures and computationally determined surface tensions which are in agreement with experimental data for different surfactant concentrations. Thus, molecular fragment dynamics is a well-suited predictive technique to study the behavior of new surfactant systems. © 2013 Elsevier Inc.view abstract doi: 10.1016/j.jcis.2013.07.069 2013 • 67 Molecular simulations of hydrated proton exchange membranes: The structure
Marchand, G. and Bopp, P.A. and Spohr, E.
Zeitschrift fur Naturforschung - Section C Journal of Biosciences 68 A 101-111 (2013)The structure of two hydrated proton exchange membranes for fuel cells (PEMFC), Nafion® (Dupont) and Hyflon® (Solvay), is studied by all-atom molecular dynamics (MD) computer simulations. Since the characteristic times of these systems are long compared to the times for which they can be simulated, several different, but equivalent, initial configurations with a large degree of randomness are generated for different water contents and then equilibrated and simulated in parallel. A more constrained structure, analog to the newest model proposed in the literature based on scattering experiments, is investigated in the same way. One might speculate that a limited degree of entanglement of the polymer chains is a key feature of the structures showing the best agreement with experiment. Nevertheless, the overall conclusion remains that the scattering experiments cannot distinguish between the several, in our view equally plausible, structural models. We thus find that the characteristic features of experimental scattering curves are, after equilibration, fairly well reproduced by all systems prepared with our method. We thus study in more detail some structural details. We attempt to characterize the spatial and size distribution of the water rich domains, which is where the proton diffusion mostly takes place, using several clustering algorithms. © 2013 Verlag der Zeitschrift für Naturforschung, Tübingen.view abstract doi: 10.5560/ZNA.2012-0089 2013 • 66 Neural network potentials for metals and oxides - First applications to copper clusters at zinc oxide
Artrith, N. and Hiller, B. and Behler, J.
Physica Status Solidi (B) Basic Research 250 1191-1203 (2013)The development of reliable interatomic potentials for large-scale molecular dynamics (MD) simulations of chemical processes at surfaces and interfaces is a formidable challenge because a wide range of atomic environments and very different types of bonding can be present. In recent years interatomic potentials based on artificial neural networks (NNs) have emerged offering an unbiased approach to the construction of potential energy surfaces (PESs) for systems that are difficult to describe by conventional potentials. Here, we review the basic properties of NN potentials and describe their construction for materials like metals and oxides. The accuracy and efficiency are demonstrated using copper and zinc oxide as benchmark systems. First results for a potential of the combined ternary CuZnO system aiming at the description of oxide-supported copper clusters are reported. Model of a copper cluster at the ZnO($10\overline {1} 0$) surface. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.view abstract doi: 10.1002/pssb.201248370 2013 • 65 On the crystallographic anisotropy of nanoindentation in pseudoelastic NiTi
Pfetzing-Micklich, J. and Somsen, C. and Dlouhy, A. and Begau, C. and Hartmaier, A. and Wagner, M.F.-X. and Eggeler, G.
Acta Materialia 61 602-616 (2013)We use a nanoindenter with a Berkovich tip to study local mechanical properties of two polycrystalline intermetallics with a B2 crystal structure, NiAl and NiTi. We use orientation imaging scanning electron microscopy to select a relevant number of grains with appropriate sizes and surface normals parallel to 〈0 0 1〉, 〈1 0 1〉 and 〈1 1 1〉. As a striking new result, we find a strong crystallographic orientation dependence for NiTi. This anisotropy is less pronounced in the case of NiAl. For NiTi, the indentation force required to impose a specific indentation depth is highest for indentation experiments performed in the 〈0 0 1〉 direction and lowest along the 〈1 1 1〉 direction. We consider transmission electron microscopy results from cross-sections below the indents and use molecular dynamics simulations and resolved shear stress calculations to discuss how this difference can be accounted for in terms of elementary deformation and transformation processes, related to dislocation plasticity (NiAl and NiTi), and in terms of the stress-induced formation and growth of martensite (NiTi). Our results show that the crystallographic anisotropy during nanoindentation of NiTi is governed by the orientation dependence of the martensitic transformation; dislocation plasticity appears to be less important. © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.view abstract doi: 10.1016/j.actamat.2012.09.081 2013 • 64 Probing the structures of hydrated nafion in different morphologies using temperature-accelerated molecular dynamics simulations
Lucid, J. and Meloni, S. and MacKernan, D. and Spohr, E. and Ciccotti, G.
Journal of Physical Chemistry C 117 774-782 (2013)We perform combined temperature-accelerated and standard molecular dynamics (MD) simulations to elucidate the atomistic structure of hydrated Nafion (hydration level λ = 6.5) in the slab and cylinder morphologies. Our samples are initially made of elongated Nafion strands with a relatively small fraction of gauche defects. Our simulations show that even very long (>50 ns) "brute force" MD simulations are insufficient to reach equilibrated structures. In fact, ∼30-40 ns long temperature-accelerated molecular dynamics (TAMD) simulations started from the same initial conditions explore more stable (lower potential energy) stationary structures. The effect of TAMD is to allow a rearrangement of the backbone consisting of an increase in gauche defects, which cannot be obtained by "brute force" MD because the trans-gauche transition is a rare event at room temperature. Associated with the backbone rearrangement, we observe a change in the structure of the water layers/tubes as measured by the size and number of bulk (four-fold coordinated water molecules) and surface-like water clusters. At equilibrium, the mean size of bulk-like water clusters is small, typically between 10 and 20 molecules, depending on the morphology. Larger clusters are also present in our samples, the largest being made of ∼350 molecules, but even the latter is too small for percolation. This suggests that the proton transport through each morphology might be a two-step process: Grotthuss-like within bulk-like water clusters and of a different type (e.g., diffusive or even transport across fluctuatively opening necks) between clusters. © 2012 American Chemical Society.view abstract doi: 10.1021/jp309038n 2013 • 63 Probing the temperature dependence of proton transfer to charged platinum electrodes by reactive molecular dynamics trajectory studies
Schmickler, W. and Wilhelm, F. and Spohr, E.
Electrochimica Acta 101 341-346 (2013)We have performed reactive trajectory calculations of proton discharge on charged platinum surfaces as a function of temperature and charge. A recently developed 9-state empirical valence bond model has been employed. The temperature dependence follows an Arrhenius law with activation energies in the range of 0.1 eV. The activation energy for the discharge reaction decreases significantly with increasing driving force as modeled by an increasingly negative surface charge on the electrode. The analysis shows that the average orientation of molecules in the adsorbed water layer reacts to the approaching proton. Within increasing temperature, configurations become more prevalent which facilitate fast proton transfer by Grotthuss style proton hops from the second to the first layer. This effect becomes more pronounced near more negatively charged surfaces and leads to the computed reduction of the activation energy. © 2013 Elsevier Ltd. All rights reserved.view abstract doi: 10.1016/j.electacta.2013.01.146 2013 • 62 Probing ultrafast carrier tunneling dynamics in individual quantum dots and molecules
Müller, K. and Bechtold, A. and Ruppert, C. and Kaldewey, T. and Zecherle, M. and Wildmann, J.S. and Bichler, M. and Krenner, H.J. and Villas-Bôas, J.M. and Abstreiter, G. and Betz, M. and Finley, J.J.
Annalen der Physik 525 49-58 (2013)Ultrafast pump-probe spectroscopy is employed to directly monitor the tunneling of charge carriers from single and vertically coupled quantum dots and probe intra-molecular dynamics. Immediately after resonant optical excitation, several peaks are observed in the pump-probe spectrum arising from Coulomb interactions between the photogenerated charge carriers. The influence of few-Fermion interactions in the photoexcited system and the temporal evolution of the optical response is directly probed in the time domain. In addition, the tunneling times for electrons and holes from the QD nanostructure are independently determined. In polarization resolved measurements, near perfect Pauli-spin blockade is observed in the spin-selective absorption spectrum as well as stimulated emission. While electron and hole tunneling from single quantum dots is shown to be well explained by the WKB formalism, for coupled quantum dots pronounced resonances in the electron tunneling rate are observed arising from elastic and inelastic electron tunneling between the different dots. © 2012 by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.view abstract doi: 10.1002/andp.201200195 2013 • 61 Single-particle fluctuations and directional correlations in driven hard-sphere glasses
Mandal, S. and Chikkadi, V. and Nienhuis, B. and Raabe, D. and Schall, P. and Varnik, F.
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 88 (2013)Via event-driven molecular dynamics simulations and experiments, we study the packing-fraction and shear-rate dependence of single-particle fluctuations and dynamic correlations in hard-sphere glasses under shear. At packing fractions above the glass transition, correlations increase as shear rate decreases: the exponential tail in the distribution of single-particle jumps broadens and dynamic four-point correlations increase. Interestingly, however, upon decreasing the packing fraction, a broadening of the exponential tail is also observed, while dynamic heterogeneity is shown to decrease. An explanation for this behavior is proposed in terms of a competition between shear and thermal fluctuations. Building upon our previous studies, we further address the issue of anisotropy of the dynamic correlations. © 2013 American Physical Society.view abstract doi: 10.1103/PhysRevE.88.022129 2013 • 60 Thermodynamic modeling of chromium: Strong and weak magnetic coupling
Körmann, F. and Grabowski, B. and Söderlind, P. and Palumbo, M. and Fries, S.G. and Hickel, T. and Neugebauer, J.
Journal of Physics Condensed Matter 25 (2013)As chromium is a decisive ingredient for stainless steels, a reliable understanding of its thermodynamic properties is indispensable. Parameter-free first-principles methods have nowadays evolved to a state allowing such thermodynamic predictions. For materials such as Cr, however, the inclusion of magnetic entropy and higher order contributions such as anharmonic entropy is still a formidable task. Employing state-of-the-art ab initio molecular dynamics simulations and statistical concepts, we compute a set of thermodynamic properties based on quasiharmonic, anharmonic, electronic and magnetic free energy contributions from first principles. The magnetic contribution is modeled by an effective nearest-neighbor Heisenberg model, which itself is solved numerically exactly by means of a quantum Monte Carlo method. We investigate two different scenarios: a weak magnetic coupling scenario for Cr, as usually presumed in empirical thermodynamic models, turns out to be in clear disagreement with experimental observations. We show that instead a mixed Hamiltonian including weak and strong magnetic coupling provides a consistent picture with good agreement to experimental thermodynamic data. © 2013 IOP Publishing Ltd.view abstract doi: 10.1088/0953-8984/25/42/425401 2013 • 59 Understanding the microscopic origin of gold nanoparticle anisotropic growth from molecular dynamics simulations
Meena, S.K. and Sulpizi, M.
