Stefan Kesselheim

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.

Efficient algorithms for electrostatic interactions including dielectric contrasts

Coarse-grained models of soft matter are usually combined with implicit solvent models that take the electrostatic polarizability into account via a dielectric background. In biophysical or nanoscale simulations that include water, this constant can vary greatly within the system. Performing molecular dynamics or other simulations that need to compute exact electrostatic interactions between charges in those systems is computationally demanding. We review here several algorithms developed by us that perform exactly this task. For planar dielectric surfaces in partial periodic boundary conditions, the arising image charges can be either treated with the MMM2D algorithm in a very efficient and accurate way or with the electrostatic layer correction term, which enables the user to use his favorite 3D periodic Coulomb solver. Arbitrarily-shaped interfaces can be dealt with using induced surface charges with the induced charge calculation (ICC*) algorithm. Finally, the local electrostatics algorithm, MEMD(Maxwell Equations Molecular Dynamics), even allows one to employ a smoothly varying dielectric constant in the systems. We introduce the concepts of these three algorithms and an extension for the inclusion of boundaries that are to be held fixed at a constant potential (metal conditions). For each method, we present a showcase application to highlight the importance of dielectric interfaces.

Applying ICC⋆ to DNA translocation: Effect of dielectric boundaries

Abstract The translocation process of a single DNA molecule through a synthetic nanopore is investigated with the help of ICC ⋆ , a fast and accurate algorithm which allows to take into account dielectric boundary forces (DBF) in molecular dynamics simulations. We show that dielectric contrast between water and membrane material is responsible for a remarkably high free energy barrier at low salt concentrations.

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.

Effects of dielectric mismatch and chain flexibility on the translocation barriers of charged macromolecules through solid state nanopores

We investigate the impact of dielectric boundary forces on the translocation process of stiff charged macromolecules through solid-state nanopores by means of coarse grained molecular dynamics simulations. We find that the low dielectric permittivity of typical pore materials (compared to the surrounding water) is able to create a high free energy barrier of more than 10kBT under low salt conditions for pore radii comparable to the Debye length. Interestingly the translocation barrier is significantly enhanced for flexible charged macromolecules. To achieve a comparable description of the free energy profile we introduce a new reaction coordinate that can describe in a consistent way the whole translocation process for flexible and stiff macromolecules, and investigate the barrier for idealized model systems of a rigid double-stranded DNA and a flexible single-stranded DNA.

A coarse-grained DNA model for the prediction of current signals in DNA translocation experiments

We present an implicit solvent coarse-grained double-stranded DNA (dsDNA) model confined to an infinite cylindrical pore that reproduces the experimentally observed current modulations of a KaCl solution at various concentrations. Our model extends previous coarse-grained and mean-field approaches by incorporating a position dependent friction term on the ions, which Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] identified as an essential ingredient to correctly reproduce the experimental data of Smeets et al. [Nano Lett. 6, 89 (2006)]. Our approach reduces the computational effort by orders of magnitude compared with all-atom simulations and serves as a promising starting point for modeling the entire translocation process of dsDNA. We achieve a consistent description of the systems electrokinetics by using explicitly parameterized ions, a friction term between the DNA beads and the ions, and a lattice-Boltzmann model for the solvent.