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Publications 2019

Non-equilibrium Markov state modeling of periodically driven biomolecules
Fabian Knoch, Thomas Speck
The Journal of Chemical Physics 150 (5), 054103 (2019);
doi:10.1063/1.5055818

Molecular dynamics simulations allow us to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained multiscale models. While systematic approaches to construct such models have become available, these typically rely on microscopic dynamics that obey detailed balance. In vivo, however, biomolecules are constantly driven away from equilibrium in order to perform specific functions and thus break detailed balance. Here we introduce a method to construct Markov state models for systems that are driven through periodically changing one (or several) external parameter. We illustrate the method for alanine dipeptide, a widely used benchmark molecule for computational methods, exposed to a time-dependent electric field.

Classical nucleation theory for the crystallization kinetics in sheared liquids
David Richard, Thomas Speck
Physical Review E 99 (6), 062801 (2019);
doi:10.1103/physreve.99.062801

While statistical mechanics provides a comprehensive framework for the understanding of equilibrium phase behavior, predicting the kinetics of phase transformations remains a challenge. Classical nucleation theory (CNT) provides a thermodynamic framework to relate the nucleation rate to thermodynamic quantities such as pressure difference and interfacial tension through the nucleation work necessary to spawn critical nuclei. However, it remains unclear whether such an approach can be extended to the crystallization of driven melts that are subjected to mechanical stresses and flows. Here, we demonstrate numerically for hard spheres that the impact of simple shear on the crystallization rate can be rationalized within the CNT framework by an additional elastic work proportional to the droplet volume. We extract the local stress and strain inside solid droplets, which yield size-dependent values for the shear modulus that are about half of the bulk value. Finally, we show that for a complete description one also has to take into account the change of interfacial work between the strained droplet and the sheared liquid. From scaling reasons, we expect this extra contribution to dominate the work formation of small nuclei but become negligible compared to the elastic work for droplets composed of a few hundreds of particles.

Thermal skyrmion diffusion used in a reshuffler device
Jakub Zázvorka, Florian Jakobs, Daniel Heinze, Niklas Keil, Sascha Kromin, Samridh Jaiswal, Kai Litzius, Gerhard Jakob, Peter Virnau, Daniele Pinna, Karin Everschor-Sitte, Levente Rózsa, Andreas Donges, Ulrich Nowak, Mathias Kläui
Nature Nanotechnology 14 (7), 658-661 (2019);
doi:10.1038/s41565-019-0436-8

Generic Model for Lamellar Self-Assembly in Conjugated Polymers: Linking Mesoscopic Morphology and Charge Transport in P3HT
Cristina Greco, Anton Melnyk, Kurt Kremer, Denis Andrienko, Kostas Ch. Daoulas
Macromolecules 52 (3), 968-981 (2019);
doi:10.1021/acs.macromol.8b01863

ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation
Horacio V. Guzman, Nikita Tretyakov, Hideki Kobayashi, Aoife C. Fogarty, Karsten Kreis, Jakub Krajniak, Christoph Junghans, Kurt Kremer, Torsten Stuehn
Computer Physics Communications 238, 66-76 (2019);
doi:10.1016/j.cpc.2018.12.017

Self-assembly mechanisms of triblock Janus particles
H. Eslami, N. Khanjari, F. Müller-Plathe
J. Chem. Theor. Comput. 15, 1345–1354 (2019);
doi:10.1021/acs.jctc.8b00713

We present a detailed model to study the nucleation of triblock Janus particles from solution. The Janus particles are modeled as cross-linked polystyrene spheres whose poles are patched with sticky alkyl groups and their middle band is covered with negative charges. To mimic the experimental conditions, solvent, counterions, and a substrate, on which the crystallization takes place, are included in the model. A many-body dissipative particle dynamics simulation technique is employed to include hydrodynamic and manybody interactions. Metadynamics simulations are performed to explore the pathways for nucleation of Kagome and hexagonal lattices. In agreement with experiment, we found that nucleation of the Kagome lattice from solution follows a two-step mechanism. The connection of colloidal particles through their patches initially generates a disordered liquid network. Subsequently, orientational rearrangements in the liquid precursors lead to the formation of ordered nuclei Biasing the potential energy of the largest crystal, a critical nucleus appears in the simulation box, whose further growth crystallizes the whole solution. The location of the phase transition point and its shift with patch width are in very good agreement with experiment. The structure of the crystallized phase depends on the patch width; in the limit of very narrow patches strings are stable aggregates, intermediate patches stabilize the Kagome lattice, and wide patches nucleate the hexagonal phase. The scaling behavior of the calculated barrier heights confirms a first-order liquid-Kagome phase transition.