Langmuir 29 14954-14961 (2013)We use molecular dynamics simulations in order to understand the microscopic origin of the asymmetric growth mechanism in gold nanorods. We provide the first atomistic model of different surfaces on gold nanoparticles in a growing electrolyte solution, and we describe the interaction of the metal with the surfactants, namely, cetyltrimethylammonium bromide (CTAB) and the ions. An innovative aspect is the inclusion of the role of the surfactants, which are explicitly modeled. We find that on all the investigated surfaces, namely, (111), (110), and (100), CTAB forms a layer of distorted cylindrical micelles where channels among micelles provide direct ion access to the surface. In particular, we show how AuCl2- ions, which are found in the growth solution, can freely diffuse from the bulk solution to the gold surface. We also find that the (111) surface exhibits a higher CTAB packing density and a higher electrostatic potential. Both elements would favor the growth of gold nanoparticles along the (111) direction. These findings are in agreement with the growth mechanisms proposed by the experimental groups of Murphy and Mulvaney. © 2013 American Chemical Society.view abstract doi: 10.1021/la403843n 2012 • 58 A neural network potential-energy surface for the water dimer based on environment-dependent atomic energies and charges
Morawietz, T. and Sharma, V. and Behler, J.
Journal of Chemical Physics 136 (2012)Understanding the unique properties of water still represents a significant challenge for theory and experiment. Computer simulations by molecular dynamics require a reliable description of the atomic interactions, and in recent decades countless water potentials have been reported in the literature. Still, most of these potentials contain significant approximations, for instance a frozen internal structure of the individual water monomers. Artificial neural networks (NNs) offer a promising way for the construction of very accurate potential-energy surfaces taking all degrees of freedom explicitly into account. These potentials are based on electronic structure calculations for representative configurations, which are then interpolated to a continuous energy surface that can be evaluated many orders of magnitude faster. We present a full-dimensional NN potential for the water dimer as a first step towards the construction of a NN potential for liquid water. This many-body potential is based on environment-dependent atomic energy contributions, and long-range electrostatic interactions are incorporated employing environment-dependent atomic charges. We show that the potential and derived properties like vibrational frequencies are in excellent agreement with the underlying reference density-functional theory calculations. © 2012 American Institute of Physics.view abstract doi: 10.1063/1.3682557 2012 • 57 A novel approach to study dislocation density tensors and lattice rotation patterns in atomistic simulations
Begau, C. and Hua, J. and Hartmaier, A.
Journal of the Mechanics and Physics of Solids 60 711-722 (2012)Crystal plasticity caused by the nucleation and interaction of dislocations is an important aspect in crystal deformation. Recent nanoindentation experiments in single crystals of copper or aluminum revealed large deviations in the lattice rotation and an inhomogeneous distribution of the dislocation density in the plastic zone under the indenter tip. Molecular dynamics simulations offer the possibility to study the origin of these phenomena on an atomistic scale, but require sophisticated analysis routines in order to deal with the massive amount of generated data. Here a new efficient approach to analyze atomistic data on the fly during the simulation is introduced. This approach allows us to identify the dislocation network including Burgers vectors on the timescale of picoseconds and below. This data does not only reveal the evolution of dislocation structures, but it offers the possibility to quantify local dislocation density tensors calculated on an atomic level. The numerical results are compared with experimental data from the literature. The presented approach provides useful insight into the active deformation mechanisms during plastic deformation that will help us to bridge simulations on atomic scales and continuum descriptions. © 2012 Elsevier Ltd. All rights reserved.view abstract doi: 10.1016/j.jmps.2011.12.005 2012 • 56 A scheme to combine molecular dynamics and dislocation dynamics
Brinckmann, S. and Mahajan, D.K. and Hartmaier, A.
Modelling and Simulation in Materials Science and Engineering 20 (2012)Many engineering challenges occur on multiple interacting length scales, e.g. during fracture atoms separate on the atomic scale while plasticity develops on the micrometer scale. To investigate the details of these events, a concurrent multiscale model is required which studies the problem at appropriate length- and time-scales: the atomistic scale and the dislocation dynamics scale. The AtoDis multiscale model is introduced, which combines atomistics and dislocation dynamicsinto a fully dynamic model that is able to simulate deformation mechanisms at finite temperature. The model uses point forces to ensure mechanical equilibrium and kinematic continuity at the interface. By resolving each interface atom analytically, and not numerically, the framework uses a coarse FEM mesh and intrinsically filters out atomistic vibrations. This multiscale model allows bi-directional dislocation transition at the interface of both models with no remnant atomic disorder. Thereby, the model is able to simulate a larger plastic zone than conventional molecular dynamics while reducing the need for constitutive dislocation dynamics equations. This contribution studies dislocation nucleation at finite temperature and investigates the absorption of dislocations into the crack wake. © 2012 IOP Publishing Ltd.view abstract doi: 10.1088/0965-0393/20/4/045001 2012 • 55 Activity coefficients of complex molecules by molecular simulation and Gibbs-Duhem integration
Hempel, S. and Fischer, J. and Paschek, D. and Sadowski, G.
Soft Materials 10 26-41 (2012)Activity coefficients of solvents and solutes in different aqueous solutions of alcohols and polymers are determined by molecular dynamic simulations. These data are often not accessible by simulation due to unacceptably high computational demands. Therefore, we applied a combination of two methods: water activity coefficients were determined directly via Overlapping Distribution Method, while counter-component activity coefficients were calculated indirectly by Gibbs-Duhem integration of the respective water activities. Results are in good agreement with experimental data. The method can easily be applied to determine activity coefficients of very complex components in water or other simple solvents. © 2012 Copyright Taylor and Francis Group, LLC.view abstract doi: 10.1080/1539445X.2011.599698 2012 • 54 Aqueous redox chemistry and the electronic band structure of liquid water
Adriaanse, C. and Cheng, J. and Chau, V. and Sulpizi, M. and Vandevondele, J. and Sprik, M.
Journal of Physical Chemistry Letters 3 3411-3415 (2012)The electronic states of aqueous species can mix with the extended states of the solvent if they are close in energy to the band edges of water. Using density functional theory-based molecular dynamics simulation, we show that this is the case for OH- and Cl-. The effect is, however, badly exaggerated by the generalized gradient approximation leading to systematic underestimation of redox potentials and spurious nonlinearity in the solvent reorganization. Drawing a parallel to charged defects in wide gap solid oxides, we conclude that misalignment of the valence band of water is the main source of error turning the redox levels of OH- and Cl- in resonant impurity states. On the other hand, the accuracy of energies of levels corresponding to strongly negative redox potentials is acceptable. We therefore predict that mixing of the vertical attachment level of CO2 and the unoccupied states of water is a real effect. © 2012 American Chemical Society.view abstract doi: 10.1021/jz3015293 2012 • 53 Atomistic simulation of the influence of nanomachining-induced deformation on subsequent nanoindentation
Zhang, J.J. and Sun, T. and Hartmaier, A. and Yan, Y.D.
Computational Materials Science 59 14-21 (2012)In this paper it is demonstrated how nanoindentation can be used to assess the subsurface damage induced by nanomachining. To accomplish this, a characteristic difference in the nanoindentation response between plastically deformed and undeformed material is exploited. Classical molecular dynamics simulations are performed to investigate the elementary mechanisms of the irreversible plastic processes that occur during nanomachining of a copper single crystal. To mimic the experimental characterization of subsurface damage, we perform nanoindentation simulations into the machined surface. The results show that the critical contact pressure required for dislocation nucleation, i.e. the pop-in load, decreases continuously with increasing machining depth, while the indentation hardness seems widely unaffected by prior nanomachining. © 2012 Elsevier B.V. All rights reserved.view abstract doi: 10.1016/j.commatsci.2012.02.024 2012 • 52 Construction of high-dimensional neural network potentials using environment-dependent atom pairs
Jose, K.V.J. and Artrith, N. and Behler, J.
Journal of Chemical Physics 136 (2012)An accurate determination of the potential energy is the crucial step in computer simulations of chemical processes, but using electronic structure methods on-the-fly in molecular dynamics (MD) is computationally too demanding for many systems. Constructing more efficient interatomic potentials becomes intricate with increasing dimensionality of the potential-energy surface (PES), and for numerous systems the accuracy that can be achieved is still not satisfying and far from the reliability of first-principles calculations. Feed-forward neural networks (NNs) have a very flexible functional form, and in recent years they have been shown to be an accurate tool to construct efficient PESs. High-dimensional NN potentials based on environment-dependent atomic energy contributions have been presented for a number of materials. Still, these potentials may be improved by a more detailed structural description, e.g., in form of atom pairs, which directly reflect the atomic interactions and take the chemical environment into account. We present an implementation of an NN method based on atom pairs, and its accuracy and performance are compared to the atom-based NN approach using two very different systems, the methanol molecule and metallic copper. We find that both types of NN potentials provide an excellent description of both PESs, with the pair-based method yielding a slightly higher accuracy making it a competitive alternative for addressing complex systems in MD simulations. © 2012 American Institute of Physics.view abstract doi: 10.1063/1.4712397 2012 • 51 Continuum simulation of the evolution of dislocation densities during nanoindentation
Engels, P. and Ma, A. and Hartmaier, A.
International Journal of Plasticity 38 159-169 (2012)When nanoindenting dislocation-free regions of single crystals a so-called pop-in phenomenon is commonly observed. Molecular dynamics (MD) studies have revealed homogeneous nucleation of dislocations in a perfect crystal as a mechanism causing such pop-in behavior. In this work we transfer this knowledge gained on the atomic scale into a dislocation nucleation model that is applied within a dislocation density based crystal plasticity description. Furthermore, we develop a non-local formulation of a crystal plasticity model that is devised to yield a valid description of plasticity also in situations where the dislocation density is small or even vanishing and where conventional plasticity models fail. This is accomplished by studying the evolution of statistically stored and geometrically necessary dislocation densities separately. We apply this non-local crystal plasticity model to investigate the evolution of dislocation densities in the early stages of nanoindentation. The results of our continuum model show good agreement with MD simulations for cases where nanoindentation into an initially dislocation-free crystal is studied, i.e. where a pop-in occurs when the critical stress underneath the indenter reaches the critical value for homogeneous dislocation nucleation. After thus validating our model we study the influence of pre-existing homogeneous and local dislocation densities. Both cases show a good qualitative agreement with recent experimental findings and it is concluded that pre-existing local dislocations densities reduce the load at which a pop-in occurs and - more importantly - change the mechanism from homogeneous dislocation nucleation to rapid dislocation multiplication. In general, our results show that continuum plasticity formulations can be extended such that applications to nanoscale volumes become possible. © 2012 Elsevier Ltd. All rights reserved.view abstract doi: 10.1016/j.ijplas.2012.05.010 2012 • 50 Critical motor number for fractional steps of cytoskeletal filaments in gliding assays
Li, X. and Lipowsky, R. and Kierfeld, J.
