We introduce a scheme to simulate the spatial and temporal evolution of the densities of charged species, taking into account diffusion, thermal fluctuations, coupling to a carrier fluid, and chemical reactions. To this end, the diffusive fluxes in the electrokinetic model by Capuani et al. [1] are supplemented with thermal fluctuations. Chemical reactions are included via an additional source term in the mass balance equation. The diffusion-reaction model is then coupled to a solver for fluctuating hydrodynamics based on the lattice Boltzmann method. This combination is particularly useful for soft matter simulations, due to the ability to couple particles to the lattice-Boltzmann fluid. These could, e.g., be charged colloids or polymers, which then interact with an ion distribution. We describe one implementations based on the automatic code generation tools pystencils and lbmpy, and another one that is contained in the molecular dynamics package ESPResSo and that allows for an easy coupling of particles to the density fields. We validate our implementations by comparing to several known analytic results. Our method can be applied to coarse-grained catalysis problems as well as to many other multi-scale problems that require the coupling of explicit-particle simulations to flow fields, diffusion, and reaction problems in arbitrary geometries.

We investigate the salt-dependent current modulation of bundled DNA nanostructures in a nanopore. To this end, we developed four simulation models for a 2 × 2 origami structure with increasing level of detail ranging from the mean-field level to an all-atom representation of the DNA structure. We observe a consistent pore conductivity as a function of salt concentration for all four models. However, a comparison of our data to recent experimental investigations on similar systems displays significant deviations. We discuss possible reasons for the discrepancies and propose extensions to our models for future investigations.

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 ESPResSo, the extensible simulation package for research on soft matter, for molecular dynamics simulations 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 with theoretical estimates.

Dieses Positionspapier ist aus Sicht von Forschenden an der Universität Stuttgart geschrieben. Wir empfehlen die Einrichtung einer Organisationseinheit „Forschungssoftware-Entwicklung“ an der Universität Stuttgart und eines daran angegliederten Stellenpools von Research Software Engineers (RSEs). Dazu schlagen wir Maßnahmen zur Schaffung und Finanzierung entsprechender neuer RSE-Stellen, zur Integration bestehender Stellen sowie zur Gewinnung und Förderung geeigneter Personen vor. RSEs sind Personen, die sich um Konzeption, Organisation, Implementierung, Testen, Dokumentation und Wartung von Forschungssoftware kümmern. Die institutionelle Förderung von Forschungssoftware-Entwicklung ist notwendig, da die Bedeutung von Software für die Forschung und Anforderungen an die entsprechende Software, u.a. durch die DFG, stetig zunimmt, siehe Abschnitt 1. In Abschnitt 2 erläutern wir, warum der aktuelle Zustand der Forschungssoftware-Entwicklung diesen Anforderungen nicht gerecht wird. Aufbauend auf den in Abschnitt 3 geschilderten grundlegenden Anforderungen an Forschungssoftware und Research Software Engineers schlagen wir in Abschnitt 4 konkreten Maßnahmen und deren Umsetzung vor. Durch diese kann die Universität Stuttgart ihre Forschenden von zentraler Stelle aus umfassend unterstützen und eine Vorreiterrolle in diesem Bereich übernehmen.

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 allow for many applications, e.g., in engineering and biomedicine. Due to their inherent complexity, computer simulations are a commonly used tool to study these materials. A well-known bottleneck for the numerics is the demanding calculation of dipolar interactions. For periodic boundary conditions there exist established algorithms, 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 periodic boundary conditions where the gel has no boundary out entirely for some research questions. In this article we will employ the recently developed dipolar variant of the (PNFFT)-N-2 method for 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 (PNFFT)-N-2 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 relevance 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 we will apply the method to a magnetic gel. Here, adapting the method to the change in shape of the gel during the course of a simulation is of particular importance. (C) 2019 Elsevier Inc. All rights reserved.

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 [H.J. 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 3.1 [A. Arnold et al., Meshfree methods for partial di_erential equations VI, Lect. Notes Comput. Sci. Eng. 89, 1 (2013)], the software has undergone considerable restructuring. The biggest change is the replacement of the Tcl scripting interface with a much more powerful Python interface. In addition, many new simulation methods have been implemented. In this article, we highlight the changes and improvements made to the interface and code, as well as the new simulation techniques that enable a user of ESPResSo 4.0 to simulate physics that is at the forefront of soft matter research.

