2016 - Publications
Deduplication Potential of HPC Applications' Checkpoints
Jürgen Kaiser, Ramy Gad, Tim Süß, Federico Padua, Lars Nagel and André Brinkmann
IEEE International Conference on Cluster Computing (Cluster'16), Pages413--422,IEEE Press (2016)
Link: https://doi.org/10.1109/CLUSTER.2016.32
Oscillatory Interaction Between Two Like-Charged Nanoparticles Induced by Polyelectrolyte Brush-Solvent Interface
Zengju Lian, Shuanhu Qi
J. Pol. Sci. B 54, 1458-1468 (2016)
Link: https://doi.org/10.1002/polb.24036
Adsorption of polyiodobenzene molecules on the Pt(111) surface using van der Waals density functional theory
Karen Johnston, Rengin Pekoz, Davide Donadio
Surface Science 644, 113-121 (2016)
Link: https://doi.org/10.1016/j.susc.2015.09.017
Gold nanorods as plasmonic sensors for particle diffusion
Verena Wulf, Fabian Knoch, Thomas Speck, Carsten Sönnichsen
The Journal of Physical Chemistry Lett. 7, 4951-4955 (2016)
Link: https://doi.org/10.1021/acs.jpclett.6b02165
Special Issue on Structure in Glassy and Jammed Systems
Patrick C. Royall and Thomas Speck
J. Stat. Mech. 054045 (2016)
Link: https://doi.org/10.1088/1742-5468/2016/05/054045
Study of Hydrophobic Clustering in Partially Sulfonated Polystyrene Solutions with a Systematic Coarse-Grained Model
Ran Zhang, Nico F. A. van der Vegt
Macromolecules 49 (19), 7571-7580 (2016)
Link: https://doi.org/10.1021/acs.macromol.6b01132
Computing bulk and shear viscosities from simulations of fluids with dissipative and stochastic interactions
Gerhard Jung, Friederike Schmid
The Journal of Chemical Physics 144 (20), 204104 (2016)
Link: https://doi.org/10.1063/1.4950760
Droplets pinned at chemically inhomogenous substrates: A simulation study of the two-dimensional Ising cas
M.L. Trobi, E.Z. Albano, K. Binder
Physical Review E 93, 052805 (2016)
Link: https://doi.org/10.1103/PhysRevE.93.052805
A new force field including charge directionality for TMAO in aqueous solution
Kota Usui, Yuki Nagata, Johannes Hunger, Mischa Bonn and Marialore Sulpizi
The Journal of Chemical Physics 145, 064103 (2016)
Link: https://doi.org/10.1063/1.4960207
Molecular Dynamics Simulations of SFG Librational Modes Spectra of Water at the Water–Air Interface
Rémi Khatib, Taisuke Hasegawa, Marialore Sulpizi, Ellen H. G. Backus, Mischa Bonn, and Yuki Nagata
The Journal of Physical Chemistry C120 (33), 18665–18673 (2016)
Link: https://doi.org/10.1021/acs.jpcc.6b06371
Revisiting the droplet simulation approach to derive force-field parameters for water on molybdenum disulfide from wetting angle measurements
Frédéric Leroy
The Journal of Chemical Physics 145 (16), 164705 (2016)
Link: http://doi.org/10.1063/1.4966215
Research update: Computational materials discovery in soft matter
T. Bereau, D. Andrienko, K. Kremer
APL Materials 4, 053101 (2016)
Link: https://doi.org/10.1063/1.4943287
Concurrent parametrization against static and kinetic information leads to more robust coarse-grained force fields
J.F. Rudzinski, T. Bereau
The European Physical Journal Special Topics 225 (8-9), 1373-1389 (2016)
Link: https://doi.org/10.1140/epjst/e2016-60114-5
Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information
Joseph F. Rudzinski, Kurt Kremer, Tristan Bereau
The Journal of Chemical Physics 144 (5), 051102 (2016)
Link: https://doi.org/10.1063/1.4941455
Polydisperse hard spheres: crystallization kinetics in small systems and role of local structure
Matteo Campo, Thomas Speck