PLoS ONE 7 (2012)In gliding assays, filaments are pulled by molecular motors that are immobilized on a solid surface. By varying the motor density on the surface, one can control the number N of motors that pull simultaneously on a single filament. Here, such gliding assays are studied theoretically using Brownian (or Langevin) dynamics simulations and taking the local force balance between motors and filaments as well as the force-dependent velocity of the motors into account. We focus on the filament stepping dynamics and investigate how single motor properties such as stalk elasticity and step size determine the presence or absence of fractional steps of the filaments. We show that each gliding assay can be characterized by a critical motor number, Nc. Because of thermal fluctuations, fractional filament steps are only detectable as long as N < Nc. The corresponding fractional filament step size is ℓ/N where ℓ is the step size of a single motor. We first apply our computational approach to microtubules pulled by kinesin-1 motors. For elastic motor stalks that behave as linear springs with a zero rest length, the critical motor number is found to be Nc=4, and the corresponding distributions of the filament step sizes are in good agreement with the available experimental data. In general, the critical motor number Nc depends on the elastic stalk properties and is reduced to Nc=3 for linear springs with a nonzero rest length. Furthermore, Nc is shown to depend quadratically on the motor step size ℓ. Therefore, gliding assays consisting of actin filaments and myosin-V are predicted to exhibit fractional filament steps up to motor number N=31. Finally, we show that fractional filament steps are also detectable for a fixed average motor number 〈N〉 as determined by the surface density (or coverage) of the motors on the substrate surface. © 2012 Li et al.view abstract doi: 10.1371/journal.pone.0043219 2012 • 49 Flow and Rheological Response of Model Glasses
Varnik, F. and Mandal, S. and Gross, M.
Transactions of the Indian Ceramic Society 71 222-224 (2012)Results of molecular dynamics simulations on the response of glassy materials to an externally imposed steady shear are presented. The work highlights on one hand how the competition of the time scale imposed by the flow and the inherent structural relaxation time determines the linear or non-linear nature of the rheological response. On the other hand, the issue of flow heterogeneity in a shear melted glass is also studied. © 2012 Copyright The Indian Ceramic Society.view abstract doi: 10.1080/0371750X.2013.772745 2012 • 48 Heterogeneous shear in hard sphere glasses
Mandal, S. and Gross, M. and Raabe, D. and Varnik, F.
Physical Review Letters 108 (2012)There is growing evidence that the flow of driven amorphous solids is not homogeneous, even if the macroscopic stress is constant across the system. Via event-driven molecular dynamics simulations of a hard sphere glass, we provide the first direct evidence for a correlation between the fluctuations of the local volume fraction and the fluctuations of the local shear rate. Higher shear rates do preferentially occur at regions of lower density and vice versa. The temporal behavior of fluctuations is governed by a characteristic time scale, which, when measured in units of strain, is independent of shear rate in the investigated range. Interestingly, the correlation volume is also roughly constant for the same range of shear rates. A possible connection between these two observations is discussed. © 2012 American Physical Society.view abstract doi: 10.1103/PhysRevLett.108.098301 2012 • 47 Human high temperature requirement serine protease A1 (HTRA1) degrades tau protein aggregates
Tennstaedt, A. and Pöpsel, S. and Truebestein, L. and Hauske, P. and Brockmann, A. and Schmidt, N. and Irle, I. and Saccà, B. and Niemeyer, C.M. and Brandt, R. and Ksiezak-Reding, H. and Tirniceriu, A.L. and Egensperger, R. and ...
Journal of Biological Chemistry 287 20931-20941 (2012)Protective proteases are key elements of protein quality control pathways that are up-regulated, for example, under various protein folding stresses. These proteases are employed to prevent the accumulation and aggregation of misfolded proteins that can impose severe damage to cells. The high temperature requirement A (HtrA) family of serine proteases has evolved to perform important aspects of ATP-independent protein quality control. So far, however, no HtrA protease is known that degrades protein aggregates. We show here that human HTRA1 degrades aggregated and fibrillar tau, a protein that is critically involved in various neurological disorders. Neuronal cells and patient brains accumulate less tau, neurofibrillary tangles, and neuritic plaques, respectively, when HTRA1 is expressed at elevated levels. Furthermore, HTRA1 mRNA and HTRA1 activity are up-regulated in response to elevated tau concentrations. These data suggest that HTRA1 is performing regulated proteolysis during protein quality control, the implications of which are discussed. © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.view abstract doi: 10.1074/jbc.M111.316232 2012 • 46 Mechanisms of crazing in glassy polymers revealed by molecular dynamics simulations
Mahajan, D.K. and Hartmaier, A.
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 86 (2012)Mechanisms leading to initiation of crazing type failure in a glassy polymer are not clearly understood. This is mainly due to the difficulty in characterizing the stress state and polymer configuration sufficiently locally at the craze initiation site. Using molecular dynamics simulations, we have now been able to access this information and have shown that the local heterogeneous deformation leads to craze initiation in glassy polymers. We found that zones of high plastic activity are constrained by their neighborhood and become unstable, initiating crazing from these sites. Furthermore, based on the constant flow stresses observed in the unstable zones, we conclude that microcavitation is the essential local deformation mode to trigger crazing in glassy polymers. Our results demonstrate the basic difference in the local deformation mode as well as the conditions that lead to either shear-yielding or crazing type failures in glassy polymers. We anticipate our paper to help in devising a new criterion for craze initiation that not only considers the stress state, but also considers local deformation heterogeneities that form the necessary condition for crazing in glassy polymers. © 2012 American Physical Society.view abstract doi: 10.1103/PhysRevE.86.021802 2012 • 45 Molecular dynamics and experimental study of conformation change of poly(N -isopropylacrylamide) hydrogels in mixtures of water and methanol
Walter, J. and Sehrt, J. and Vrabec, J. and Hasse, H.
Journal of Physical Chemistry B 116 5251-5259 (2012)The conformation transition of poly(N-isopropylacrylamide) hydrogel as a function of the methanol mole fraction in water/methanol mixtures is studied both experimentally and by atomistic molecular dynamics simulation with explicit solvents. The composition range in which the conformation transition of the hydrogel occurs is determined experimentally at 268.15, 298.15, and 313.15 K. In these experiments, cononsolvency, i.e., collapse at intermediate methanol concentrations while the hydrogel is swollen in both pure solvents, is observed at 268.15 and 298.15 K. The composition range in which cononsolvency is present does not significantly depend on the amount of cross-linker. The conformation transition of the hydrogel is caused by the conformation transition of the polymer chains of its backbone. Therefore, conformation changes of single backbone polymer chains are studied by massively parallel molecular dynamics simulations. The hydrogel backbone polymer is described with the force field OPLS-AA, water with the SPC/E model, and methanol with the model of the GROMOS-96 force field. During simulation, the mean radius of gyration of the polymer chains is monitored. The conformation of the polymer chains is studied at 268, 298, and 330 K as a function of the methanol mole fraction. Cononsolvency is observed at 268 and 298 K, which is in agreement with the present experiments. The structure of the solvent around the hydrogel backbone polymer is analyzed using H-bond statistics and visualization. It is found that cononsolvency is caused by the fact that the methanol molecules strongly attach to the hydrogels backbone polymer, mainly with their hydroxyl group. This leads to the effect that the hydrophobic methyl groups of methanol are oriented toward the bulk solvent. The hydrogel+solvent shell hence appears hydrophobic and collapses in water-rich solvents. As more methanol is present in the solvent, the effect disappears again. © 2012 American Chemical Society.view abstract doi: 10.1021/jp212357n 2012 • 44 Molecular dynamics investigation of the thermo-responsive polymer poly(N-isopropylacrylamide)
Alaghemandi, M. and Spohr, E.
Macromolecular Theory and Simulations 21 106-112 (2012)Using molecular dynamics simulations with an OPLS force field, the lower critical solution temperature (LCST) of single- and multiple-chain PNIPAM solutions in water is investigated. The sample containing ten polymer chains shows a sudden drop in size and volume at 305 K. Such an effect is absent in the single-chain system. Large fluctuations of the physical properties of a short single-chain prevent any clear detection of the LCST for the chosen model system, at least on the time scale of 200 ns. The results provide evidence that a critical number of PNIPAM monomer units must be present in the simulated system before MD simulations are capable to detect conformational changes unambiguously. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.view abstract doi: 10.1002/mats.201100071 2012 • 43 On the effect of molecular and hydrocarbon-bonded hydrogen on carbon particle formation in C 3O 2 pyrolysis behind shock waves
Böhm, H. and Emelianov, A. and Eremin, A. and Schulz, C. and Jander, H.
Combustion and Flame 159 932-939 (2012)The effect of H 2 and C 2H 2 addition on particle formation in the pyrolysis of C 3O 2/Ar mixtures was studied behind reflected shock waves. An existing reaction mechanism for the pyrolysis of highly-diluted C 3O 2 in argon was expanded to conditions with higher C 3O 2 concentrations (up to 33volume%) at elevated pressures and high temperatures and was validated against experimental data. The simulations for the gas-phase chemistry were performed with the program CHEMKIN. The heterogeneous particle formation was modeled by post-processing using the program PREDICI relying on the Galerkin method. It was found that in C 3O 2/H 2/Ar pyrolysis, the induction times and rate constants of particle formation do not differ significantly from those of pure C 3O 2/Ar pyrolysis. However, the presence of H 2 reduced the particle volume fraction, the mean diameter of particles, the particle number density, and the maximum temperature rise of the mixture. Hydrocarbon-bonded hydrogen in C 3O 2/C 2H 2/Ar pyrolysis caused significantly increased induction times for particle formation, decreased particle volume fractions, and decreased temperature rises. The different reaction channels for carbon particle formation were identified in view of the role of hydrogen. An alternating reaction channel including C 2 species played an important role in forming polycyclic aromatic hydrocarbons (PAH) in the mixtures. © 2011 The Combustion Institute.view abstract doi: 10.1016/j.combustflame.2011.09.012 2012 • 42 Oxide/water interfaces: How the surface chemistry modifies interfacial water properties
Gaigeot, M.-P. and Sprik, M. and Sulpizi, M.
