TRR 146 – Publications 2018

Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment
Hima Bindu Kolli, Antonio de Nicola, Sigbjørn Løland Bore, Ken Schäfer, Gregor Diezemann, Jürgen Gauss, Toshihiro Kawakatsu, Zhong-Yuan Lu, You-Liang Zhu, Giuseppe Milano, Michele Cascella
Journal of Chemical Theory and Computation 14 (9), 4928-4937 (2018);
doi:10.1021/acs.jctc.8b00466

↓ Show Abstract↑ Hide Abstract We develop and test specific coarse-grained models for charged amphiphilic systems such as palmitoyloleoylphosphatidylglycer- ol (POPG) lipid bilayer and sodium dodecyl sulfate (SDS) surfactant in an aqueous environment, to verify the ability of the hybrid particle-field method to provide a realistic description of polyelectrolytes. According to the hybrid approach, the intramolecular interactions are treated by a standard molecular Hamiltonian, and the nonelectrostatic intermolec- ular forces are described by density fields. Electrostatics is introduced as an additional external field obtained by a modified particle-mesh Ewald procedure, as recently proposed [Zhu et al. Phys. Chem. Chem. Phys. 2016, 18, 9799]. Our results show that, upon proper calibration of key parameters, electrostatic forces can be correctly reproduced. Molecular dynamics simulations indicate that the methodology is robust with respect to the choice of the relative dielectric constant, yielding the same correct qualitative behavior for a broad range of values. In particular, our methodology reproduces well the organization of the POPG bilayer, as well as the SDS concentration-dependent change in the morphology of the micelles from spherical to microtubular aggregates. The inclusion of explicit electrostatics with good accuracy and low computational cost paves the way for a significant extension of the hybrid particle-field method to biological systems, where the polyelectrolyte component plays a fundamental role for both structural and dynamical molecular properties.

Fluctuations, Finite-Size Effects and the Thermodynamic Limit in Computer Simulations: Revisiting the Spatial Block Analysis Method
Maziar Heidari, Kurt Kremer, Raffaello Potestio, Robinson Cortes-Huerto
Entropy 20 (4), 222 (2018);
doi:10.3390/e20040222

Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations
Maziar Heidari, Robinson Cortes-Huerto, Kurt Kremer, Raffaello Potestio
The European Physical Journal E 41 (5), (2018);
doi:10.1140/epje/i2018-11675-x

Spatially Resolved Thermodynamic Integration: An Efficient Method To Compute Chemical Potentials of Dense Fluids
Maziar Heidari, Kurt Kremer, Robinson Cortes-Huerto, Raffaello Potestio
Journal of Chemical Theory and Computation 14 (7), 3409-3417 (2018);
doi:10.1021/acs.jctc.8b00002

Finite-size integral equations in the theory of liquids and the thermodynamic limit in computer simulations
M. Heidari, K. Kremer, R. Potestio, R. Cortes-Huerto
Molecular Physics 116 (21-22), 3301-3310 (2018);
doi:10.1080/00268976.2018.1482429

Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding
Fabian Knoch, Ken Schäfer, Gregor Diezemann, Thomas Speck
The Journal of Chemical Physics 148 (4), 044109 (2018);
doi:10.1063/1.5010435

Bottom-up approach to represent dynamic properties in coarse-grained molecular simulations
Gregor Deichmann and Nico F. A. van der Vegt
J. Chem. Phys. 149, 244114 (2018);
doi:10.1063/1.5064369

Intrinsic conformational preferences and interactions in alpha-synuclein fibrils: Insights from molecular dynamics simulations
Ioana M. Ilie, Divya Nayar, Wouter K. den Otter, Nico F. A. van der Vegt, Wim J. Briels
J. Chem. Theory Comp. 14, 3298-3310 (2018);
doi:10.1021/acs.jctc.8b00183

Cosolute effects on polymer hydration drive hydrophobic collapse
Divya Nayar and Nico F. A. van der Vegt
J. Phys. Chem. B 122, 3587-3595 (2018);
doi:10.1021/acs.jpcb.7b10780

