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.

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  • 2020 • 193 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 abstractdoi: 10.1063/1.5129769
  • 2020 • 192 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 abstractdoi: 10.1111/jace.16696
  • 2020 • 191 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 abstractdoi: 10.1038/s41586-020-2082-6
  • 2020 • 190 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 abstractdoi: 10.1016/j.bpc.2019.106258
  • 2020 • 189 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 abstractdoi: 10.1039/c9cp06785j
  • 2020 • 188 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 abstractdoi: 10.1103/PhysRevMaterials.4.013605
  • 2020 • 187 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 abstractdoi: 10.1039/d0ra00932f
  • 2020 • 186 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 abstractdoi: 10.1088/1361-651X/ab7150
  • 2020 • 185 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 abstractdoi: 10.1016/j.ceramint.2020.02.009
  • 2019 • 184 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 abstractdoi: 10.3390/ma12020215
  • 2019 • 183 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 abstractdoi: 10.3390/ma12020215
  • 2019 • 182 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 abstractdoi: 10.1039/c9cp00036d
  • 2019 • 181 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 abstractdoi: 10.1038/s41467-019-08752-7
  • 2019 • 180 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 abstractdoi: 10.1021/acscentsci.9b00497
  • 2019 • 179 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 abstractdoi: 10.1016/j.tsf.2019.06.030
  • 2019 • 178 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 abstractdoi: 10.1103/PhysRevB.99.094107
  • 2019 • 177 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 abstractdoi: 10.1039/c8cc07946c
  • 2019 • 176 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 abstractdoi: 10.1103/PhysRevLett.123.195502
  • 2019 • 175 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. © 2019
    view abstractdoi: 10.1016/j.bpc.2019.106260
  • 2019 • 174 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 abstractdoi: 10.1063/1.5050090
  • 2019 • 173 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 abstractdoi: 10.1103/PhysRevB.100.104110
  • 2019 • 172 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 abstractdoi: 10.1108/ILT-03-2019-0096
  • 2019 • 171 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 abstractdoi: 10.1016/j.actamat.2019.06.008
  • 2019 • 170 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 abstractdoi: 10.1038/s41467-019-10012-7
  • 2019 • 169 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 abstractdoi: 10.1016/j.tsf.2019.05.016
  • 2019 • 168 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 abstractdoi: 10.1021/jacs.9b09225
  • 2019 • 167 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 abstractdoi: 10.1016/j.molliq.2019.04.068
  • 2019 • 166 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 abstractdoi: 10.1021/acs.chemmater.9b02047
  • 2019 • 165 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 Ltd
    view abstractdoi: 10.1016/j.tibtech.2019.04.015
  • 2019 • 164 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 abstractdoi: 10.1021/acs.jpcc.8b12015
  • 2019 • 163 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 abstractdoi: 10.1063/1.5063476
  • 2018 • 162 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, Weinheim
    view abstractdoi: 10.1002/cbic.201700596
  • 2018 • 161 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 abstractdoi: 10.1038/s41467-018-07140-x
  • 2018 • 160 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 abstractdoi: 10.1016/j.ijplas.2018.03.008
  • 2018 • 159 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 abstractdoi: 10.1016/j.nimb.2018.04.027
  • 2018 • 158 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 abstractdoi: 10.1016/j.commatsci.2018.08.055
  • 2018 • 157 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 abstractdoi: 10.1021/acs.jpcc.8b08590
  • 2018 • 156 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 abstractdoi: 10.1021/acs.jcim.7b00413
  • 2018 • 155 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 SAS
    view abstractdoi: 10.1016/j.ejmech.2018.09.072
  • 2018 • 154 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 abstractdoi: 10.1088/1367-2630/aadd5a
  • 2018 • 153 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 abstractdoi: 10.1021/acs.jpcb.7b11697
  • 2018 • 152 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 abstractdoi: 10.1021/acs.jpcb.7b11697
  • 2018 • 151 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 abstractdoi: 10.1038/s41467-018-03591-4
  • 2018 • 150 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 abstractdoi: 10.1038/s41467-018-04544-7
  • 2018 • 149 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, Weinheim
    view abstractdoi: 10.1002/celc.201800158
  • 2018 • 148 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 abstractdoi: 10.1016/j.apsusc.2018.04.191
  • 2018 • 147 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 abstractdoi: 10.1016/j.actamat.2018.03.038