Journal of Physics Condensed Matter 24 (2012)The organization of water at the interface with silica and alumina oxides is analysed using density functional theory-based molecular dynamics simulation (DFT-MD). The interfacial hydrogen bonding is investigated in detail and related to the chemistry of the oxide surfaces by computing the surface charge density and acidity. We find that water molecules hydrogen-bonded to the surface have different orientations depending on the strength of the hydrogen bonds and use this observation to explain the features in the surface vibrational spectra measured by sum frequency generation spectroscopy. In particular, ice-like and liquid-like features in these spectra are interpreted as the result of hydrogen bonds of different strengths between surface silanols/aluminols and water. © 2012 IOP Publishing Ltd.view abstract doi: 10.1088/0953-8984/24/12/124106 2012 • 41 Relevance of lysine snorkeling in the outer transmembrane domain of small viral potassium ion channels
Gebhardt, M. and Henkes, L.M. and Tayefeh, S. and Hertel, B. and Greiner, T. and Van Etten, J.L. and Baumeister, D. and Cosentino, C. and Moroni, A. and Kast, S.M. and Thiel, G.
Biochemistry 51 5571-5579 (2012)Transmembrane domains (TMDs) are often flanked by Lys or Arg because they keep their aliphatic parts in the bilayer and their charged groups in the polar interface. Here we examine the relevance of this so-called " snorkeling" of a cationic amino acid, which is conserved in the outer TMD of small viral K+ channels. Experimentally, snorkeling activity is not mandatory for KcvPBCV-1 because K29 can be replaced by most of the natural amino acids without any corruption of function. Two similar channels, KcvATCV-1 and KcvMT325, lack a cytosolic N-terminus, and neutralization of their equivalent cationic amino acids inhibits their function. To understand the variable importance of the cationic amino acids, we reanalyzed molecular dynamics simulations of KcvPBCV-1 and N-terminally truncated mutants; the truncated mutants mimic KcvATCV-1 and KcvMT325. Structures were analyzed with respect to membrane positioning in relation to the orientation of K29. The results indicate that the architecture of the protein (including the selectivity filter) is only weakly dependent on TMD length and protonation of K29. The penetration depth of Lys in a given protonation state is independent of the TMD architecture, which leads to a distortion of shorter proteins. The data imply that snorkeling can be important for K+ channels; however, its significance depends on the architecture of the entire TMD. The observation that the most severe N-terminal truncation causes the outer TMD to move toward the cytosolic side suggests that snorkeling becomes more relevant if TMDs are not stabilized in the membrane by other domains. © 2012 American Chemical Society.view abstract doi: 10.1021/bi3006016 2012 • 40 Thermal conductivity of polyamide-6,6 in the vicinity of charged and uncharged graphene layers: A molecular dynamics analysis
Alaghemandi, M. and Gharib-Zahedi, M.R. and Spohr, E. and Böhm, M.C.
Journal of Physical Chemistry C 116 14115-14122 (2012)The thermal conductivity (λ) of nanoconfined polyamide-6,6 (PA) oligomers in polymer-graphene nanocomposites has been investigated by reverse nonequilibrium molecular dynamics (RNEMD) simulations. The preferential alignment of the PA chains parallel to the graphene plane as well as their elongation implies that λ of the polymer in nanocomposites is larger than that in the neat polymer system. The ordering of the polymer phase is enhanced in an arrangement of charged graphene surfaces made of one layer with a charge deficit and one with a charge excess. The consequence of the enhanced polymer ordering as well as the denser packing is an increase in λ in the polymer network. Differences in the thermal conductivity for an armchair and zigzag arrangement of the graphene sheets in the direction of the heat transfer are almost negligible. In contrast with this insensitivity, the present RNEMD simulations predict the largest value of λ for composites with the smallest number of PA chains between adjacent graphene sheets. The modifications in the polymer thermal conductivity are rationalized via several structural parameters such as PA bond orientation relative to the graphene sheets, end-to-end distance of polymer chains, and density profiles. © 2012 American Chemical Society.view abstract doi: 10.1021/jp301452z 2012 • 39 Thermodynamic and physical properties of FeAl and Fe 3Al: An atomistic study by EAM simulation
Ouyang, Y. and Tong, X. and Li, C. and Chen, H. and Tao, X. and Hickel, T. and Du, Y.
Physica B: Condensed Matter 407 4530-4536 (2012)With this work we present a newly developed potential for the Fe-Al system, which is based on the analytical embedded atom method (EAM) with long range atomic interactions. The potential yields for the two most relevant phases B2-FeAl and D0 3-Fe 3Al lattice constants, elastic constants, as well as bulk and point defect formation enthalpies, which are in good agreement with experimental and other theoretical data. In addition, the phonon dispersions for B2-FeAl and D0 3-Fe 3Al show a good agreement with available experiments. The calculated lattice constants and formation enthalpy for disordered Fe-Al alloys are in good agreement with experimental data or other theoretical calculations. This indicates that the present EAM potentials of Fe-Al system is suitable for atomistic simulations of structural and kinetic properties for the Fe-Al system. © 2012 Elsevier B.V.view abstract doi: 10.1016/j.physb.2012.08.025 2012 • 38 Variational constitutive updates for microstructure evolution in hcp metals
Mosler, J. and Homayonifar, M.
GAMM Mitteilungen 35 43-58 (2012)Magnesium and its alloys are promising materials for lightweight applications. Unfortunately, the macroscopic formability of such materials is relatively poor at room temperature and these metals are characterized by a complex mechanical response. This response is a result of the interplay between different deformation modes at the microscale. Since magnesium is a material showing a hexagonal close-packed (hcp) structure of the underlying atomic lattice, plasticity caused by dislocations and deformation-induced twinning are the most relevant deformation modes. Within the present paper, two different recently advocated modeling approaches suitable for capturing such modes at the microscale are analyzed. It is shown that both models can be rewritten into a variationally consistent format where every aspect is naturally driven by energy minimization. In addition to this already known feature, it turns out that both models are based on the same minimization problem. The difference between the models results from different constraints enforced within the variational principle. For getting further insight into the interaction between dislocations and twinning interfaces, accompanying atomistic simulations based on molecular dynamics are also performed. The results of such simulations enter the micromechanical model through the initial plastic deformation within the twinned phase. ©c 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.view abstract doi: 10.1002/gamm.201210004 2012 • 37 Water activity coefficients in aqueous amino acid solutions by molecular dynamics simulation: 1. Force field development
Hempel, S. and Sadowski, G.
Molecular Simulation 38 132-138 (2012)New force fields for molecular dynamics (MD) simulation of aqueous zwitterionic amino acid simulations were developed. These were especially designed to calculate activity coefficient of water in amino acid solutions with high accuracy. For example, aqueous solutions of the following amino acids were considered: glycine, alanine, α-aminobutyric acid, α- aminovalerianic acid, valine and leucine. The force fields were obtained by quantum chemical calculations using B3LYP/6-31G and MP2/6-311(d,p) model theories in combination with the Merz-Kollmann-Singh scheme. To further increase the accuracy of the force field, a polarised continuum was considered in all quantum chemical calculations. Water activity coefficients obtained from MD using different all-purpose literature force fields, namely, OPLS, AMBER ff03 and GROMOS 53A6 as well as experimental data are compared with the results utilising the new force field. The new force field is shown to give better results compared with experimental data than existing force fields. Copyright © 2012 Taylor and Francis Group, LLC.view abstract doi: 10.1080/08927022.2011.608670 2011 • 36 A density functional theory based estimation of the anharmonic contributions to the free energy of a polypeptide helix
Ismer, L. and Ireta, J. and Neugebauer, J.
Journal of Chemical Physics 135 (2011)We have employed density functional theory to determine the temperature dependence of the intrinsic stability of an infinite poly-L-alanine helix. The most relevant helix types, i.e., the - and the 310 - helix, and several unfolded conformations, which serve as reference for the stability analysis, have been included. For the calculation of the free energies for the various chain conformations we have explicitly included both, harmonic and anharmonic contributions. The latter have been calculated by means of a thermodynamic integration approach employing stochastic Langevin molecular dynamics, which is shown to provide a dramatic increase in the computational efficiency as compared to commonly employed deterministic molecular dynamics schemes. Employing this approach we demonstrate that the anharmonic part of the free energy amounts to the order of 0.1-0.4 kcal/mol per peptide unit for all analysed conformations. Although small, the anharmonic contribution stabilizes the helical conformations with respect to the fully extended structure. © 2011 American Institute of Physics.view abstract doi: 10.1063/1.3629451 2011 • 35 A molecular dynamics investigation of kinetic electron emission from silver surfaces under varying angle of projectile impact
Duvenbeck, A. and Hanke, S. and Weidtmann, B. and Wucher, A.
Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms 269 1661-1664 (2011)We present a computer simulation study on the influence of the impact angle of the projectile on kinetic electron emission yields for 5-keV Ag → Ag bombardment. By means of a hybrid computer simulation model incorporating (i) the particle dynamics following the primary particle impact, (ii) the kinetically induced electronic substrate excitations via electronic friction and electron promotion and (iii) the transport of excitation energy away from the spot of generation, a full three-dimensional electron temperature profile within the volume affected by the atomic collision cascade is calculated. This profile is evaluated at the very surface of the target and taken as input for a thermionic model ('hot-spot-model') for kinetic electron emission. Averaging the results for different choices of the polar angle of incidence Θ over a large set of impact points, the obtained kinetic electron emission yields can be compared with experimental data and predictions from simple geometrical calculations. The presented simulation results appear to be reasonable in comparison with experimental data as well as with simple geometrical considerations of kinetic electron emission under oblique incidence. © 2010 Elsevier B.V. All rights reserved.view abstract doi: 10.1016/j.nimb.2010.11.082 2011 • 34 Ab initio molecular dynamics of proton networks in narrow polymer electrolyte pores
Ilhan, M.A. and Spohr, E.
