TRR 146 – Publications 2015

Flows and mixing in channels with misaligned superhydrophobic walls
Tatiana V. Nizkaya, Evgeny S. Asmolov, Jiajia Zhou, Friederike Schmid, Olga I. Vinogradova
Physical Review E 91 (3), (2015);
doi:10.1103/physreve.91.033020

A molecular dynamics simulations study on the relations between dynamical heterogeneity, structural relaxation, and self-diffusion in viscous liquids
Patrick Henritzi, André Bormuth, Felix Klameth, Michael Vogel
The Journal of Chemical Physics 143 (16), 164502 (2015);
doi:10.1063/1.4933208

Computer simulations of single particles in external electric fields
Jiajia Zhou, Friederike Schmid
Soft Matter 11 (34), 6728-6739 (2015);
doi:10.1039/c5sm01485a

Solvent Determines Nature of Effective Interactions between Nanoparticles in Polymer Brushes
Zengju Lian, Shuanhu Qi, Jiajia Zhou, Friederike Schmid
The Journal of Physical Chemistry B 119 (10), 4099-4108 (2015);
doi:10.1021/jp511911g

Flows and mixing in channels with misaligned superhydrophobic walls
Tatiana V. Nizkaya, Evgeny S. Asmolov, Jiajia Zhou, Friederike Schmid, Olga I. Vinogradova
Physical Review E 91 (3), (2015);
doi:10.1103/physreve.91.033020

A molecular dynamics simulations study on the relations between dynamical heterogeneity, structural relaxation, and self-diffusion in viscous liquids
Patrick Henritzi, André Bormuth, Felix Klameth, Michael Vogel
The Journal of Chemical Physics 143 (16), 164502 (2015);
doi:10.1063/1.4933208

The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption
Stephan Köhler, Friederike Schmid, Giovanni Settanni
PLOS Computational Biology 11 (9), e1004346 (2015);
doi:10.1371/journal.pcbi.1004346

The role of shear in crystallization kinetics: From suppression to enhancement
David Richard, Thomas Speck
Sci. Rep. 5, 14610 (2015);
doi:10.1038/srep14610

Reply to comments by R. Klein on Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations
K. Kreis, A. C. Fogarty, K. Kremer, R. Potestio
The European Physical Journal Special Topics 224 (12), 2505-2506 (2015);
doi:10.1140/epjst/e2015-02533-5

Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations
K. Kreis, A. C. Fogarty, K. Kremer, R. Potestio
The European Physical Journal Special Topics 224 (12), 2289-2304 (2015);
doi:10.1140/epjst/e2015-02412-1

Analysis and numerical solution of the Peterlin viscoelastic model (PhD Thesis)
Mizerova Hana
JGU (2015);
URL: http://ubm.opus.hbz-nrw.de/volltexte/2015/4231/

↓ Show Abstract↑ Hide Abstract Liquids and gasses form a vital part of nature. Many of these are complex fluids with non-Newtonian behaviour. We introduce a mathematical model describing the unsteady motion of an incompressible polymeric fluid. Each polymer molecule is treated as two beads connected by a spring. For the nonlinear spring force it is not possible to obtain a closed system of equations, unless we approximate the force law. The Peterlin approximation replaces the length of the spring by the length of the average spring. Consequently, the macroscopic dumbbell-based model for dilute polymer solutions is obtained. The model consists of the conservation of mass and momentum and time evolution of the symmetric positive definite conformation tensor, where the diffusive effects are taken into account. In two space dimensions we prove global in time existence of weak solutions. Assuming more regular data we show higher regularity and consequently uniqueness of the weak solution. For the Oseen-type Peterlin model we propose a linear pressure-stabilized characteristics finite element scheme. We derive the corresponding error estimates and we prove, for linear finite elements, the optimal first order accuracy. Theoretical error of the pressure-stabilized characteristic finite element scheme is confirmed by a series of numerical experiments.

Mechanical unfolding pathway of a model β-peptide foldamer
Lalita Uribe, Stefan Jaschonek, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics 142 (20), 204901 (2015);
doi:10.1063/1.4921371

Comparative Study of the Mechanical Unfolding Pathways of α- and β-Peptides
Lalita Uribe, Jürgen Gauss, Gregor Diezemann
The Journal of Physical Chemistry B 119 (26), 8313-8320 (2015);
doi:10.1021/acs.jpcb.5b04044

Analysis of the ECMWF Storage Landscape
Matthias Grawinkel, Lars Nagel, Markus Mäsker, Federico Padua, André Brinkmann, Lennart Sorth
in Proceedings of the 13th USENIX Conference on File and Storage Technologies {FAST} 2015, Santa Clara, CA, USA, Pages 15 - 27, Usenix (2015);

Molecular Mechanism of Water Evaporation
Yuki Nagata, Kota Usui, Mischa Bonn
Phys. Rev. Lett. 115 (23), 236102 (2015);
doi:10.1103/physrevlett.115.236102

The surface roughness, but not the water molecular orientation varies with temperature at the water–air interface
Yuki Nagata, Taisuke Hasegawa, Ellen H. G. Backus, Kota Usui, Seiji Yoshimune, Tatsuhiko Ohto, Mischa Bonn
Phys. Chem. Chem. Phys. 17 (36), 23559-23564 (2015);
doi:10.1039/c5cp04022a

