@article{44987, author = {{Brehm, Martin and Sebastiani, D.}}, journal = {{J. Chem. Phys.}}, pages = {{193802}}, title = {{{Simulating Structure and Dynamics in Small Droplets of 1-Ethyl-3-Methylimidazolium Acetate}}}, doi = {{10.1063/1.5010342}}, volume = {{148}}, year = {{2018}}, } @inproceedings{1590, abstract = {{We present the submatrix method, a highly parallelizable method for the approximate calculation of inverse p-th roots of large sparse symmetric matrices which are required in different scientific applications. Following the idea of Approximate Computing, we allow imprecision in the final result in order to utilize the sparsity of the input matrix and to allow massively parallel execution. For an n x n matrix, the proposed algorithm allows to distribute the calculations over n nodes with only little communication overhead. The result matrix exhibits the same sparsity pattern as the input matrix, allowing for efficient reuse of allocated data structures. We evaluate the algorithm with respect to the error that it introduces into calculated results, as well as its performance and scalability. We demonstrate that the error is relatively limited for well-conditioned matrices and that results are still valuable for error-resilient applications like preconditioning even for ill-conditioned matrices. We discuss the execution time and scaling of the algorithm on a theoretical level and present a distributed implementation of the algorithm using MPI and OpenMP. We demonstrate the scalability of this implementation by running it on a high-performance compute cluster comprised of 1024 CPU cores, showing a speedup of 665x compared to single-threaded execution.}}, author = {{Lass, Michael and Mohr, Stephan and Wiebeler, Hendrik and Kühne, Thomas and Plessl, Christian}}, booktitle = {{Proc. Platform for Advanced Scientific Computing (PASC) Conference}}, isbn = {{978-1-4503-5891-0/18/07}}, keywords = {{approximate computing, linear algebra, matrix inversion, matrix p-th roots, numeric algorithm, parallel computing}}, location = {{Basel, Switzerland}}, publisher = {{ACM}}, title = {{{A Massively Parallel Algorithm for the Approximate Calculation of Inverse p-th Roots of Large Sparse Matrices}}}, doi = {{10.1145/3218176.3218231}}, year = {{2018}}, } @article{13238, abstract = {{A numerically efficient yet highly accurate implementation of the crystal orbital Hamilton population (COHP) scheme for plane-wave calculations is presented. It is based on the projector-augmented wave (PAW) formalism in combination with norm-conserving pseudopotentials and allows to extract chemical interactions between atoms from band-structure calculations even for large and complex systems. The potential of the present COHP implementation is demonstrated by an in-depth analysis of the intensively investigated metal-insulator transition in atomic-scale indium wires self-assembled on the Si(111) surface. Thereby bond formation between In atoms of adjacent zigzag chains is found to be instrumental for the phase change. © 2017 Wiley Periodicals, Inc.}}, author = {{Lücke, Andreas and Gerstmann, Uwe and Kühne, Thomas D. and Schmidt, Wolf G.}}, journal = {{Journal of Computational Chemistry}}, keywords = {{density functional theory, bonding, crystal orbital Hamilton population, indium nanowires, phase transition}}, number = {{26}}, pages = {{2276--2282}}, title = {{{Efficient PAW-based bond strength analysis for understanding the In/Si(111)(8 × 2) – (4 × 1) phase transition}}}, doi = {{10.1002/jcc.24878}}, volume = {{38}}, year = {{2017}}, } @article{13239, author = {{Azadi, Sam and Kühne, Thomas D.}}, journal = {{The Journal of Chemical Physics}}, number = {{8}}, pages = {{084503}}, title = {{{High-pressure hydrogen sulfide by diffusion quantum Monte Carlo}}}, doi = {{10.1063/1.4976836}}, volume = {{146}}, year = {{2017}}, } @article{44983, author = {{Brehm, Martin and Saddiq, G. and Watermann, T. and Sebastiani, D.}}, journal = {{J. Phys. Chem. B}}, pages = {{8311--8321}}, title = {{{Influence of Small Fluorophilic and Lipophilic Organic Molecules on Dipalmitoylphosphatidylcholine Bilayers}}}, doi = {{10.1021/acs.jpcb.7b06520}}, volume = {{121 (35)}}, year = {{2017}}, } @article{44982, author = {{Brehm, Martin and Thomas, M.}}, journal = {{J. Phys. Chem. Lett.}}, pages = {{3409--3414}}, title = {{{Computing Bulk Phase Raman Optical Activity Spectra from ab initio Molecular Dynamics Simulations}}}, doi = {{10.1021/acs.jpclett.7b01616}}, volume = {{8 (14)}}, year = {{2017}}, } @article{44981, author = {{Slawik, C. and Rickmeyer, C. and Brehm, Martin and Böhme, A. and Schüürmann, G.