Journal of Physics Condensed Matter 23 (2011)It is well established that proton conductivity in fuel cell membrane materials such as Nafion decreases strongly with decreasing water content. Proton transport in almost dry membranes is thought to proceed through narrow channels. In the present work we investigate proton structure and dynamics in two narrow cylindrical pores, which differ by their radius and the spacing of SO3H groups inside the channel. Pores are modelled through eight CF3CF3 and four CF3SO3H entities in a helical arrangement. The water content λ (the ratio between the number of water molecules and the number of sulfonic acid groups) in the pores varies between 2.5 and 4.5. We observe a transition from the undissociated acid at very low λ through more or less localized H3O+ entities to more delocalized H5O2 + entities for the investigated range of λ. In the narrower pore, where S-S distances vary in a more favourable range (between 6 and 8.5) than in the wider pore, we find that the molecular mobility is significantly higher, even at a rather high density of water molecules inside the pore. © 2011 IOP Publishing Ltd.view abstract doi: 10.1088/0953-8984/23/23/234104 2011 • 33 Artificial synthetic receptors as regulators of protein activity
Dutt, S. and Wilch, C. and Schrader, T.
Chemical Communications 47 5376-5383 (2011)This article discusses most recent work and progress in the direction of a rational design of small molecule receptors that efficiently interfere with the biological function of a particular receptor or enzyme - some of which are therapeutically relevant. More specifically, the following topics are highlighted here: the inhibition of voltage-dependent potassium channels of the Kv1.x family by designed porphyrin and calix[4]arene ligands, the structural and functional recovery of the tetramerization domain of mutated P53 protein by tailored calix[4]arene ligands and the control over LDH activity by supramolecular signaling. Finally a new way to modulate NAD+- dependent enzymatic activities by molecular clips and tweezers is presented. © 2011 The Royal Society of Chemistry.view abstract doi: 10.1039/c0cc05812b 2011 • 32 Atom-centered symmetry functions for constructing high-dimensional neural network potentials
Behler, J.
Journal of Chemical Physics 134 (2011)Neural networks offer an unbiased and numerically very accurate approach to represent high-dimensional ab initio potential-energy surfaces. Once constructed, neural network potentials can provide the energies and forces many orders of magnitude faster than electronic structure calculations, and thus enable molecular dynamics simulations of large systems. However, Cartesian coordinates are not a good choice to represent the atomic positions, and a transformation to symmetry functions is required. Using simple benchmark systems, the properties of several types of symmetry functions suitable for the construction of high-dimensional neural network potential-energy surfaces are discussed in detail. The symmetry functions are general and can be applied to all types of systems such as molecules, crystalline and amorphous solids, and liquids. © 2011 American Institute of Physics.view abstract doi: 10.1063/1.3553717 2011 • 31 Atomistic processes of dislocation generation and plastic deformation during nanoindentation
Begau, C. and Hartmaier, A. and George, E.P. and Pharr, G.M.
Acta Materialia 59 934-942 (2011)To enable plastic deformation during nanoindentation of an initially defect-free crystal, it is necessary first to produce dislocations. While it is now widely accepted that the nucleation of the first dislocations occurs at the start of the pop-in event frequently observed in experiments, it is unclear how these initial dislocations multiply during the early stages of plastic deformation and produce pop-in displacements that are typically much larger than the magnitude of the Burgers vector. This uncertainty about the complex interplay between dislocation multiplication and strain hardening during nanoindentation makes a direct correlation between force-displacement curves and macroscopic material properties difficult. In this paper, we study the early phase of plastic deformation during nanoindentation with the help of large-scale molecular dynamics simulations. A skeletonization method to simplify defect structures in atomistic simulations enables the direct observation and quantitative analysis of dislocation nucleation and multiplication processes occurring in the bulk as well as at the surface. © 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.view abstract doi: 10.1016/j.actamat.2010.10.016 2011 • 30 Diffusion of poly(ethylene glycol) and ectoine in NIPAAm hydrogels with confocal Raman spectroscopy
Poggendorf, S. and Adama Mba, G. and Engel, D. and Sadowski, G.
Colloid and Polymer Science 289 545-559 (2011)The diffusion behavior of poly(ethylene glycol) (PEG) in N-isopropylacrylamide (NIPAAm) hydrogels was investigated using confocal Raman spectroscopy with regard to temperature (25°C, 30°C and 35°C), PEG concentration (10 and 40 wt.%), PEG molecular weight (2,000 and 12,000 g/mol) and addition of the compatible solute ectoine (0.1 and 2 wt.%). Swelling and shrinking of the gels was observed by means of confocal Raman spectroscopy. The swelling behavior of NIPAAm gels in aqueous solutions of PEG and ectoine was found to resemble the swelling behavior in pure water with regard to temperature, i.e., the gel shrinks with increasing temperature. However, the presence and concentration of PEG and ectoine influence the swelling behavior by lowering the volume phase-transition temperature of the gel and facilitating shrinking. In some cases, a re-swelling of the gel was observed after the initial shrinking at the onset of PEG diffusion, which can be explained by PEG changing the chemical potential in the gel phase as it diffuses into the sample allowing the water to re-enter. The expulsion of water from the gel during shrinking and the so-caused increase of PNIPAAm and PEG concentrations in some cases led to the PEG diffusion seemingly being faster in more shrunken gels despite of their higher diffusion resistance. © Springer-Verlag 2011.view abstract doi: 10.1007/s00396-011-2399-7 2011 • 29 Hydrogen bonding in narrow protonated polymer electrolyte pores
Ilhan, M.A. and Spohr, E.
Journal of Electroanalytical Chemistry 660 347-351 (2011)Proton conductivity in fuel cell membrane materials such as Nafion® decreases dramatically with decreasing water content. At very low water content proton transport is thought to occur through narrow necks, which can be either static or fluctuatively formed temporarily. In the present work we investigate the properties of hydrogen bonding and protons in a one-dimensional narrow model pore by using ab initio Car-Parrinello molecular dynamics. The pore consists of eight suitably arranged CF3-CF3 and four CF 3-SO3H entities and is filled with water at varying water content λ (the ratio between the number of water molecules and the number of sulfonic acid groups) between 2.5 and 4.5. Proton mobilization in this pore occurs in two steps. First, around λ = 3 sulfonic acid groups dissociate to form sulfonate groups and hydronium ions which form mostly contact ion pairs. Second, increasing the water content to λ = 4.5 leads to an increase of the population of Zundel-like H5O2+ configurations with more or less symmetrically shared protons. Simultaneously, the number of hydrogen bonds increases and the hydrogen bond network becomes more liquid-like. © 2010 Elsevier B.V. All rights reserved.view abstract doi: 10.1016/j.jelechem.2011.03.035 2011 • 28 Influence of dislocation density on the pop-in behavior and indentation size effect in CaF2 single crystals: Experiments and molecular dynamics simulations
Lodes, M.A. and Hartmaier, A. and Göken, M. and Durst, K.
Acta Materialia 59 4264-4273 (2011)In this work, the indentation size effect and pop-in behavior are studied for indentations in undeformed and locally pre-deformed CaF2 single crystals, using both nanoindentation experiments and molecular dynamics simulations. To study the influence of dislocation density on the indentation behavior, small-scale indentations are carried out inside the plastic zone of larger indentations. This experiment is mimicked in the simulations by indenting a small sphere into the center of the residual impression of a larger sphere. The undeformed material shows the well-known pop-in behavior followed by the indentation size effect. Pre-deforming the material leads to a reduction in the indentation size effect both for experiments and simulations, which is in accordance with the Nix-Gao theory. Furthermore, the pop-in load is reduced in the experiments, whereas a smooth transition from elastic to plastic deformation is found in the simulations. There, plasticity is initiated by the movement of pre-existing dislocation loops in the vicinity of the plastic zone. The simulations thus give a detailed insight into the deformation mechanism during indentation and highlight the importance of the dislocation microstructure for the indentation size effect and dislocation nucleation. © 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.view abstract doi: 10.1016/j.actamat.2011.03.050 2011 • 27 Minimal art: Or why small viral K+ channels are good tools for understanding basic structure and function relations
Thiel, G. and Baumeister, D. and Schroeder, I. and Kast, S.M. and Van Etten, J.L. and Moroni, A.
Biochimica et Biophysica Acta - Biomembranes 1808 580-588 (2011)Some algal viruses contain genes that encode proteins with the hallmarks of K+ channels. One feature of these proteins is that they are less than 100 amino acids in size, which make them truly minimal for a K+ channel protein. That is, they consist of only the pore module present in more complex K+ channels. The combination of miniature size and the functional robustness of the viral K+ channels make them ideal model systems for studying how K+ channels work. Here we summarize recent structure/function correlates from these channels, which provide insight into functional properties such as gating, pharmacology and sorting in cells. © 2010 Elsevier B.V. All rights reserved.view abstract doi: 10.1016/j.bbamem.2010.04.008 2011 • 26 Modeling proton transfer to charged silver electrodes
Wilhelm, F. and Schmickler, W. and Nazmutdinov, R. and Spohr, E.
Electrochimica Acta 56 10632-10644 (2011)Density functional theory (DFT) and molecular dynamics (MD) techniques are used to study proton transfer from an aqueous solution to an Ag(1 1 1) surface. DFT is applied to study Ag-water and Ag-hydronium interactions as well as proton transfer for small systems based on the cluster model. The data gained are then used to adjust an empirical Ag-water interaction potential and to reparametrize an empirical valence-bond (EVB) model, which has been successfully applied for the study of proton transfer to a Pt(1 1 1) surface before. Employing these force fields in MD simulations enables dynamic modeling of the electrolyte-metal interface on a scale large enough to give realistic results. Results from a MD trajectory study on Ag(1 1 1) are reported and compared to the analogous study for platinum. Low discharge rates on Ag(1 1 1) are observed, and the potential range for hydrogen evolution can be estimated. The different behavior relative to Pt(1 1 1) can be traced to features of the respective potential energy surfaces and to the different structural properties of the aqueous/metallic interfaces. © 2011 Elsevier Ltd. All rights reserved.view abstract doi: 10.1016/j.electacta.2011.04.036 2011 • 25 Molecular dynamics simulation study of microstructure evolution during cyclic martensitic transformations
Kastner, O. and Eggeler, G. and Weiss, W. and Ackland, G.J.
