ESPResSo is an extensible simulation package for research on soft matter. This versatile molecular dynamics program was originally developed for coarse-grained simulations of charged systems [Limbach et al., Comput. Phys. Commun. 174, 704 (2006)]. The scope of the software has since broadened considerably: ESPResSo can now be used to simulate systems with length scales spanning from the molecular to the colloidal. Examples include, self-propelled particles in active matter, membranes in biological systems, and the aggregation of soot particles in process engineering. ESPResSo also includes solvers for hydrodynamic and electrokinetic problems, both on the continuum and on the explicit particle level. Since our last description of version 3.

Molecular dynamics (MD) simulations represent a powerful investigation tool in the field of soft matter. By using shear flows, one can probe the bulk rheology of complex fluids, also beyond the linear response regime, in a way that imitates laboratory experiments. One solution to impose a shear flow in particle-based simulations is the Lees-Edwards technique which ensures that particles experience shear by imposing rules for motion and interactions across the boundary in the direction of the shear plane. Despite their presentation in 1972, a readily available public implementation of Lees-Edwards boundary conditions has been missing from MD simulation codes. In this article, we present our implementation of the Lees-Edwards technique and discuss the relevant technical choices. We used the ESPResSo software package for Molecular Dynamics simulation of soft matter system, which can be used as a reference for other implementers. We illustrate our implementation using bulk dissipative particle dynamics fluids, compare different viscosity measurement techniques, and observe the anomalous diffusion in our samples during continuous and oscillatory shear, in good comparison to theoretical estimates.

Magnetic gels are soft elastic materials consisting of magnetic particles embedded in a polymer network. Their shape and elasticity can be controlled by an external magnetic field, which gives rise to both, engineering and biomedical applications. Computer simulations are a commonly used tool to study these materials. A well-known bottleneck of these simulations is the demanding calculation of dipolar interactions. Under periodic boundary conditions established algorithms are available for doing this, however, at the expense of restricting the way in which the gels can deform in an external magnetic field. Moreover, the magnetic properties depend on the sample shape, ruling out periodic boundary conditions entirely for some research questions. In this article we will employ the recently developed dipolar variant of the P 2 NFFT method that is able to calculate dipolar interactions under open boundary conditions with an N log N scaling in the number of particles, rather than the expensive N 2 scaling of a direct summation of pair forces. The dipolar P 2 NFFT method has been implemented within the ScaFaCoS library. The molecular dynamics software ESPResSo has been extended to make use of the library.After a short summary of the method, we will discuss its value for studying magnetic soft matter systems. A particular focus is put on developing a tuning strategy to reach the best performance of the method at a predefined accuracy, and lastly applying the method to a magnetic gel model. Here, adapting to the gel's change in shape during the course of a simulation is of particular interest.

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 system's electrokinetics by using explicitly parameterized ions, a friction term between the DNA beads and the ions, and a lattice-Boltzmann model for the solvent.

We present a coarse-grained (CG) model of a charged double-stranded DNA immersed in an electrolyte solution that can be used for a variety of electrokinetic applications. The model is based on an earlier rigid and immobile model of Weik et al. and includes now semi-flexibility and mobility, so that DNA dynamics can be sufficiently captured to simulate a full nanopore translocation process. To this end we couple the DNA hydrodynamically via a raspberry approach to a lattice-Boltzmann fluid and parametrize the counterions with a distant dependent friction. The electrokinetic properties of the CG DNA model inside an infinite cylinder is fitted against experimental data from Smeets et al. and all-atom simulation data from Kesselheim et al. The stiffness of our CG DNA is modeled via a harmonic angle potential fitted against experimental data of Brunet et al. Finally, the quality of our tuned parameters is tested by measuring the electrophoretic mobility of our DNA model for various numbers of base pairs and salt concentrations. Our results compare excellently with the experimental data sets of Stellwagen et al. and Hoagland et al.