  • 2018 • 146 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 abstractdoi: 10.1103/PhysRevLett.121.125902
  • 2018 • 145 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 abstractdoi: 10.1039/c7cp04971d
  • 2017 • 144 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 abstractdoi: 10.1021/jacs.7b07939
  • 2017 • 143 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 abstractdoi: 10.1063/1.4979982
  • 2017 • 142 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 abstractdoi: 10.1063/1.4987005
  • 2017 • 141 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 abstractdoi: 10.1063/1.4972963
  • 2017 • 140 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 abstractdoi: 10.1016/j.molliq.2016.09.089
  • 2017 • 139 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 abstractdoi: 10.1016/j.molliq.2016.09.067
  • 2017 • 138 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 abstractdoi: 10.1021/acs.jcim.6b00765
  • 2017 • 137 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 abstractdoi: 10.1088/1361-651X/aa865a
  • 2017 • 136 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 abstractdoi: 10.3390/polym9010015
  • 2017 • 135 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 abstractdoi: 10.1016/j.bpc.2017.05.016
  • 2017 • 134 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 abstractdoi: 10.1016/j.procs.2017.05.152
  • 2017 • 133 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 abstractdoi: 10.1021/jacs.7b01158
  • 2017 • 132 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 abstractdoi: 10.1088/1361-648X/aa72cb
  • 2017 • 131 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 abstractdoi: 10.1038/ncomms14472
  • 2017 • 130 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 abstractdoi: 10.1021/acs.jproteome.6b00587
  • 2017 • 129 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 Ltd
    view abstractdoi: 10.1016/j.carbon.2016.12.015
  • 2017 • 128 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, Weinheim
    view abstractdoi: 10.1002/ejoc.201601596
  • 2017 • 127 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, Weinheim
    view abstractdoi: 10.1002/anie.201706662
  • 2017 • 126 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 abstractdoi: 10.1016/j.commatsci.2017.01.043
  • 2016 • 125 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 abstractdoi: 10.1021/acs.jpcc.5b12331
  • 2016 • 124 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 abstractdoi: 10.1016/j.jcp.2016.02.065
  • 2016 • 123 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 abstractdoi: 10.1021/acs.jpcc.6b08609
  • 2016 • 122 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 abstractdoi: 10.1116/1.4953404
  • 2016 • 121 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 abstractdoi: 10.1002/mawe.201600481
  • 2016 • 120 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 Group
    view abstractdoi: 10.1080/00268976.2016.1167266
  • 2016 • 119 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 abstractdoi: 10.1002/pssa.201532469
  • 2016 • 118 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 abstractdoi: 10.1021/acs.langmuir.6b02076
  • 2016 • 117 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 abstractdoi: 10.1002/biot.201500086
  • 2016 • 116 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 abstractdoi: 10.1063/1.4944991
  • 2016 • 115 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 abstractdoi: 10.1016/j.actamat.2015.11.047
  • 2016 • 114 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 abstractdoi: 10.3762/bjnano.7.63
  • 2016 • 113 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 abstractdoi: 10.1039/c6ra16966j
  • 2016 • 112 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 abstractdoi: 10.1088/0953-8984/28/34/344004
  • 2016 • 111 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 abstractdoi: 10.1016/j.actamat.2016.03.052
  • 2016 • 110 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 Ltd
    view abstractdoi: 10.1016/j.bmcl.2016.06.051
  • 2016 • 109 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 abstractdoi: 10.1016/j.susc.2016.01.031
  • 2016 • 108 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 abstractdoi: 10.1021/acs.jpcc.6b02652
  • 2015 • 107 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 abstractdoi: 10.1016/j.cpc.2015.01.009
  • 2015 • 106 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 abstractdoi: 10.1016/j.micromeso.2015.02.042
  • 2015 • 105 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 abstractdoi: 10.1007/s10295-015-1621-x
  • 2015 • 104 The dynamics of TiNx (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 abstractdoi: 10.1016/j.tsf.2015.05.013
  • 2015 • 103 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 abstractdoi: 10.1021/acs.jpcc.5b06249
  • 2015 • 102 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 abstractdoi: 10.1021/acs.jpclett.5b01939
  • 2015 • 101 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 abstractdoi: 10.1115/IMECE2015-53118
  • 2015 • 100 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 abstractdoi: 10.1016/j.bbamem.2015.09.015
  • 2015 • 99 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 abstractdoi: 10.1016/j.scriptamat.2015.02.016