Ultrafast Vibrational Dynamics of Water Disentangled by Reverse Nonequilibrium Ab Initio Molecular Dynamics Simulations
Yuki Nagata, Seiji Yoshimune, Cho-Shuen Hsieh, Johannes Hunger, Mischa Bonn
Physical Review X 5 (2), 021002 (2015);
doi:10.1103/physrevx.5.021002

Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function
Tatsuhiko Ohto, Kota Usui, Taisuke Hasegawa, Mischa Bonn, Yuki Nagata
The Journal of Chemical Physics 143 (12), 124702 (2015);
doi:10.1063/1.4931106

Ab Initio Liquid Water Dynamics in Aqueous TMAO Solution
Kota Usui, Johannes Hunger, Marialore Sulpizi, Tatsuhiko Ohto, Mischa Bonn, and Yuki Nagata
J. Phys. Chem. B 119 (33), 10597–10606 (2015);
doi: 10.1021/acs.jpcb.5b02579

↓ Show Abstract↑ Hide Abstract Ab initio molecular dynamics (AIMD) simulations in trimethylamine N-oxide (TMAO)–D2O solution are employed to elucidate the effects of TMAO on the reorientational dynamics of D2O molecules. By decomposing the O–D groups of the D2O molecules into specific subensembles, we reveal that water reorientational dynamics are retarded considerably in the vicinity of the hydrophilic TMAO oxygen (OTMAO) atom, due to the O–D···OTMAO hydrogen-bond. We find that this reorientational motion is governed by two distinct mechanisms: The O–D group rotates (1) after breaking the O–D···OTMAO hydrogen-bond, or (2) together with the TMAO molecule while keeping this hydrogen-bond intact. While the orientational slow-down is prominent in the AIMD simulation, simulations based on force field models exhibit much faster dynamics. The simulated angle-resolved radial distribution functions illustrate that the O–D···OTMAO hydrogen-bond has a strong directionality through the sp3 orbital configuration in the AIMD simulation, and this directionality is not properly accounted for in the force field simulation. These results imply that care must be taken when modeling negatively charged oxygen atoms as single point charges; force field models may not adequately describe the hydration configuration and dynamics.

Lipid Carbonyl Groups Terminate the Hydrogen Bond Network of Membrane-Bound Water
Tatsuhiko Ohto, Ellen H. G. Backus, Cho-Shuen Hsieh, Marialore Sulpizi, Mischa Bonn, and Yuki Nagata
J. Phys. Chem. Lett., 6 (22), 4499–4503 (2015);
doi:10.1021/acs.jpclett.5b02141

↓ Show Abstract↑ Hide Abstract We present a combined experimental sum-frequency generation (SFG) spectroscopy and ab initio molecular dynamics simulations study to clarify the structure and orientation of water at zwitterionic phosphatidylcholine (PC) lipid and amine N-oxide (AO) surfactant monolayers. Simulated O–H stretch SFG spectra of water show good agreement with the experimental data. The SFG response at the PC interface exhibits positive peaks, whereas both negative and positive bands are present for the similar zwitterionic AO interface. The positive peaks at the water/PC interface are attributed to water interacting with the lipid carbonyl groups, which act as efficient hydrogen bond acceptors. This allows the water hydrogen bond network to reach, with its (up-oriented) O–H groups, into the headgroup of the lipid, a mechanism not available for water underneath the AO surfactant. This highlights the role of the lipid carbonyl group in the interfacial water structure at the membrane interface, namely, stabilizing the water hydrogen bond network.

Mechanism of Polymer Collapse in Miscible Good Solvents
Francisco Rodríguez-Ropero, Timir Hajari, Nico F. A. van der Vegt
The Journal of Physical Chemistry B 119 (51), 15780-15788 (2015);
doi:10.1021/acs.jpcb.5b10684

Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method
Vikram Reddy Ardham, Gregor Deichmann, Nico F. A. van der Vegt, Frédéric Leroy
The Journal of Chemical Physics 143 (24), 243135 (2015);
doi:10.1063/1.4936253

Parametrizing Nonbonded Interactions from Wetting Experiments via the Work of Adhesion: Example of Water on Graphene Surfaces
Frédéric Leroy, Shengyuan Liu, Jianguo Zhang
J. Phys. Chem. C 119 (51), 28470-28481 (2015);
doi:10.1021/acs.jpcc.5b10267

Cycle representatives for the coarse-graining of systems driven into a non-equilibrium steady state
Fabian Knoch, Thomas Speck
New Journal of Physics 17 (11), 115004 (2015);
doi:10.1088/1367-2630/17/11/115004

Stimuli-Responsive Brushes with Active Minority Components: Monte Carlo Study and Analytical Theory
Shuanhu Qi, Leonid I. Klushin, Alexander M. Skvortsov, Alexey A. Polotsky, Friederike Schmid
Macromolecules 48 (11), 3775-3787 (2015);
doi:10.1021/acs.macromol.5b00563

Publications 2015

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