All-atom molecular dynamics (MD) simulations of double stranded DNA (dsDNA) translocating through a cylindrical nanopore by Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] have revealed that ions close to the surface of the DNA experience an additional friction contribution when compared to their bulk value. This friction is a key ingredient in reproducing the 2006 experimentally observed current modifications by Smeets and coworkers. While these findings were already incorporated into a coarse-grained model by Weik et al. [J. Chem. Phys. 145, 194106 (2016)], we now present an extended mean-field model for solving the electrokinetic equations of a dsDNA confined to a structureless cylindrical pore. This is done by incorporating a suitably constructed friction term into the Nernst-Planck equation. Solving the modified electrokinetic equations using a finite element method, we demonstrate that this model is able to reproduce experimental and atomistic MD results for dsDNA current modulations. The advantage of our model is that it allows a fast evaluation of new geometric arrangements of the DNA within the cylinder.

1 General Remarks 1 2 Thermostats 2 2.1 Andersen Thermostat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 2.2 Berendsen Thermostat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 3 Simple Sampling – Integration 3 4 Importance Sampling – Metropolis-Hastings Algorithm 4 5 Simulating the Ising Model 6 5.1 Exact Summation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 5.2 Monte-Carlo Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1 General Remarks • Deadline for the report is Monday, January 23, 2017 • On this worksheet, you can achieve a maximum of 19 points. • The report should be written as though it would be read by a fellow student who attends to the lecture, but does not do the tutorials. • To hand in your report, send it to your tutor via email – Florian (fweik@icp.uni-stuttgart.de) (Thursday 11:30-13:00) – Michael (mkuron@icp.uni-stuttgart.de) (Friday 14:00-15:30)

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.

Hybrid parallel program models that combine message passing and multithreading (MP+MT) are becoming more popular, extending the basic message passing (MP) model that uses single-threaded processes for both inter- and intra-node parallelism. A consequence is that coupled parallel applications increasingly comprise MP libraries together with MP+MT libraries with differing preferred degrees of threading, resulting in thread-level heterogeneity. Retroactively matching threading levels between independently developed and maintained libraries is difficult; the challenge is exacerbated because contemporary parallel job launchers provide only static resource binding policies over entire application executions. A standard approach for accommodating thread-level heterogeneity is to under-subscribe compute resources such that the library with the highest degree of threading per process has one processing element per thread. This results in libraries with fewer threads per process utilizing only a fraction of the available compute resources. We present and evaluate a novel approach for accommodating thread-level heterogeneity. Our approach enables full utilization of all available compute resources throughout an application's execution by providing programmable facilities to dynamically reconfigure runtime environments for compute phases with differing threading factors and memory affinities. We show that our approach can improve overall application performance by up to 5.8x in real-world production codes. Furthermore, the practicality and utility of our approach has been demonstrated by continuous production use for over one year, and by more recent incorporation into a number of production codes.

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 the minimally-invasive exchange of the regular Cartesian grid in the lattice-Boltzmann solver of ESPResSo by a dynamically-adaptive octree grid.Octree grids are favoured by computer scientists over other grid types as they are very memory-efficient.In addition, they represent a natural generalisation of regular Cartesian grids, such that most discretisation details of a regular grid solver can be maintained.Optimised codes, however, require a special tree-oriented grid traversal, which typically conflicts with existing simulation codes using various iterators, some for only parts of the grid, e.g., boundaries.ESPResSo is a large software package developed for soft-matter simulations involving fluid flow, electrostatic, and electrokinetic effects, and molecular dynamics.The currently used regular Cartesian grid hinders the simulation of realistic domain sizes and significant time periods, a problem that can be solved using grid adaptivity.In a first step, we focus on the lattice-Boltzmann flow solver in ESPResSo.p4est is a grid framework, that already provides dynamically adaptive quadtree and octree grids together with high-level interfaces for flexible grid traversals with direct neighbour access in all grid components.In this paper, we first describe extensions of p4est that were necessary to fulfill certain application requirements.The second part of our work consists of the minimally-invasive changes in ESPResSo preserving the expertise accumulated in the software's implementation over years.Our numerical results demonstrate physical correctness of the implementation, good parallel scalability and low overhead of the dynamical grid adaptivity.These are prerequisites to actually profit from grid adaptivity in terms of being able to simulate larger domains over longer time periods with limited computational resources.Thus, the current status forms a solid basis for further steps such as the development of refinement criteria, the setup of more realistic application scenarios, and a GPU implementation.

1 General Remarks 1 2 Introduction 2 3 Saving and Restarting the Simulation 3 4 Simple Observables 3 5 Equilibration 5 6 Molecular Dynamics at a Desired Temperature 6 7 Setting up and Warming up the System 7 8 Radial Distribution Function 9 9 Measuring Equilibrium Mean Values of the Observables 11 1 General Remarks • Deadline for the report is Monday, December 12, 2016 • In this worksheet, you can achieve a maximum of 20 points. • The report should be written as though it would be read by a fellow student who attends the lecture, but doesn’t do the tutorials. • To hand in your report, send it to your tutor via email.