  • 2015 • 98 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 abstractdoi: 10.1063/1.4927084
  • 2015 • 97 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 abstractdoi: 10.1038/ncomms8349
  • 2015 • 96 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 abstractdoi: 10.1016/j.bbamem.2015.06.008
  • 2015 • 95 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 abstractdoi: 10.1016/j.micromeso.2015.02.043
  • 2015 • 94 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 abstractdoi: 10.1016/j.actamat.2015.03.050
  • 2015 • 93 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 • 92 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 abstractdoi: 10.1038/ncomms7409
  • 2015 • 91 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 abstractdoi: 10.1038/ncomms7577
  • 2015 • 90 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 abstractdoi: 10.1021/ci5006096
  • 2015 • 89 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 abstractdoi: 10.1016/j.surfcoat.2015.08.034
  • 2015 • 88 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 abstractdoi: 10.1016/j.susc.2014.06.016
  • 2015 • 87 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 abstractdoi: 10.1016/j.wear.2015.02.023
  • 2014 • 86 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 abstractdoi: 10.1088/1367-2630/16/1/015021
  • 2014 • 85 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 &amp; Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/chem.201304980
  • 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 abstractdoi: 10.1016/j.tsf.2014.02.053
  • 2014 • 83 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 abstractdoi: 10.1088/0965-0393/22/3/034005
  • 2014 • 82 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 abstractdoi: 10.1073/pnas.1411620111
  • 2014 • 81 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 abstractdoi: 10.1016/j.commatsci.2014.02.031
  • 2014 • 80 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 abstractdoi: 10.1016/j.actamat.2013.11.037
  • 2014 • 79 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 abstractdoi: 10.1088/0965-0393/22/3/034001
  • 2014 • 78 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 abstractdoi: 10.1016/j.molliq.2013.05.022
  • 2014 • 77 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 abstractdoi: 10.1038/ncomms5435
  • 2014 • 76 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 abstractdoi: 10.1063/1.4869800
  • 2014 • 75 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 abstractdoi: 10.1016/j.susc.2014.01.007
  • 2014 • 74 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 abstractdoi: 10.1007/s00340-013-5745-2
  • 2014 • 73 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 abstractdoi: 10.1115/HT2013-17246
  • 2014 • 72 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 abstractdoi: 10.1016/j.cplett.2013.11.025
  • 2014 • 71 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 abstractdoi: 10.1088/0965-0393/22/3/035011
  • 2014 • 70 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 abstractdoi: 10.1016/j.micromeso.2013.11.045
  • 2014 • 69 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 abstractdoi: 10.3762/bjnano.5.111
  • 2013 • 68 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 abstractdoi: 10.1016/j.cplett.2013.07.017
  • 2013 • 67 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 abstractdoi: 10.1039/c3ra22266g
  • 2013 • 66 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 abstractdoi: 10.1063/1.4821229
  • 2013 • 65 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 abstractdoi: 10.1038/nature12610
  • 2013 • 64 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 abstractdoi: 10.1088/0953-8984/25/42/425401
  • 2013 • 63 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 abstractdoi: 10.1016/j.bpj.2012.11.3834
  • 2013 • 62 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 abstractdoi: 10.1021/jp309038n
  • 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 abstractdoi: 10.1103/PhysRevE.88.022129
  • 2013 • 60 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 abstractdoi: 10.5560/ZNA.2012-0089
  • 2013 • 59 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 abstractdoi: 10.1002/andp.201200195
  • 2013 • 58 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 abstractdoi: 10.1002/bip.22131
  • 2013 • 57 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 abstractdoi: 10.1016/j.actamat.2012.09.081
  • 2013 • 56 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 abstractdoi: 10.1073/pnas.1220301110
  • 2013 • 55 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 abstractdoi: 10.1016/j.electacta.2013.01.146
  • 2013 • 54 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 abstractdoi: 10.1103/PhysRevE.87.030101
  • 2013 • 53 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 abstractdoi: 10.1021/am4010094
  • 2013 • 52 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 abstractdoi: 10.1007/s11249-012-0085-7
  • 2013 • 51 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 abstractdoi: 10.1016/j.jcis.2013.07.069
  • 2013 • 50 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 abstractdoi: 10.1088/0965-0393/21/6/065001