Journal of the Mechanics and Physics of Solids 59 1888-1908 (2011)Shape memory alloys (SMA) exhibit a number of features which are not easily explained by equilibrium thermodynamics, including hysteresis in the phase transformation and reverse shape memory in the high symmetry phase. Processing can change these features: repeated cycling can train the reverse shape memory effect, while changing the amount of hysteresis and other functional properties. These effects are likely to be due to formations of localised defects and these can be studied by atomistic methods. Here we present a molecular dynamics simulation study of such behaviour employing a two-dimensional, binary LennardJones model. Our atomistic model exhibits a symmetry breaking, displacive phase transition from a high temperature, entropically stabilised, austenite-like phase to a low temperature martensite-like phase. The simulations show transformations in this model material proceed by non-diffusive nucleation and growth processes and produce distinct microstructures. We observe the generation of persistent lattice defects during forward-and-reverse transformations which serve as nucleation centres in subsequent transformation processes. These defects interfere the temporal and spatial progression of transformations and thereby affect subsequent product morphologies. During cyclic transformations we observe accumulations of lattice defects so as to establish new microstructural elements which represent a memory of the previous morphologies. These new elements are self-organised and they provide a basis of the reversible shape memory effect in the model material. © 2011 Elsevier Ltd.view abstract doi: 10.1016/j.jmps.2011.05.009 2011 • 24 NMR studies of benzene mobility in metal-organic framework MOF-5
Hertel, S. and Wehring, M. and Amirjalayer, S. and Gratz, M. and Lincke, J. and Krautscheid, H. and Schmid, R. and Stallmach, F.
EPJ Applied Physics 55 (2011)The concentration and temperature dependence of the self-diffusion of benzene adsorbed in the metal-organic framework MOF-5 (IRMOF-1) is studied by pulsed field gradient (PFG) NMR spectroscopy. When increasing the loading from 10 to 20 molecules per unit cell of MOF-5, the experimental diffusion data drop by a factor of about 3 while current molecular dynamic (MD) simulations predict slightly increasing diffusion coefficients for this range of loadings. The observation is rationalized using the recently predicted clustering of adsorbate molecules in microporous systems for temperatures well below the adsorbate critical temperature. Necessary improvements of molecular simulation models for predicting diffusivities under such conditions are discussed. © EDP Sciences, 2011.view abstract doi: 10.1051/epjap/2011100370 2011 • 23 On the formation of vacancies by edge dislocation dipole annihilation in fatigued copper
Brinckmann, S. and Sivanesapillai, R. and Hartmaier, A.
International Journal of Fatigue 33 1369-1375 (2011)Fatigue experiments on copper have shown that vacancy production leads to the evolution of extrusions, which are the preferred sites for fatigue crack initiation. However, experimental, analytical and numerical results for the critical edge-dislocation dipole annihilation distance vastly differ. This study performs molecular statics and molecular dynamics simulations at elevated temperature to investigate the discrepancies in annihilation distance. Vacancy forming edge dislocation dipoles are stable if their spacing exceeds 2 lattice spacings. If the dislocation dipole is perpendicular to the free surface in a thin sheet of material, jogs on edge dislocations lead to dipole annihilation. Our main conclusion is that dislocation generation, glide and stable edge dislocation dipoles are sufficient to lead to that extrusion growth, which results in fatigue crack initiation.view abstract doi: 10.1016/j.ijfatigue.2011.05.004 2011 • 22 Quantitative, label-free and site-specific monitoring of molecular recognition: A multivariate resonance Raman approach
Niebling, S. and Kuchelmeister, H.Y. and Schmuck, C. and Schlücker, S.
Chemical Communications 47 568-570 (2011)A site-specific and quantitative approach for label-free monitoring of molecular recognition is presented. Specifically, the binding site of an artificial receptor is probed selectively by UVRR spectroscopy. The ligand binding constant can be determined by non-negative matrix factorization. © 2011 The Royal Society of Chemistry.view abstract doi: 10.1039/c0cc02052d 2011 • 21 Rational design of β-sheet ligands against Aβ42- induced toxicity
Hochdörffer, K. and März-Berberich, J. and Nagel-Steger, L. and Epple, M. and Meyer-Zaika, W. and Horn, A.H.C. and Sticht, H. and Sinha, S. and Bitan, G. and Schrader, T.
Journal of the American Chemical Society 133 4348-4358 (2011)A β-sheet-binding scaffold was equipped with long-range chemical groups for tertiary contacts toward specific regions of the Alzheimer's Aβ fibril. The new constructs contain a trimeric aminopyrazole carboxylic acid, elongated with a C-terminal binding site, whose influence on the aggregation behavior of the Aβ42 peptide was studied. MD simulations after trimer docking to the anchor point (F19/F20) suggest distinct groups of complex structures each of which featured additional specific interactions with characteristic Aβ regions. Members of each group also displayed a characteristic pattern in their antiaggregational behavior toward Aβ. Specifically, remote lipophilic moieties such as a dodecyl, cyclohexyl, or LPFFD fragment can form dispersive interactions with the nonpolar cluster of amino acids between I31 and V36. They were shown to strongly reduce Thioflavine T (ThT) fluorescence and protect cells from Aβ lesions (MTT viability assays). Surprisingly, very thick fibrils and a high β-sheet content were detected in transmission electron microscopy (TEM) and CD spectroscopic experiments. On the other hand, distant single or multiple lysines which interact with the ladder of stacked E22 residues found in Aβ fibrils completely dissolve existing β-sheets (ThT, CD) and lead to unstructured, nontoxic material (TEM, MTT). Finally, the triethyleneglycol spacer between heterocyclic β-sheet ligand and appendix was found to play an active role in destabilizing the turn of the U-shaped protofilament. Fluorescence correlation spectroscopy (FCS) and sedimentation velocity analysis (SVA) provided experimental evidence for some smaller benign aggregates of very thin, delicate structure (TEM, MTT). A detailed investigation by dynamic light scattering (DLS) and other methods proved that none of the new ligands acts as a colloid. The evolving picture for the disaggregation mechanism by these new hybrid ligands implies transformation of well-ordered fibrils into less structured aggregates with a high molecular weight. In the few cases where fibrillar components remain, these display a significantly altered morphology and have lost their acute cellular toxicity. © 2011 American Chemical Society.view abstract doi: 10.1021/ja107675n 2011 • 20 Robustness and optimal use of design principles of arthropod exoskeletons studied by ab initio-based multiscale simulations
Nikolov, S. and Fabritius, H. and Petrov, M. and Friák, M. and Lymperakis, L. and Sachs, C. and Raabe, D. and Neugebauer, J.
Journal of the Mechanical Behavior of Biomedical Materials 4 129-145 (2011)Recently, we proposed a hierarchical model for the elastic properties of mineralized lobster cuticle using (i) ab initio calculations for the chitin properties and (ii) hierarchical homogenization performed in a bottom-up order through all length scales. It has been found that the cuticle possesses nearly extremal, excellent mechanical properties in terms of stiffness that strongly depend on the overall mineral content and the specific microstructure of the mineral-protein matrix. In this study, we investigated how the overall cuticle properties changed when there are significant variations in the properties of the constituents (chitin, amorphous calcium carbonate (ACC), proteins), and the volume fractions of key structural elements such as chitin-protein fibers. It was found that the cuticle performance is very robust with respect to variations in the elastic properties of chitin and fiber proteins at a lower hierarchy level. At higher structural levels, variations of design parameters such as the volume fraction of the chitin-protein fibers have a significant influence on the cuticle performance. Furthermore, we observed that among the possible variations in the cuticle ingredients and volume fractions, the experimental data reflect an optimal use of the structural variations regarding the best possible performance for a given composition due to the smart hierarchical organization of the cuticle design. © 2010 Elsevier Ltd.view abstract doi: 10.1016/j.jmbbm.2010.09.015 2011 • 19 Structural plasticity of staphylococcal nuclease probed by perturbation with pressure and pH
Kitahara, R. and Hata, K. and Maeno, A. and Akasaka, K. and Chimenti, M.S. and Garcia-Moreno, E.B. and Schroer, M.A. and Jeworrek, C. and Tolan, M. and Winter, R. and Roche, J. and Roumestand, C. and Montet de Guillen, K. and Royer, C.A.
Proteins: Structure, Function and Bioinformatics 79 1293-1305 (2011)The ionization of internal groups in proteins can trigger conformational change. Despite this being the structural basis of most biological energy transduction, these processes are poorly understood. Small angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy experiments at ambient and high hydrostatic pressure were used to examine how the presence and ionization of Lys-66, buried in the hydrophobic core of a stabilized variant of staphylococcal nuclease, affect conformation and dynamics. NMR spectroscopy at atmospheric pressure showed previously that the neutral Lys-66 affects slow conformational fluctuations globally, whereas the effects of the charged form are localized to the region immediately surrounding position 66. Ab initio models from SAXS data suggest that when Lys-66 is charged the protein expands, which is consistent with results from NMR spectroscopy. The application of moderate pressure (<2 kbar) at pH values where Lys-66 is normally neutral at ambient pressure left most of the structure unperturbed but produced significant nonlinear changes in chemical shifts in the helix where Lys-66 is located. Above 2 kbar pressure at these pH values the protein with Lys-66 unfolded cooperatively adopting a relatively compact, albeit random structure according to Kratky analysis of the SAXS data. In contrast, at low pH and high pressure the unfolded state of the variant with Lys-66 is more expanded than that of the reference protein. The combined global and local view of the structural reorganization triggered by ionization of the internal Lys-66 reveals more detectable changes than were previously suggested by NMR spectroscopy at ambient pressure. Proteins 2011. © 2011 Wiley-Liss, Inc.view abstract doi: 10.1002/prot.22966 2011 • 18 The object-oriented DFT program library S/PHI/nX
Boeck, S. and Freysoldt, C. and Dick, A. and Ismer, L. and Neugebauer, J.
Computer Physics Communications 182 543-554 (2011)In order to simplify the development and implementation process of quantum mechanical algorithms, we developed a set of object-oriented C++ libraries which can exploit modern computer architectures. The libraries are characterized as follows: (i) State-of-the-art computer science techniques have been applied or developed in this work to provide language elements to express algebraic expressions efficiently on modern computer platforms. (ii) Quantum mechanical algorithms are crucial in the field of materials research. The new libraries support the Dirac notation to implement such algorithms in the native language of physicists. (iii) The libraries are completed by elements to express equations of motions efficiently which is required for implementing structural algorithms such as molecular dynamics. Based on these libraries we introduce the DFT program package S/PHI/nX. © 2010 Elsevier B.V. All rights reserved.view abstract doi: 10.1016/j.cpc.2010.09.016 2011 • 17 The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode
Costanzo, F. and Sulpizi, M. and Valle, R.G.D. and Sprik, M.
