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Publikationen 2016

Gold Nanorods as Plasmonic Sensors for Particle Diffusion
Verena Wulf, Fabian Knoch, Thomas Speck, Carsten Sönnichsen
The Journal of Physical Chemistry Letters, 4951-4955 (2016);
doi:10.1021/acs.jpclett.6b02165

Polydisperse hard spheres: crystallization kinetics in small systems and role of local structure
Matteo Campo, Thomas Speck
J. Stat. Mech. 2016 (8), 084007 (2016);
doi: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);
doi:10.1039/c6sm00485g

Numerical reduction of self-consistent field models of macromolecular systems
A. Disterhoft, T. Raasch, F. Schmid
Proc. Appl. Math. Mech. 16, 915-916 (2016);
doi:10.1002/pamm.201610446

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
J. Chem. Theory Comput. 12 (7), 3030-3039 (2016);
doi: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);
doi: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
J. Chem. Theory Comput. 12 (8), 3441-3448 (2016);
doi:10.1021/acs.jctc.6b00205

Determining Factors for the Unfolding Pathway of Peptides, Peptoids, and Peptidic Foldamers
Lalita Uribe, Jürgen Gauss, Gregor Diezemann
The Journal of Physical Chemistry B 120 (40), 10433-10441 (2016);
doi:10.1021/acs.jpcb.6b06784

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);
URL: http://scitation.aip.org/content/aip/journal/jcp/145/16/10.1063/1.4966215
doi:10.1063/1.4966215

Deduplication Potential of HPC Applications' Checkpoints
Jürgen Kaiser, Ramy Gad, Tim Süß, Federico Padua, Lars Nagel and André Brinkmann
in IEEE Int. Conf. on Cluster Computing (Cluster'16), Seiten 413--422, IEEE Press (2016);

A new force field including charge directionality for TMAO in aqueous solution
Kota Usui, Yuki Nagata, Johannes Hunger, Mischa Bonn and Marialore Sulpizi
J. Chem. Phys. 145, 064103 (2016);
doi:10.1063/1.4960207

We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (OTMAO) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around OTMAO to mimic the OTMAO lone pairs and we migrate the negative charge on the OTMAO to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasing TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions.

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
J. Phys. Chem. C 120 (33), 18665–18673 (2016);
doi:10.1021/acs.jpcc.6b06371

At the water–air interface, the hydrogen-bond network of water molecules is interrupted, and accordingly, the structure and dynamics of the interfacial water molecules are altered considerably compared with the bulk. Such interfacial water molecules have been studied by surface-specific vibrational sum-frequency generation (SFG) spectroscopy probing high-frequency O–H stretch and H–O–H bending modes. In contrast, the low-frequency librational mode has been much less studied with SFG. Because this mode is sensitive to the hydrogen-bond connectivity, understanding the librational mode of the interfacial water is crucial for unveiling a microscopic view of the interfacial water. Here, we compute the SFG librational mode spectra at the water–air interface by using molecular dynamics simulation. We show that the modeling of the polarizability has a drastic effect on the simulated librational mode spectra, whereas the spectra are less sensitive to the force field models and the modeling of the dipole moment. The simulated librational spectra display a peak centered at ∼700 cm–1, which is close to the infrared peak frequency of the liquid water librational mode of 670 cm–1. This indicates that the librational mode of the interfacial water at the water–air interface closely resembles that of bulk liquid water.

Energy dissipative characteristic schemes for the diffusive Oldroyd-B viscoelastic fluid
Maria Lukacova-Medvidova, Hirofumi Notsu, Bangwei She
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS 81, 523-557 (2016);
URL: wileyonlinelibrary.com
doi:10.1002/fld.4195

In this paper, we propose new energy dissipative characteristic numerical methods for the approximation of diffusive Oldroyd-B equations that are based either on the finite element or finite difference discretization. We prove energy stability of both schemes and illustrate their behavior on a series of numerical experiments. Using both the diffusive model and the logarithmic transformation of the elastic stress, we are able to obtain methods that converge as mesh parameter is refined.

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 B 120 (34), 8757-8767 (2016);
doi:10.1021/acs.jpcb.6b04100

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);
doi:10.1021/acs.macromol.6b01132

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);
doi:10.1140/epjst/e2016-60120-1

Computational materials discovery in soft matter
T. Bereau, D. Andrienko, K. Kremer
APL Mat 4, 053101 (2016);
doi:10.1063/1.4943287

Soft matter embodies a wide range of materials, which all share the common characteristics of weak interaction energies determining their supramolecular structure. This complicates structure-property predictions and hampers the direct application of data-driven approaches to their modeling. We present several aspects in which these methods play a role in designing soft-matter materials: drug design as well as information-driven computer simulations, e.g., histogram reweighting. We also discuss recent examples of rational design of soft-matter materials fostered by physical insight and assisted by data-driven approaches. We foresee the combination of data-driven and physical approaches a promising strategy to move the field forward.

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);
doi: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);
doi:10.1063/1.4941455

Comparison of systematic coarse-graining strategies for soluble conjugated polymers
Christoph Scherer and Denis Andrienko
Eur. Phys. J. Spec. Top. 225, 1441-1461, (2016);
doi:10.1140/epjst/e2016-60154-9

We assess several systematic coarse-graining approaches by coarse-graining poly(3-hexylthiophene-2,5-diyl) (P3HT), a polymer showing π-stacking of the thiophene rings and lamellar ordering of the π-stacked structures. All coarse-grained force fields are ranked according to their ability of preserving the experimentally known crystalline molecular arrangement of P3HT. The coarse-grained force fields parametrized in the amorphous melt turned out to accurately reproduce the structural quantities of the melt, as well as to preserve the lamellar ordering of the P3HT oligomers in π-stacks. However, the exact crystal structure is not reproduced. The combination of Boltzmann inversion for bonded and iterative Boltzmann inversion with pressure correction for nonbonded degrees of freedom gives the best coarse-grained model.

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);
doi:10.1063/1.4950760

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);
doi:10.1140/epjst/e2016-60096-8

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