Journal of Statistical Mechanics: Theory and Experiment 2016 (8), 084007 (2016)
Link: https://doi.org/10.1088/1742-5468/2016/8/084007
Nucleation pathway and kinetics of phase-separating active Brownian particles
David Richard, Hartmut Löwen, Thomas Speck
Soft Matter 12 (24), 5257-5264 (2016)
Link: https://doi.org/10.1039/c6sm00485g
Comparison of Different TMAO Force Fields and Their Impact on the Folding Equilibrium of a Hydrophobic Polymer
Francisco Rodríguez-Ropero, Philipp Rötzscher, Nico F. A. van der Vegt
The Journal of Physical Chemistry B120 (34), 8757-8767 (2016)
Link: https://doi.org/10.1021/acs.jpcb.6b04100
Comparison of iterative inverse coarse-graining methods
David Rosenberger, Martin Hanke, Nico F.A. van der Vegt
The European Physical Journal Special Topics 225 (8-9), 1323-1345 (2016)
Link: https://doi.org/10.1140/epjst/e2016-60120-1
Comparison of systematic coarse-graining strategies for soluble conjugated polymers
Christoph Scherer and Denis Andrienko
The European Physical Journal Special Topics 225, 1441-1461, (2016)
Link: https://doi.org/10.1140/epjst/e2016-60154-9
Determining Factors for the Unfolding Pathway of Peptides, Peptoids, and Peptidic Foldamers
Lalita Uribe, Jürgen Gauss, Gregor Diezemann
The Journal of Physical Chemistry B120 (40),10433-10441 (2016);
Link: https://doi.org/10.1021/acs.jpcb.6b06784
From Classical to Quantum and Back: A Hamiltonian Scheme for Adaptive Multiresolution Classical/Path-Integral Simulations
Karsten Kreis, Mark E. Tuckerman, Davide Donadio, Kurt Kremer, Raffaello Potestio
Journal of Chemical Theory and Computationut. 12 (7), 3030-3039 (2016)
Link: https://doi.org/10.1021/acs.jctc.6b00242
Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations
M. Heidari, R. Cortes-Huerto, D. Donadio, R. Potestio
The European Physical Journal Special Topics 225 (8-9), 1505-1526 (2016)
Link: https://doi.org/10.1140/epjst/e2016-60151-6
Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials
Jelle M. Boereboom, Raffaello Potestio, Davide Donadio, Rosa E. Bulo
Journal of Chemical Theory and Computationut. 12 (8), 3441-3448 (2016)
Link: https://doi.org/10.1021/acs.jctc.6b00205
Polydisperse Polymer Brushes: Internal structure, critical behavior, and interaction with flow
Shuanhu Qi, Leonid I. Klushin, Alexander M. Skvortsov, Friederike Schmid
Macromolecules 49, 9665-9683 (2016)
Link: https://doi.org/10.1021/acs.macromol.6b02026
Numerical reduction of self-consistent field models of macromolecular systems
A. Disterhoft, T. Raasch, F. Schmid
Proceedings in Applied Mathematics and Mechanics 16, 915-916 (2016)
Link: https://doi.org/10.1002/pamm.201610446
A hybrid particle-continuum resolution method and its application to a homopolymer solution
S. Qi, H. Behringer, T. Raasch, F. Schmid
The European Physical Journal Special Topics 225 (8-9), 1527-1549 (2016)
Link: https://doi.org/10.1140/epjst/e2016-60096-8
The Cassie-Wenzel transition of fluids on nanostructured substrates: Macroscopic force balance versus microscopic density-functional theory
Nikita Tretyakov, Periklis Papadopoulos, Doris Vollmer, Hans-Jürgen Butt, Burkhard Dünweg, Kostas Ch. Daoulas
The Journal of Chemical Physics 145 (13), 134703 (2016)
Link: https://doi.org/10.1063/1.4963792
Energy dissipative characteristic schemes for the diffusive Oldroyd-B viscoelastic fluid
Mária Lukáčová-Medvid'ová, Hirofumi Notsu, Bangwei She
International Journal for Numerical Methods in Fluids, 523-557 (2016)
Link: https://doi.org/10.1002/fld.4195