Gaussian charge distributions for incorporation of electrostatic interactions in dissipative particle dynamics: Application to self-assembly of surfactants
H. Eslami, M. Khani, F. Müller-Plathe
J. Chem. Theor. Comput. 15, 4197−4207 (2019);
doi:10.1021/acs.jctc.9b0017

The point charges are distributed over the soft dissipative particle dynamics (DPD) beads using a Gaussian of tunable width. Screening the Gaussian smeared charge distributions, with wider Gaussians of opposite charge, splits the electrostatic interaction into the real- and the reciprocal-space contributions. This method is validated against model test systems in the literature. The method has also been employed to study self-assembly in solutions of sodium dodecyl sulfate (SDS) in water. The critical micelle concentration (CMC) and the equilibrium concentration of free surfactants, in solutions with SDS concentrations varying from CMC to ≈20 times larger than CMC, are in close agreement with experiment. The microscopic structure of the micelles and the distributions of its hydrophobic/hydrophilic groups and counterions at the water interface are in agreement with experiment. The dynamics of monomer exchange between micelles and solution is examined in terms of the intermittent and continuous correlation functions for the fluctuation of micelle size with time. Two discrete relaxation processes, whose relaxation times differ by 2 orders of magnitude are found. Using the natural DPD time unit, defined in terms of thermal velocity, the relaxation times are an order of magnitude shorter than experimental relaxation times for monomer exchange and establishment of equilibrium between surfactants in the solution and micelles through diffusion of surfactants. However, experimentally comparable relaxation times are obtained by defining the DPD time scale such that the calculated diffusion coefficient of water corresponds to its experimental value.

Controlling stability and transport of magnetic microswimmers by an external field
Fabian R. Koessel, Sara Jabbari-Farouji
EPL (Europhysics Letters) 125 (2), 28001 (2019);
doi:10.1209/0295-5075/125/28001

Heterogeneous Interactions between Gas-Phase Pyruvic Acid and Hydroxylated Silica Surfaces: A Combined Experimental and Theoretical Study
Yuan Fang, Dominika Lesnicki, Kristin J. Wall, Marie-Pierre Gaigeot, Marialore Sulpizi, Veronica Vaida, Vicki H. Grassian
The Journal of Physical Chemistry A 123 (5), 983-991 (2019);
doi:10.1021/acs.jpca.8b10224

Understanding the Acidic Properties of the Amorphous Hydroxylated Silica Surface
Maciej Gierada, Frank De Proft, Marialore Sulpizi, Frederik Tielens
The Journal of Physical Chemistry C 123 (28), 17343-17352 (2019);
doi:10.1021/acs.jpcc.9b04137

A hybrid mass transport finite element method for Keller–Segel type systems
J.A. Carrillo, N. Kolbe, M. Lukacova-Medvidova
J. Sci. Comp 80, 1777-1804 (2019);
doi:10.1007/s10915-019-00997-0

We propose a new splitting scheme for general reaction–taxis–diffusion systems in one spatial dimension capable to deal with simultaneous concentrated and diffusive regions as well as travelling waves and merging phenomena. The splitting scheme is based on a mass transport strategy for the cell density coupled with classical finite element approximations for the rest of the system. The built-in mass adaption of the scheme allows for an excellent performance even with respect to dedicated mesh-adapted AMR schemes in original variables.

Convergence of a finite volume scheme for the compressible Navier-Stokes system
E.Feireisl, M. Lukacova-Medvidova, H. Mizerova
ESAIM: Math. Model. Num. 53, 1957–1979 (2019);
doi: https://doi.org/10.1051/m2an/2019043

We study convergence of a finite volume scheme for the compressible (barotropic) Navier–Stokes system. First we prove the energy stability and consistency of the scheme and show that the numerical solutions generate a dissipative measure-valued solution of the system. Then by the dissipative measure-valued-strong uniqueness principle, we conclude the convergence of the numerical solution to the strong solution as long as the latter exists. Numerical experiments for standard benchmark tests support our theoretical results.