Journal of Chemical Physics 134 (2011)The thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H+) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H3O+). Using the computed solvation free energy of H+ as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pKa and normal hydrogen electrode (NHE) potentials. This conversion requires certain thermochemical corrections which were first presented in a similar study of the oxidation of hydrobenzoquinone [J. Cheng, M. Sulpizi, and M. Sprik, J. Chem. Phys. 131, 154504 (2009)]10.1063/1.3250438. Taking a different view of the thermodynamic status of the hydronium ion, these thermochemical corrections are revised in the present work. The key difference with the previous scheme is that the hydronium is now treated as an intermediate in the transfer of the proton from solution to the gas-phase. The accuracy of the method is assessed by a detailed comparison of the computed pKa, NHE potentials and dehydrogenation free energies to experiment. As a further application of the technique, we have analyzed the role of the solvent in the oxidation of tyrosine by the tryptophan radical. The free energy change computed for this hydrogen atom transfer reaction is very similar to the gas-phase value, in agreement with experiment. The molecular dynamics results however, show that the minimal solvent effect on the reaction free energy is accompanied by a significant reorganization of the solvent. © 2011 American Institute of Physics.view abstract doi: 10.1063/1.3597603 2011 • 16 Thermodynamics and molecular dynamics investigation of a possible new critical size for surface and inner cohesive energy of Al nanoparticles
Chamaani, A. and Marzbanrad, E. and Rahimipour, M. R. and Yaghmaee, M. S. and Aghaei, A. and Kamachali, R. D. and Behnamian, Y.
Journal of Nanoparticle Research 13 6059--6067 (2011)In this study, the authors first review the previously developed, thermodynamics-based theory for size dependency of the cohesion energy of free-standing spherically shaped Al nanoparticles. Then, this model is extrapolated to the cubic and truncated octahedron Al nanoparticle shapes. A series of computations for Al nanoparticles with these two new shapes are presented for particles in the range of 1-100 nm. The thermodynamics computational results reveal that there is a second critical size around 1.62 and 1 nm for cubes and truncated octahedrons, respectively. Below this critical size, particles behave as if they consisted only of surface-energy-state atoms. A molecular dynamics simulation is used to verify this second critical size for Al nanoparticles in the range of 1-5 nm. MD simulation for cube and truncated octahedron shapes shows the second critical point to be around 1.63 and 1.14 nm, respectively. According to the modeling and simulation results, this second critical size seems to be a material property characteristic rather than a shape-dependent feature.view abstract doi: 10.1007/s11051-011-0258-6 2010 • 15 Development of a method to determine Burgers vectors from atomistic data
Hua, J. and Hartmaier, A.
Journal of Physics: Conference Series 240 (2010)Large-scale molecular dynamics simulations have been widely used to investigate the mechanical behaviour of materials. But complex datasets, involving the positions of millions of atoms, generated during the simulations make quantitative data analysis quite a challenge. This paper presents a novel method to determine not only dislocations in the crystal, but also to quantify their Burgers vectors. This is achieved by combining geometrical methods to determine the atoms lying in the dislocations cores, like for example the common neighbour analysis or the bond angle analysis, with the slip vector analysis. The first methods are used to filter out the atoms lying in undisturbed regions of the crystal; the latter method yields the relative slip of the remaining atoms and thus indicates the Burgers vector of those atoms lying in the dislocation cores. The validity of the method is demonstrated here on a single edge dislocation in a relatively small sample. Furthermore a way will be sketched how this analysis can be used to determine densities of statistically stored and geometrically necessary dislocations, respectively. Hence, this method can be expected to provide valuable input for strain gradient plasticity models. © 2010 IOP Publishing Ltd.view abstract doi: 10.1088/1742-6596/240/1/012010 2010 • 14 Experimental and computer simulation determination of the structural changes occurring through the liquid-glass transition in Cu-Zr alloys
Mendelev, M.I. and Kramer, M.J. and Ott, R.T. and Sordelet, D.J. and Besser, M.F. and Kreyssig, A. and Goldman, A.I. and Wessels, V. and Sahu, K.K. and Kelton, K.F. and Hyers, R.W. and Canepari, S. and Rogers, J.R.
Philosophical Magazine 90 3795-3815 (2010)Molecular dynamics (MD) simulations were performed of the structural changes occurring through the liquid-glass transition in Cu-Zr alloys. The total scattering functions (TSF), and their associated primary diffuse scattering peak positions (Kp), heights (Kh) and full-widths at half maximum (KFWHM) were used as metrics to compare the simulations to high-energy X-ray scattering data. The residuals of difference between the model and experimental TSFs are ∼0.03 for the liquids and about 0.07 for the glasses. Over the compositional range studied, Zr1-xCux (0.1 ≤ x ≤ 0.9), Kp, Kh and KFWHM show a strong dependence on composition and temperature. The simulation and experimental data correlate well between each other. MD simulation revealed that the Cu-Zr bonds undergo the largest changes during cooling of the liquid, whereas the Cu-Cu bonds change the least. Changes in the partial-pair correlations are more readily seen in the second and third shells. The Voronoi polyhedra (VP) in glasses are dominated by only a few select types that are compositionally dependent. The relative concentrations of the dominant VPs rapidly change in their relative proportion in the deeply undercooled liquid. The experimentally determined region of best glass formability, xCu 65%, shows the largest temperature dependent changes for the deeply undercooled liquid in the MD simulation. This region also exhibits very strong temperature dependence for the diffusivity and the total energy of the system. These data point to a strong topological change in the best glass-forming alloys and a concurrent change in the VP chemistry in the deeply undercooled liquid. © 2010 Taylor & Francis.view abstract doi: 10.1080/14786435.2010.494585 2010 • 13 High-throughput parallel-I/O using sionlib for mesoscopic particle dynamics simulations on massively parallel computers
Freche, J. and Frings, W. and Sutmann, G.
Advances in Parallel Computing 19 371-378 (2010)The newly developed parallel Input/Output-libray SIONlib is applied to the highly scalable parallel multiscale code MP2C, which couples a mesoscopic fluid method based on multi-particle collision dynamics to molecular dynamics. It is demonstrated that for fluid-benchmark systems, a significant improvement of scalability under production conditions can be achieved. It is shown that for the BlueGene/P architecture at Jülich a performance close to the bandwidth capacity of 4.7 GByte/sec can be obtained. The article discusses the ease of use of SIONlib from the point of view of application. © 2010 The authors and IOS Press. All rights reserved.view abstract doi: 10.3233/978-1-60750-530-3-371 2010 • 12 Molecular dynamics simulations of the shape memory effect in a chain of Lennard-Jones crystals
Kastner, O. and Eggeler, G.
Multidiscipline Modeling in Materials and Structures 6 78-91 (2010)Purpose - Shape memory alloys are a fascinating class of materials because they combine both structural and functional properties. These properties strongly depend on temperature. One consequence of this dependency yields the characteristic shape-memory effect: shape memory alloys can recover processed reference configurations after significant plastic deformations simply upon a change of temperature. For real materials, such processes incorporate characteristic hysteresis. This paper aims at an understanding of these materials from an atomistic point of view. Design/methodology/approach - 2D molecular-dynamics (MD) simulations describing a chain consisting of 32 linked Lennard-Jones crystals are presented. The crystals consist of nested lattices of two atom species. Distinct lattice structures can be identified, interpreted as austenite and (variants of) martensite. Temperature and/or load-induced phase transitions between these configurations are observed in MD simulations. Previously, the thermal equation of state of one isolated crystal was investigated and its phase stability was discussed in detail. In the multi-crystal chain considered in the present paper, individual crystals contribute collectively to the thermo-mechanical behavior of the assembly. Findings - The paper presents the results of numerical experiments with this polycrystalline chain under strain-, load- and/or temperature-control. The results show that with the assumption of simple Lennard-Jones potentials of interaction between atoms in individual crystals and linking these crystals allows to reproduce the features associated with the fascinating behavior of shape memory alloys, including pseudo-plasticity, pseudo-elasticity and the shape memory effect. Originality/value - Owing to the special setup chosen, interfaces are missing between adjacent crystals in the chain assembly. The paper shows that in this situation load-induced austenite/ martensite transitions do not exhibit hysteresis in tension/compression cycles. This observation indirectly supports mesoscopic-level work in the literature which explicitly introduces interface energy to model such hysteresis. © Emerald Group Publishing Limited.view abstract doi: 10.1108/15736101011055275 2010 • 11 Multiscale simulations on the grain growth process in nanostructured materials
Kamachali, R.D. and Hua, J. and Steinbach, I. and Hartmaier, A.
International Journal of Materials Research 101 1332-1338 (2010)In this work, multi-phase field and molecular dynamics simulations have been used to investigate nanoscale grain growth mechanisms. Based on experimental observations, the combination of grain boundary expansion and vacancy diffusion has been considered in the multi-phase field model. The atomistic mechanism of boundary movement and the free volume redistribution during the growth process have been investigated using molecular dynamics simulations. According to the multi-phase field results, linear grain growth in nanostructured materials at low temperature can be explained by vacancy diffusion in the stress field around the grain boundaries. Molecular dynamics simulations confirm the observation of linear grain growth for nanometresized grains. The activation energy of grain boundary motion in this regime has been determined to be of the order of onetenth of the self-diffusion activation energy, which is consistent with experimental data. Based on the simulation results, the transition from linear to normal grain growth is discussed in detail and a criterion for this transition is proposed. © Carl Hanser Verlag GmbH & Co. KG.view abstract doi: 10.3139/146.110419 2010 • 10 Nonlinear reaction coordinate analysis in the reweighted path ensemble
Lechner, W. and Rogal, J. and Juraszek, J. and Ensing, B. and Bolhuis, P.G.
Journal of Chemical Physics 133 (2010)We present a flexible nonlinear reaction coordinate analysis method for the transition path ensemble based on the likelihood maximization approach developed by Peters and Trout [J. Chem. Phys. 125, 054108 (2006)]. By parametrizing the reaction coordinate by a string of images in a collective variable space, we can optimize the likelihood that the string correctly models the committor data obtained from a path sampling simulation. The collective variable space with the maximum likelihood is considered to contain the best description of the reaction. The use of the reweighted path ensemble [J. Rogal, J. Chem. Phys. 133, 174109 (2010)] allows a complete reaction coordinate description from the initial to the final state. We illustrate the method on a z-shaped two-dimensional potential. While developed for use with path sampling, this analysis method can also be applied to regular molecular dynamics trajectories. © 2010 American Institute of Physics.view abstract doi: 10.1063/1.3491818 2010 • 9 Particle based simulations of complex systems with MP2C: Hydrodynamics and electrostatics
Sutmann, G. and Westphal, L. and Bolten, M.
