Peter Košovan

ESPResSo 3.1: Molecular Dynamics Software for Coarse-Grained Models

ESPResSo is a package for Molecular Dynamics (MD) simulations of coarse-grained models. We present the most recent version 3.1 of our software, highlighting some recent algorithmic extensions to version 1.0 presented in a previous paper (Limbach et al. Comput Phys Commun 174:704–727, 2006). A major strength of our package is the multitude of implemented methods for calculating Coulomb and dipolar interactions in periodic and partially periodic geometries. Here we present some more recent additions which include methods for systems with dielectric contrasts that frequently occur in coarse-grained models of charged systems with implicit water models, and an alternative, completely local electrostatic solver that is based on the electrodynamic equations. We also describe our approach to rigid body dynamics that uses MD particles with fixed relative positions. ESPResSo now gained the ability to add bonds during the integration, which allows to study e.g. agglomeration. For hydrodynamic interactions, a thermalized lattice Boltzmann solver has been built into ESPResSo, which can be coupled to the MD particles. This computationally expensive algorithm can be greatly accelerated by using Graphics Processing Units. For the analysis of time series spanning many orders of magnitude in time scales, we implemented a hierarchical generic correlation algorithm for user-configurable observables.

Coarse-grained simulations of an ionic liquid-based capacitor: I. Density, ion size, and valency effects

We introduce a hierarchy of generic coarse-grained models of ionic liquids of increasing complexity. We use them in molecular dynamics simulations to study the differential capacitance of a capacitor consisting of an ionic liquid between two planar electrodes. The primary goal is to explain the complex dependence of the differential capacitance Cd on the electrode potential U in simple terms, e.g. in terms of the size and valency of the ions. For this purpose we introduce the symmetric model A, which qualitatively reproduces the Cd(U) dependence predicted by the mean-field theory but also reveals strong quantitative deviations. We further introduce size asymmetry in model A by increasing the cation size. In model B we vary the cation valency, keeping the sizes of both ions constant. We show that simultaneous increases in size and valency may compensate for each other, leading to a Cd(U) very similar to that for the symmetric case. We interpret distinct features in Cd(U) on the basis of the density profiles of the ions and charge density profiles. We focus on the first two ion layers at the electrode, and demonstrate that the polarization of the ionic liquid proceeds through replacement of one ion type by the other, in contrast to the simple increase in ion concentrations typical for dilute systems. The understanding gained for the simple models serves as a reference for interpretation of complex effects of ion size, valency and shape. This is carried through in part II (a separate article) where we show how the planar shape of ions in model C brings new features to the Cd(U) curve and also to the polarization mechanism.

Polymers in focus: fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy has been increasingly used in polymer science. In the present perspective, the principles of the method are briefly reviewed, and the temporal and spatial resolutions are critically discussed. Examples of recent findings are summarized, focusing on polymer solutions, environmental parameters, combination with other techniques, near-interface measurements, simulations, and modeling. Finally, desirable new developments are discussed.

Molecular dynamics simulations of a polyelectrolyte star in poor solvent

We used Molecular Dynamics (MD) simulations to investigate the conformations of a star polyelectrolyte in poor solvent. We observed several distinct morphologies: at low number of arms, pearl-necklace structures are formed on individual arms; at higher number of arms inter-arm bundling is the dominant structural motif.

Coarse-grained simulations of an ionic liquid-based capacitor: II. Asymmetry in ion shape and charge localization

In this work, which is a continuation of part I, we introduce a primitive model for an ionic liquid (IL) that can account for the planar shape of cations typical for ILs like imidazolium. The model consists of a spherical anion and a triangular cation consisting of three spheres, where one or all three vertices of the triangle can carry electric charge. We use molecular dynamics simulations to study the differential capacitance Cd of an ionic liquid confined between two planar electrodes. Our goal is to elucidate the complex dependence of Cd on the electrode potential U in terms of simple entities such as the shape and charge distribution of the ions. For this purpose, we compare the results from the current model to the results based on the models with spherical cations that possess asymmetry in ion valence and shape that were analyzed in detail in part I of this work. We show that the various possible stackings of the triangles near the cathode lead to noticeable new features in Cd(U) as compared to the spherical models. Different distributions of charges on the triangle lead to different preferred orientations of the cations near the cathode that are moreover potential dependent.