Shear Modulus of an Irreversible Diblock Copolymer Network from Self-Consistent Field Theory
Shuanhu Qi, Jiajia Zhou, Friederike Schmid
Macromolecules 52 (24), 9569-9577 (2019);
doi:10.1021/acs.macromol.9b01985

Using self-consistentfield theory, we investigate thestretching-induced microphase separation in an irreversibly cross-linkedpolymer network composed of diblock copolymer chains and estimate itsshear modulus. The topology of the network isfixed to a planar square lattice.The monomer density, the distribution of cross-links, and the free energy ofthe system are calculated. Wefind that the system develops circular domainsat equilibrium, which may merge to lamellae upon compression or stretching.The lamellae are oriented perpendicular to the stretching direction. Cross-links are localized, but their distribution may be anisotropic. For asymmetricstrands, the distributions of different type of cross-links differ from eachother, indicating that the cross-linkfluctuations are inhomogeneous. Thestress is evaluated from the derivative of the free energy of stretched systemswith respect to the deformation in the stretching direction. Using theelasticity theory of isotropic solids allows us to estimate the shear modulus.Wefind that the shear modulus increases if the networkfluctuations are inhomogeneous. Ourfindings may provide guidance forthe design of stiffer soft matter materials.

Order–Order Phase Transitions Induced by Supercritical Carbon Dioxide in Triblock Copolymer Thin Films
Anabella A. Abate, Giang Thi Vu, Cristian M. Piqueras, María Cecilia del Barrio, Leopoldo R. Gómez, Gabriel Catalini, Friederike Schmid, Daniel A. Vega
Macromolecules 52 (20), 7786-7797 (2019);
doi:10.1021/acs.macromol.9b01278

We study the influence of supercritical carbon dioxide(scCO2) on the phase behavior of a cylinder-forming polystyrene-block-polybutadiene-b-polystyrene triblock copolymer thinfilm. Solventannealing with scCO2can produce patterns with long-range order butthese structures become unstable for thinfilms with small thicknesses.These results are in good agreement with self-consistent meanfieldcalculations, which indicate that a drying transition occurs forthicknesses below the radius of gyration of the molecule. Afterdecompression and solvent extraction, the initially swollen polymernanostructure suffers a strong reduction in the average domain spacing, which has a deleterious effect on the degree of order inthe resulting pattern. Both, experiments and Cahn−Hilliard simulations suggest that during decompression the pattern suffersan order−order instability where the collapse of the lattice constant leads to uncommon patterns with long-range orientationalorder but structural distortions at small-length scales.

Surface of Half-Neutralized Diamine Triflate Ionic Liquids. A Molecular Dynamics Study of Structure, Thermodynamics, and Kinetics of Water Absorption and Evaporation
N. C. Forero-Martinez, R. Cortes-Huerto, J. F. Mora Cardozo, P. Ballone
The Journal of Physical Chemistry B 123 (40), 8457-8471 (2019);
doi:10.1021/acs.jpcb.9b06619

Steering a solute between coexisting solvation states: Revisiting nonequilibrium work relations and the calculation of free energy differences
Maziar Heidari, Robinson Cortes-Huerto, Raffaello Potestio, Kurt Kremer
The Journal of Chemical Physics 151 (14), 144105 (2019);
doi:10.1063/1.5117780

On the relevance of electrostatic interactions for the structural relaxation of ionic liquids: A molecular dynamics simulation study
Tamisra Pal, Michael Vogel
The Journal of Chemical Physics 150 (12), 124501 (2019);
doi:10.1063/1.5085508

A note on the uniqueness result for the inverse Henderson problem
F. Frommer, M. Hanke, S. Jansen
Journal of Mathematical Physics 60 (9), 093303 (2019);
Highlighted on Scilight, see https://aip.scitation.org/doi/10.1063/1.5134789
doi:10.1063/1.5112137

The inverse Henderson problem of statistical mechanics is the theoretical foundation for many bottom-up coarse-graining techniques for the numerical simulation of complex soft matter physics. This inverse problem concerns classical particles in continuous space which interact according to a pair potential depending on the distance of the particles. Roughly stated, it asks for the interaction potential given the equilibrium pair correlation function of the system. In 1974 Henderson proved that this potential is uniquely determined in a canonical ensemble and he claimed the same result for the thermodynamical limit of the physical system. Here we provide a rigorous proof of a slightly more general version of the latter statement using Georgii's variant of the Gibbs variational principle.