AIP Conference Proceedings 1281 1768-1772 (2010)Particle based simulation methods are well established paths to explore system behavior on microscopic to mesoscopic time and length scales. With the development of new computer architectures it becomes more and more important to concentrate on local algorithms which do not need global data transfer or reorganisation of large arrays of data across processors. This requirement strongly addresses long-range interactions in particle systems, i.e. mainly hydrodynamic and electrostatic contributions. In this article, emphasis is given to the implementation and parallelization of the Multi-Particle Collision Dynamics method for hydrodynamic contributions and a splitting scheme based on Multigrid for electrostatic contributions. Implementations are done for massively parallel architectures and are demonstrated for the IBM Blue Gene/P architecture Jugene in Jülich. © 2010 American Institute of Physics.view abstract doi: 10.1063/1.3498216 2010 • 8 Prediction of tautomer ratios by embedded-cluster integral equation theory
Kast, S.M. and Heil, J. and Güssregen, S. and Schmidt, K.F.
Journal of Computer-Aided Molecular Design 24 343-353 (2010)The "embedded cluster reference interaction site model" (EC-RISM) approach combines statistical-mechanical integral equation theory and quantum-chemical calculations for predicting thermodynamic data for chemical reactions in solution. The electronic structure of the solute is determined self-consistently with the structure of the solvent that is described by 3D RISM integral equation theory. The continuous solvent-site distribution is mapped onto a set of discrete background charges ("embedded cluster") that represent an additional contribution to the molecular Hamiltonian. The EC-RISM analysis of the SAMPL2 challenge set of tautomers proceeds in three stages. Firstly, the group of compounds for which quantitative experimental free energy data was provided was taken to determine appropriate levels of quantum-chemical theory for geometry optimization and free energy prediction. Secondly, the resulting workflow was applied to the full set, allowing for chemical interpretations of the results. Thirdly, disclosure of experimental data for parts of the compounds facilitated a detailed analysis of methodical issues and suggestions for future improvements of the model. Without specifically adjusting parameters, the EC-RISM model yields the smallest value of the root mean square error for the first set (0.6 kcal mol-1) as well as for the full set of quantitative reaction data (2.0 kcal mol-1) among the SAMPL2 participants. © 2010 Springer Science+Business Media B.V.view abstract doi: 10.1007/s10822-010-9340-x 2010 • 7 Proapoptotic influenza A virus protein PB1-F2 forms a nonselective ion channel
Henkel, M. and Mitzner, D. and Henklein, P. and Meyer-Almes, F.-J. and Moroni, A. and DiFrancesco, M.L. and Henkes, L.M. and Kreim, M. and Kast, S.M. and Schubert, U. and Thiel, G.
PLoS ONE 5 (2010)Background: PB1-F2 is a proapoptotic influenza A virus protein of approximately 90 amino acids in length that is located in the nucleus, cytosol and in the mitochondria membrane of infected cells. Previous studies indicated that the molecule destabilizes planar lipid bilayers and has a strong inherent tendency for multimerization. This may be correlate with its capacity to induce mitochondrial membrane depolarization. Methodology/Principal Findings: Here, we investigated whether PB1-F2 is able to form ion channels within planar lipid bilayers and microsomes. For that purpose, a set of biologically active synthetic versions of PB1-F2 (sPB1-F2) derived from the IAV isolates A/Puerto Rico/8/34(H1N1) (IAVPR8), from A/Brevig Mission/1/1918(H1N1) (IAVSF2) or the H5N1 consensus sequence (IAVBF2) were used. Electrical and fluorimetric measurements show that all three peptides generate in planar lipid bilayers or in liposomes, respectively, a barely selective conductance that is associated with stochastic channel type fluctuations between a closed state and at least two defined open states. Unitary channel fluctuations were also generated when a truncated protein comprising only the 37 c-terminal amino acids of sPB1-F2 was reconstituted in bilayers. Experiments were complemented by extensive molecular dynamics simulations of the truncated fragment in a lipid bilayer. The results indicate that the c-terminal region exhibits a slightly bent helical fold, which is stable and remains embedded in the bilayer for over 180 ns. Conclusion/Significance: The data support the idea that PB1-F2 is able to form protein channel pores with no appreciable selectivity in membranes and that the c-terminus is important for this function. This information could be important for drug development. © 2010 Henkel et al.view abstract doi: 10.1371/journal.pone.0011112 2010 • 6 Proton transfer to charged platinum electrodes. A molecular dynamics trajectory study
Wilhelm, F. and Schmickler, W. and Spohr, E.
Journal of Physics Condensed Matter 22 (2010)A recently developed empirical valence bond(EVB) model for proton transfer on Pt(111) electrodes (Wilhelm et al 2008 J. Phys. Chem. C 112 10814) has been applied in molecular dynamics(MD) simulations of a water film in contact with a charged Pt surface. A total of seven negative surface charge densities σ between - 7.5 and - 18.9νCcm-2 were investigated. For each value of σ, between 30 and 84 initial conditions of a solvated proton within a water slab were sampled, and the trajectories were integrated until discharge of a proton occurred on the charged surfaces. We have calculated the mean rates for discharge and for adsorption of solvated protons within the adsorbed water layer in contact with the metal electrode as a function of surface charge density. For the less negative values of σ we observe a Tafel-like exponential increase of discharge rate with decreasing σ. At the more negative values this exponential increase levels off and the discharge process is apparently transport limited. Mechanistically, the Tafel regime corresponds to a stepwise proton transfer: first, a proton is transferred from the bulk into the contact water layer, which is followed by transfer of a proton to the charged surface and concomitant discharge. At the more negative surface charge densities the proton transfer into the contact water layer and the transfer of another proton to the surface and its discharge occur almost simultaneously. © 2010 IOP Publishing Ltd.view abstract doi: 10.1088/0953-8984/22/17/175001 2010 • 5 Salt bridges in the miniature viral channel Kcv are important for function
Hertel, B. and Tayefeh, S. and Kloss, T. and Hewing, J. and Gebhardt, M. and Baumeister, D. and Moroni, A. and Thiel, G. and Kast, S.M.
European Biophysics Journal 39 1057-1068 (2010)The viral potassium channel Kcv comprises only 94 amino acids, which represent the pore module of more complex K+channels. As for Kir-type channels, Kcv also has a short N-terminal helix exposed to the cytoplasm, upstream of the Wrst transmembrane domain. Here we show that this helix is relevant for Kcv function. The presence of charged amino acids, which form dynamic inter- and intrasubunit salt bridges is crucial. Electrophysiological measurements, yeast rescue experiments and molecular dynamics simulations show that mutants in which the critical salt bridge formation is impaired have no or reduced channel activity. We conclude that these salt bridges destabilise the complexation of K+ions by negative charges on the inner transmembrane domain at the entrance into the cavity. This feature facilitates a continuous and coordinated transfer of ions between the cavity and the cytoplasm for channels without the canonical bundle crossing. © European Biophysical Societies' Association 2009.view abstract doi: 10.1007/s00249-009-0451-z 2010 • 4 Semidilute polymer solutions at equilibrium and under shear flow
Huang, C.-C. and Winkler, R.G. and Sutmann, G. and Gompper, G.
Macromolecules 43 10107-10116 (2010)The properties of semidilute polymer solutions are investigated at equilibrium and under shear flow by mesoscale simulations, which combine molecular dynamics simulations and the multiparticle collision dynamics approach. In semidilute solution, intermolecular hydrodynamic and excluded volume interactions become increasingly important due to the presence of polymer overlap. At equilibrium, the dependence of the radius of gyration, the structure factor, and the zero-shear viscosity on the polymer concentration is determined and found to be in good agreement with scaling predictions. In shear flow, the polymer alignment and deformation are calculated as a function of concentration. Shear thinning, which is related to flow alignment and finite polymer extensibility, is characterized by the shear viscosity and the normal stress coefficients. © 2010 American Chemical Society.view abstract doi: 10.1021/ma101836x 2010 • 3 The reweighted path ensemble
Rogal, J. and Lechner, W. and Juraszek, J. and Ensing, B. and Bolhuis, P.G.
Journal of Chemical Physics 133 (2010)We introduce a reweighting scheme for the path ensembles in the transition interface sampling framework. The reweighting allows for the analysis of free energy landscapes and committor projections in any collective variable space. We illustrate the reweighting scheme on a two dimensional potential with a nonlinear reaction coordinate and on a more realistic simulation of the Trp-cage folding process. We suggest that the reweighted path ensemble can be used to optimize possible nonlinear reaction coordinates. © 2010 American Institute of Physics.view abstract doi: 10.1063/1.3491817 2009 • 2 Redox potentials and pKa for benzoquinone from density functional theory based molecular dynamics
Cheng, J. and Sulpizi, M. and Sprik, M.
Journal of Chemical Physics 131 (2009)The density functional theory based molecular dynamics (DFTMD) method for the computation of redox free energies presented in previous publications and the more recent modification for computation of acidity constants are reviewed. The method uses a half reaction scheme based on reversible insertion/removal of electrons and protons. The proton insertion is assisted by restraining potentials acting as chaperones. The procedure for relating the calculated deprotonation free energies to Brønsted acidities (pKa) and the oxidation free energies to electrode potentials with respect to the normal hydrogen electrode is discussed in some detail. The method is validated in an application to the reduction of aqueous 1,4-benzoquinone. The conversion of hydroquinone to quinone can take place via a number of alternative pathways consisting of combinations of acid dissociations, oxidations, or dehydrogenations. The free energy changes of all elementary steps (ten in total) are computed. The accuracy of the calculations is assessed by comparing the energies of different pathways for the same reaction (Hess's law) and by comparison to experiment. This two-sided test enables us to separate the errors related with the restrictions on length and time scales accessible to DFTMD from the errors introduced by the DFT approximation. It is found that the DFT approximation is the main source of error for oxidation free energies. © 2009 American Institute of Physics.view abstract doi: 10.1063/1.3250438 2009 • 1 The electron attachment energy of the aqueous hydroxyl radical predicted from the detachment energy of the aqueous hydroxide anion
Adriaanse, C. and Sulpizi, M. and VandeVondele, J. and Sprik, M.
Journal of the American Chemical Society 131 6046-6047 (2009)Combining photoemission and electrochemical data from the literature we argue that the difference between the vertical and adiabatic ionization energy of the aqueous hydroxide anion is 2.9 eV. We then use density functional theory based molecular dynamics to show that the solvent response to ionization is nonlinear. Adding this to the experimental data we predict a 4.1 eV difference between the energy for vertical attachment of an electron to the aqueous hydroxyl radical and the corresponding adiabatic electron affinity. This places the state accepting the electron only 2.2 eV below vacuum or 7.7 eV above the edge of the valence band of water. © 2009 American Chemical Society.view abstract doi: 10.1021/ja809155k