}}, journal = {{Environ. Sci. Technol.}}, pages = {{4018--4026}}, title = {{{Glutathione Adduct Patterns of Michael-Acceptor Carbonyls}}}, doi = {{10.1021/acs.est.6b04981}}, volume = {{51 (7)}}, year = {{2017}}, } @article{44985, author = {{Brehm, Martin and Kafka, A. and Bamler, M. and Kühne, R. and Schüürmann, G. and Sikk, L. and Burk, J. and Burk, P. and Tamm, T. and Tämm, K. and Pokhrel, S. and Mädler, L. and Kahru, A. and Aruoja, V. and Sihtmäe, M. and Scott-Fordsmand, J. and Sorensen, P. B. and Escorihuela, L. and Roca, C. P. and Fernández, A. and Giralt, F. and Rallo, R.}}, journal = {{Adv. Exp. Med. Biol.}}, pages = {{257--301}}, title = {{{An Integrated Data-Driven Strategy for Safe-by-Design Nanoparticles: The FP7 MODERN Project.}}}, doi = {{10.1007/978-3-319-47754-1_9}}, volume = {{947}}, year = {{2017}}, } @article{45183, abstract = {{We investigated the effect of fluorinated molecules on dipalmitoylphosphatidylcholine (DPPC) bilayers by force-field molecular dynamics simulations. In the first step, we developed all-atom force-field parameters for additive molecules in membranes to enable an accurate description of those systems. On the basis of this force field, we performed extensive simulations of various bilayer systems containing different additives. The additive molecules were chosen to be of different size and shape, and they included small molecules such as perfluorinated alcohols, but also more complex molecules. From these simulations, we investigated the structural and dynamic effects of the additives on the membrane properties, as well as the behavior of the additive molecules themselves. Our results are in good agreement with other theoretical and experimental studies, and they contribute to a microscopic understanding of interactions, which might be used to specifically tune membrane properties by additives in the future.}}, author = {{Peschel, Christopher and Brehm, Martin and Sebastiani, Daniel}}, issn = {{2073-4360}}, journal = {{Polymers}}, keywords = {{Polymers and Plastics, General Chemistry}}, number = {{9}}, publisher = {{MDPI AG}}, title = {{{Polyphilic Interactions as Structural Driving Force Investigated by Molecular Dynamics Simulation (Project 7)}}}, doi = {{10.3390/polym9090445}}, volume = {{9}}, year = {{2017}}, } @article{16319, author = {{Zimmer, Peter and Müller, Patrick and Burkhardt, Lukas and Schepper, Rahel and Neuba, Adam and Steube, Jakob and Dietrich, Fabian and Flörke, Ulrich and Mangold, Stefan and Gerhards, Markus and Bauer, Matthias}}, issn = {{1434-1948}}, journal = {{European Journal of Inorganic Chemistry}}, pages = {{1504--1509}}, title = {{{N-Heterocyclic Carbene Complexes of Iron as Photosensitizers for Light-Induced Water Reduction}}}, doi = {{10.1002/ejic.201700064}}, year = {{2017}}, } @article{13417, author = {{Lücke, Andreas and Gerstmann, Uwe and Kühne, Thomas D. and Schmidt, Wolf Gero}}, issn = {{0192-8651}}, journal = {{Journal of Computational Chemistry}}, pages = {{2276--2282}}, title = {{{Efficient PAW-based bond strength analysis for understanding the In/Si(111)(8 × 2) - (4 × 1) phase transition}}}, doi = {{10.1002/jcc.24878}}, year = {{2017}}, } @article{19842, abstract = {{Non-trivial electronic properties of silver telluride and other chalcogenides, such as the presence of a topological insulator state, electronic topological transitions, metallization, and the possible emergence of superconductivity under pressure have attracted attention in recent years. In this work, we studied the electronic properties of silver selenide (Ag2Se). We performed direct current electrical resistivity measurements, in situ Raman spectroscopy, and synchrotron x-ray diffraction accompanied by ab initio calculations to explore pressure-induced changes to the atomic and electronic structure of Ag2Se. The temperature dependence of the electrical resistivity was measured up to 30 GPa in the 4–300 K temperature interval. Resistivity data showed an unusual increase in the thermal energy gap of phase I, which is a semiconductor under ambient conditions. Recently, a similar effect was reported for the 3D topological insulator Bi2Se3. Raman spectroscopy studies revealed lattice instability in phase I indicated by the softening of observed vibrational modes with pressure. Our hybrid functional band structure calculations predicted that phase I of Ag2Se would be a narrow band gap semiconductor, in accordance with experimental results. At a pressure of ~7.5 GPa, Ag2Se underwent a structural transition to phase II with an orthorhombic Pnma structure. The temperature dependence of the resistivity of Ag2Se phase II demonstrated its metallic character. Ag2Se phase III, which is stable above 16.5 GPa, is also metallic according to the resistivity data. No indication of the superconducting transition is found above 4 K in the studied pressure range.