Mechanical and Structural Tuning of Reversible Hydrogen Bonding in Interlocked Calixarene Nanocapsules
Stefan Jaschonek, Ken Schäfer, Gregor Diezemann
The Journal of Physical Chemistry B 123 (22), 4688-4694 (2019);
doi:10.1021/acs.jpcb.9b02676

Temperature dependent mechanical unfolding of calixarene nanocapsules studied by molecular dynamics simulations
Takashi Kato, Ken Schäfer, Stefan Jaschonek, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics 151 (4), 045102 (2019);
doi:10.1063/1.5111717

Relative entropy indicates an ideal concentration for structure-based coarse graining of binary mixtures
David Rosenberger and Nico F. A. van der Vegt
Phys. Rev. E 99, 053308 (2019);
doi:10.1103/PhysRevE.99.053308

Transferability of Local Density-Assisted Implicit Solvation Models for Homogeneous Fluid Mixtures
David Rosenberger, Tanmoy Sanyal, M. Scott Shell, and Nico F. A. van der Vegt
J. Chem. Theory Comp 15, 2881-2895 (2019);
doi:10.1021/acs.jctc.8b01170

Conditional reversible work coarse-grained models with explicit electrostatics - An application to butylmethylimidazolium ionic liquids
Gregor Deichmann and Nico F. A. van der Vegt
J. Chem. Theory Comp. 15, 1187-1198 (2019);
doi:10.1021/acs.jctc.8b00881

Phase equilibria modeling with systematically coarse-grained models - A comparative study on state point transferability
Gregor Deichmann, Marco Dallavalle, David Rosenberger and Nico F. A. van der Vegt
J. Phys. Chem. B 123, 504-515 (2019);
doi:10.1021/acs.jpcb.8b07320

Polydispersity Effects on Interpenetration in Compressed Brushes
Leonid I. Klushin, Alexander M. Skvortsov, Shuanhu Qi, Torsten Kreer, Friederike Schmid
Macromolecules 52 (4), 1810-1820 (2019);
doi:10.1021/acs.macromol.8b02361

How ill-defined constituents produce well-defined nanoparticles: Effect of polymer dispersity on the uniformity of copolymeric micelles
Sriteja Mantha, Shuanhu Qi, Matthias Barz, Friederike Schmid
Physical Review Materials 3 (2), (2019);
doi:10.1103/physrevmaterials.3.026002

An asymptotic preserving scheme for kinetic chemotaxis models in two space dimensions
A. Chertock, A. Kurganov, M. Lukacova-Medvidova, S. Nur Oezcan
Kinetic and Related Models 12 (1), 195–216 (2019);
URL: http://aimsciences.org//article/doi/10.3934/krm.2019009
doi:10.3934/krm.2019009

In this paper, we study two-dimensional multiscale chemotaxis models based on a combination of the macroscopic evolution equation for chemoattractant and microscopic models for cell evolution. The latter is governed by a Boltzmann-type kinetic equation with a local turning kernel operator which describes the velocity change of the cells. The parabolic scaling yields a non-dimensional kinetic model with a small parameter, which represents the mean free path of the cells. We propose a new asymptotic preserving numerical scheme that reflects the convergence of the studied micro-macro model to its macroscopic counterpart-the Patlak-Keller-Segel system-in the singular limit. The method is based on the operator splitting strategy and a suitable combination of the higher-order implicit and explicit time discretizations. In particular, we use the so-called even-odd decoupling and approximate the stiff terms arising in the singular limit implicitly. We prove that the resulting scheme satisfies the asymptotic preserving property. More precisely, it yields a consistent approximation of the Patlak-Keller-Segel system as the mean-free path tends to 0. The derived asymptotic preserving method is used to get better insight to the blowup behavior of two-dimensional kinetic chemotaxis model.

Energy-stable linear schemes for polymer-solvent phase field models
P. Strasser, G. Tierra, B. Dünweg, M. Lukacova-Medvidova
Comp. Math. Appl. 77 (1), 125-143 (2019);
URL: https://www.sciencedirect.com/science/article/pii/S0898122118305303?via%3Dihub
doi:https://doi.org/10.1016/j.camwa.2018.09.018

We present new linear energy-stable numerical schemes for numerical simulation of complex polymer–solvent mixtures. The mathematical model proposed by Zhou et al. (2006) consists of the Cahn–Hilliard equation which describes dynamics of the interface that separates polymer and solvent and the Oldroyd-B equations for the hydrodynamics of polymeric mixtures. The model is thermodynamically consistent and dissipates free energy. Our main goal in this paper is to derive numerical schemes for the polymer–solvent mixture model that are energy dissipative and efficient in time. To this end we will propose several problem-suited time discretizations yielding linear schemes and discuss their properties.

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