New ends to the tale of tails: adsorption of comb polymers and the effect on colloidal stability

In this paper we consider the classical problem of homopolymer adsorption at the solid–liquid interface and discuss its implications for colloidal stability. More specifically, our focus is on comb-like homopolymers in the strong adsorption limit. A self-consistent field analysis shows that for relatively long side chains but still much longer backbones, the adsorbed layer is dominated by the side chains near the surface, whereas at larger distances the layer has features that belong to the backbone. As a rule, homopolymer adsorption promotes flocculation of colloids. This is attributed to the long polymer chains that form bridges between the colloidal particles. However, the free ends of the chains do not participate in the bridging and thus contribute with a small repulsive term to the mainly attractive pair interaction. For comb polymers, the free ends of the side chains amplify the repulsion dramatically. As a result, in contrast to linear adsorbed homopolymers, comb polymers typically prevent flocculation.

Tracer diffusion in a crowded cylindrical channel.

Based on a coarse-grained model, we carry out molecular dynamics simulations to analyze the diffusion of a small tracer particle inside a cylindrical channel whose inner wall is covered with randomly grafted short polymeric chains. We observe an interesting transient subdiffusive behavior along the cylindrical axis at high attraction between the tracer and the chains, however, the long-time diffusion is always normal. This process is found to be enhanced for the case that we immobilize the grafted chains, i.e., the subdiffusive behavior sets in at an earlier time and spans over a longer time period before becoming diffusive. Even if the grafted chains are replaced with a frozen sea of repulsive, nonconnected particles in the background, a transient subdiffusion is observed. The intermediate subdiffusive behavior only disappears when the grafted chains are replaced with a mobile background sea of mutually repulsive particles. Overall, the long-time diffusion coefficient of the tracer along the cylinder axis decreases with an increase in system volume fraction, the strength of the attraction between the tracer and the background, and also on freezing the background.

Molecular Simulations of Hydrogels

We review the state-of-the-art of simulational approaches to understand the complex behavior of swollen hydrogels. We concentrate on molecular simulation approaches that use coarse-grained polymer models, and atomistic simulations. Continuum, finite-element, and other modeling approaches are briefly mentioned. The current understanding of the topic, as well as open problems are highlighted.

Seawater Desalination via Hydrogels: Practical Realisation and First Coarse Grained Simulations

We investigated and described a novel approach for water desalination using charged hydrogels under externally applied mechanical forces. The desalination mechanism is based on the unequal distribution of an added salt between gel and surrounding solution phase. We synthesised acrylic acid-based hydrogels of various compositions and investigated their desalination properties with a specifically designed experimental press setup that allowed us to control online the force respective pressure exerted on the gel and to measure the water elution from the gel bed as well as the salt concentration of the eluate. A reference sodium chloride solution was used as a model for desalination applications. The experiments were augmented with a theoretical analysis within a mean-field Donnan model that can semi-quantitatively explain the salt distribution and the desalination process. In addition we performed coarse-grained simulations with explicit ions and charged bead-spring polymers. The simulations provided reference data on well defined systems which could be directly compared with the theoretical predictions. This comparison provided valuable insights into the weak points of the mean-field theory and guidelines for its further development.

Fluorescence Spectroscopy as a Tool for Investigating the Self-Organized Polyelectrolyte Systems

In this article, we outline the principles and application of several time-resolved fluorescence techniques for studying the behavior of stimuli-responsive self-assembled polymer systems. We demonstrate the high research potential of fluorescence using results of several published studies performed by the research team at the Charles University in Prague in the framework of the Marie Curie Research Training Network “Self-Organized Nanostructures of Amphiphilic Copolymers” (MRTN-CT-2003-505027). We have chosen several interesting examples of complex self-assembling systems, the behavior of which could not have been understood without the help of targeted fluorescence studies. We have chosen four different techniques, two of them relatively popular (fluorescence anisotropy and nonradiative excitation energy transfer) and two only little used in polymer science (the solvent relaxation method and fluorescence correlation spectroscopy). The last part of the article is devoted to computer simulations (Monte Carlo and molecular dynamics) aimed at the interpretation of fluorescence data.