Addressing the temperature transferability of structure based coarse graining models
David Rosenberger and Nico F. A. van der Vegt
Phys.Chem.Chem.Phys 20, 6617-6628 (2018);
doi:10.1039/c7cp08246k

Curvature as a Guiding Field for Patterns in Thin Block Copolymer Films
Giang Thi Vu, Anabella A. Abate, Leopoldo R. Gómez, Aldo D. Pezzutti, Richard A. Register, Daniel A. Vega, Friederike Schmid
Physical Review Letters 121 (8), (2018);
doi:10.1103/physrevlett.121.087801

↓ Show Abstract↑ Hide Abstract Experimental data on thin films of cylinder-forming block copolymers (BC)—free-standing BC membranes as well as supported BC films—strongly suggest that the local orientation of the BC patterns is coupled to the geometry in which the patterns are embedded. We analyze this phenomenon using general symmetry considerations and numerical self-consistent field studies of curved BC films in cylindrical geometry. The stability of the films against curvature-induced dewetting is also analyzed. In good agreement with experiments, we find that the BC cylinders tend to align along the direction of curvature at high curvatures. At low curvatures, we identify a transition from perpendicular to parallel alignment in supported films, which is absent in free-standing membranes. Hence both experiments and theory show that curvature can be used to manipulate and align BC patterns.

Generalized Langevin dynamics: construction and numerical integration of non-Markovian particle-based models
Gerhard Jung, Martin Hanke, Friederike Schmid
Soft Matter 14 (46), 9368-9382 (2018);
doi:10.1039/c8sm01817k

Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics
Tristan Bereau, Joseph F. Rudzinski
Physical Review Letters 121 (25), (2018);
doi:10.1103/physrevlett.121.256002

Phase transitions in single macromolecules: Loop-stretch transition versus loop adsorption transition in end-grafted polymer chains
Shuangshuang Zhang, Shuanhu Qi, Leonid I. Klushin, Alexander M. Skvortsov, Dadong Yan, Friederike Schmid
The Journal of Chemical Physics 148 (4), 044903 (2018);
doi:10.1063/1.5013346

Existence of global weak solutions to the kinetic Peterlin model
P. Gwiazda, M. Lukacova-Medvid'ova, H. Mizerova, A. Szwierczewska-Gwiazda
Nonlinear Analysis: Real World App. 44, 465-478 (2018);
URL: https://www.sciencedirect.com/science/article/pii/S1468121818305480?via%3Dihub
doi:https://doi.org/10.1016/j.nonrwa.2018.05.016

↓ Show Abstract↑ Hide Abstract We consider a class of kinetic models for polymeric fluids motivated by the Peterlin dumbbell theories for dilute polymer solutions with a nonlinear spring law for an infinitely extensible spring. The polymer molecules are suspended in an incompressible viscous Newtonian fluid confined to a bounded domain in two or three space dimensions. The unsteady motion of the solvent is described by the incompressible Navier–Stokes equations with the elastic extra stress tensor appearing as a forcing term in the momentum equation. The elastic stress tensor is defined by Kramer’s expression through the probability density function that satisfies the corresponding Fokker–Planck equation. In this case a coefficient depending on the average length of polymer molecules appears in the latter equation. Following the recent work of Barrett and Süli (2018) we prove the existence of global-in-time weak solutions to the kinetic Peterlin model in two space dimensions.

Understanding three-body contributions to coarse-grained force fields
Christoph Scherer, Denis Andrienko
Physical Chemistry Chemical Physics 20 (34), 22387-22394 (2018);
URL: http://dx.doi.org/10.1039/C8CP00746B
doi:10.1039/c8cp00746b

Tuning Transition Properties of Stimuli-Responsive Brushes by Polydispersity
Shuanhu Qi, Leonid I. Klushin, Alexander M. Skvortsov, Mingjie Liu, Jiajia Zhou, Friederike Schmid
Advanced Functional Materials, 1800745 (2018);
doi:10.1002/adfm.201800745