  • 2012 • 49 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 abstractdoi: 10.1021/jp301452z
  • 2012 • 48 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 abstractdoi: 10.1002/mats.201100071
  • 2012 • 47 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 abstractdoi: 10.1016/j.jmps.2011.12.005
  • 2012 • 46 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 abstractdoi: 10.1016/j.combustflame.2011.09.012
  • 2012 • 45 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 abstractdoi: 10.1088/0965-0393/20/4/045001
  • 2012 • 44 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 abstractdoi: 10.1016/j.ijplas.2012.05.010
  • 2012 • 43 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 abstractdoi: 10.1021/bi3006016
  • 2012 • 42 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 abstractdoi: 10.1080/08927022.2011.608670
  • 2012 • 41 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 abstractdoi: 10.1080/1539445X.2011.599698
  • 2012 • 40 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 abstractdoi: 10.1371/journal.pone.0043219
  • 2012 • 39 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 abstractdoi: 10.1103/PhysRevE.86.021802
  • 2012 • 38 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 abstractdoi: 10.1103/PhysRevLett.108.098301
  • 2012 • 37 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 abstractdoi: 10.1002/gamm.201210004
  • 2012 • 36 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 abstractdoi: 10.1016/j.physb.2012.08.025
  • 2012 • 35 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 abstractdoi: 10.1074/jbc.M111.316232
  • 2012 • 34 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 abstractdoi: 10.1080/0371750X.2013.772745
  • 2012 • 33 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 abstractdoi: 10.1021/jp212357n
  • 2012 • 32 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 abstractdoi: 10.1016/j.commatsci.2012.02.024
  • 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 abstractdoi: 10.1016/j.actamat.2010.10.016
  • 2011 • 30 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 abstractdoi: 10.1016/j.cpc.2010.09.016
  • 2011 • 29 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 abstractdoi: 10.1016/j.ijfatigue.2011.05.004
  • 2011 • 28 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 abstractdoi: 10.1007/s11051-011-0258-6
  • 2011 • 27 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 abstractdoi: 10.1039/c0cc05812b
  • 2011 • 26 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 abstractdoi: 10.1016/j.nimb.2010.11.082
  • 2011 • 25 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 abstractdoi: 10.1051/epjap/2011100370
  • 2011 • 24 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 abstractdoi: 10.1021/ja107675n
  • 2011 • 23 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 abstractdoi: 10.1016/j.jelechem.2011.03.035
  • 2011 • 22 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 abstractdoi: 10.1088/0953-8984/23/23/234104
  • 2011 • 21 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 abstractdoi: 10.1063/1.3629451
  • 2011 • 20 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 abstractdoi: 10.1016/j.jmps.2011.05.009
  • 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 abstractdoi: 10.1002/prot.22966
  • 2011 • 18 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 abstractdoi: 10.1016/j.actamat.2011.03.050
  • 2011 • 17 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 abstractdoi: 10.1039/c0cc02052d
  • 2011 • 16 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 abstractdoi: 10.1016/j.jmbbm.2010.09.015
  • 2011 • 15 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 abstractdoi: 10.1007/s00396-011-2399-7
  • 2011 • 14 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 abstractdoi: 10.1016/j.bbamem.2010.04.008
  • 2011 • 13 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 abstractdoi: 10.1016/j.electacta.2011.04.036
  • 2010 • 12 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 abstractdoi: 10.3233/978-1-60750-530-3-371
  • 2010 • 11 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 abstractdoi: 10.1371/journal.pone.0011112
  • 2010 • 10 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 abstractdoi: 10.1007/s00249-009-0451-z
  • 2010 • 9 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 abstractdoi: 10.1088/1742-6596/240/1/012010
  • 2010 • 8 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 abstractdoi: 10.1021/ma101836x
  • 2010 • 7 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 abstractdoi: 10.3139/146.110419
  • 2010 • 6 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 abstractdoi: 10.1007/s10822-010-9340-x
  • 2010 • 5 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 abstractdoi: 10.1108/15736101011055275
  • 2010 • 4 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 abstractdoi: 10.1063/1.3491818
  • 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 abstractdoi: 10.1063/1.3491817
  • 2010 • 2 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 abstractdoi: 10.1063/1.3498216
  • 2010 • 1 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 abstractdoi: 10.1088/0953-8984/22/17/175001