}}, author = {{Naumov, P and Barkalov, O and Mirhosseini, Hossein and Felser, C and A Medvedev, S}}, journal = {{Journal of Physics: Condensed Matter}}, number = {{38}}, pages = {{385801}}, publisher = {{{IOP} Publishing}}, title = {{{Atomic and electronic structures evolution of the narrow band gap semiconductor Ag2Se under high pressure}}}, doi = {{10.1088/0953-8984/28/38/385801}}, volume = {{28}}, year = {{2016}}, } @article{13240, abstract = {{Recently, the quantum harmonic oscillator model has been combined with maximally localized Wannier functions to account for long-range dispersion interactions in density functional theory calculations (Silvestrelli, J. Chem. Phys. 2013, 139, 054106). Here, we present a new, improved set of values for the three parameters involved in this scheme. To test the new parameter set we have computed the potential energy curves for various systems, including an isolated Ar2 dimer, two N2 dimers interacting within different configurations, and a water molecule physisorbed on pristine graphene. While the original set of parameters generally overestimates the interaction energies and underestimates the equilibrium distances, the new parameterization substantially improves the agreement with experimental and theoretical reference values. © 2016 Wiley Periodicals, Inc.}}, author = {{Partovi-Azar, Pouya and Berg, Matthias and Sanna, Simone and Kühne, Thomas D.}}, journal = {{International Journal of Quantum Chemistry}}, keywords = {{Wannier orbitals, Van der Waals interactions, density functional theory, quantum harmonic oscillator}}, number = {{15}}, pages = {{1160--1165}}, title = {{{Improved parameterization of the quantum harmonic oscillator model based on localized wannier functions to describe Van der Waals interactions in density functional theory}}}, doi = {{10.1002/qua.25150}}, volume = {{116}}, year = {{2016}}, } @article{13241, abstract = {{The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc.}}, author = {{Köster, Andreas and Spura, Thomas and Rutkai, Gábor and Kessler, Jan and Wiebeler, Hendrik and Vrabec, Jadran and Kühne, Thomas D.}}, journal = {{Journal of Computational Chemistry}}, keywords = {{liquid water, force matching, ab initio, molecular dynamics, Monte Carlo}}, number = {{19}}, pages = {{1828--1838}}, title = {{{Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations}}}, doi = {{10.1002/jcc.24398}}, volume = {{37}}, year = {{2016}}, } @article{45766, author = {{John, Christopher and Spura, Thomas and Kühne, Thomas D.}}, journal = {{Phys. Rev. E}}, title = {{{Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab Initio molecular dynamics}}}, volume = {{93}}, year = {{2016}}, } @inproceedings{25, author = {{Lass, Michael and Kühne, Thomas and Plessl, Christian}}, booktitle = {{Workshop on Approximate Computing (AC)}}, title = {{{Using Approximate Computing in Scientific Codes}}}, year = {{2016}}, } @article{44980, author = {{Cooper, M. and Wagner, A. and Wondrousch, D. and Sonntag, F. and Sonnabend, A. and Brehm, Martin and Schüürmann, G. and Adrian, L.}}, journal = {{Environ. Sci. Technol.}}, pages = {{6018--6028}}, title = {{{Anaerobic Microbial Transformation of Halogenated Aromatics and Fate Prediction Using Electron Density Modeling}}}, doi = {{10.1021/acs.est.5b00303}}, volume = {{49 (10)}}, year = {{2015}}, } @article{44977, author = {{Hollóczki, O. and Macchiagodena, M. and Weber, H. and Thomas, M. and Brehm, Martin and Stark, A. and Russina, O. and Triolo, A. and Kirchner, B.}}, journal = {{ChemPhysChem}}, pages = {{3325--3333}}, title = {{{Triphilic Ionic-Liquid Mixtures: Fluorinated and Non-Fluorinated Aprotic Ionic-Liquid Mixtures}}}, doi = {{10.1002/cphc.201500473}}, volume = {{16 (15)}}, year = {{2015}}, } @article{44978, author = {{Brehm, Martin and Weber, H. and Thomas, M. and Hollóczki, O. and Kirchner, B.}}, journal = {{ChemPhysChem}}, pages = {{3271--3277}}, title = {{{Domain Analysis in Nanostructured Liquids: A Post-Molecular Dynamics Study at the Example of Ionic Liquids}}}, doi = {{10.1002/cphc.201500471}}, volume = {{16 (15)}}, year = {{2015}}, } @article{44979, author = {{Thomas, M. and Brehm, Martin and Kirchner, B.}}, journal = {{Phys. Chem. Chem. Phys.}}, pages = {{3207--3213}}, title = {{{Voronoi Dipole Moments for the Simulation of Bulk Phase Vibrational Spectra}}}, doi = {{10.1039/C4CP05272B}}, volume = {{17}}, year = {{2015}}, }