Molecular Structure and Multi-Body Potential of Mean Force in Silica-Polystyrene Nanocomposites
Gianmarco Munao', Antonio Pizzirusso, Andreas Kalogirou, Antonio De Nicola, Toshihiro Kawakatsu, Florian Mueller-Plathe, Giuseppe Milano
Nanoscale, (2018);
doi:10.1039/c8nr05135f

Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment
Hima Bindu Kolli, Antonio de Nicola, Sigbjørn Løland Bore, Ken Schäfer, Gregor Diezemann, Jürgen Gauss, Toshihiro Kawakatsu, Zhong-Yuan Lu, You-Liang Zhu, Giuseppe Milano, Michele Cascella
Journal of Chemical Theory and Computation 14 (9), 4928-4937 (2018);
doi:10.1021/acs.jctc.8b00466

A fundamental catalytic difference between zinc and manganese dependent enzymes revealed in a bacterial isatin hydrolase
Theis Sommer, Kaare Bjerregaard-Andersen, Lalita Uribe, Michael Etzerodt, Gregor Diezemann, Jürgen Gauss, Michele Cascella, J. Preben Morth
Scientific Reports 8 (1), (2018);
doi:10.1038/s41598-018-31259-y

Structural Origin of Metal Specificity in Isatin Hydrolase from Labrenzia aggregata Investigated by Computer Simulations
Lalita Uribe, Gregor Diezemann, Jürgen Gauss, Jens Preben Morth, Michele Cascella
Chemistry - A European Journal 24 (20), 5074-5077 (2018);
doi:10.1002/chem.201705159

Intramolecular structural parameters are key modulators of the gel-liquid transition in coarse grained simulations of DPPC and DOPC lipid bilayers
Stefan Jaschonek, Michele Cascella, Jürgen Gauss, Gregor Diezemann, Giuseppe Milano
Biochemical and Biophysical Research Communications 498 (2), 327-333 (2018);
doi:10.1016/j.bbrc.2017.10.132

Convergence of a mixed finite element finite volume scheme for the isentropic Navier-Stokes system via dissipative measure-valued solutions
E. Feireisl, M. Lukacova-Medvidova
Found. Comput. Math. 18 , 703–730 (2018);
doi: DOI: 10.1007/s10208-017-9351-2

↓ Show Abstract↑ Hide Abstract We study convergence of a mixed finite element-finite volume numerical scheme for the isentropic Navier-Stokes system under the full range of the adiabatic exponent. We establish suitable stability and consistency estimates and show that the Young measure generated by numerical solutions represents a dissipative measure-valued solutions of the limit system. In particular, using the recently established weak{strong uniqueness principle in the class of dissipative measure-valued solutions we show that the numerical solutions converge strongly to a strong solutions of the limit system as long as the latter exists.

Asymptotic preserving error estimates for numerical solutions of compressible Navier-Stokes equations in the low Mach number regime
E. Feireisl, M. Lukacova-Medvidova, S. Necasova, A. Novotny, B. She
SIAM Multiscale Model. Simul. 16 (1), 150–183 (2018);
URL: https://epubs.siam.org/doi/10.1137/16M1094233

↓ Show Abstract↑ Hide Abstract We study the convergence of numerical solutions of the compressible Navier-Stokes system to its incompressible limit. The numerical solution is obtained by a combined finite element-finite volume method based on the linear Crouzeix-Raviart finite element for the velocity and piecewise constant approximation for the density. The convective terms are approximated using upwinding. The distance between a numerical solution of the compressible problem and the strong solution of the incompressible Navier-Stokes equations is measured by means of a relative energy functional. For barotropic pressure exponent larger than 3/2 and for well-prepared initial data we obtain uniform convergence of order. Extensive numerical simulations confirm that the numerical solution of the compressible problem converges to the solution of the incompressible Navier-Stokes equations as the discretization parameters and the Mach number tend to zero.

Unfolding dynamics of small peptides biased by constant mechanical forces
Fabian Knoch, Thomas Speck
Molecular Systems Design & Engineering, (2018);
doi:10.1039/c7me00080d

Publications 2018

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