Many problems in soft matter research involve particles suspended in a solvent, where hydrodynamic interactions play a crucial role. A well-established simulation approach for such systems combines molecular dynamics for the particles with the lattice-Boltzmann method for the solvent. We present the coupling of the coarse-grained molecular dynamics code ESPResSo to the waLBerla library, a high-performance framework for lattice-Boltzmann and other stencil-based methods. This coupling code, developed in the context of the EuroHPC Centre of Excellence MultiXscale, enables large-scale, multi-GPU simulations of coupled particle–fluid systems within ESPResSo. Beyond hydrodynamics, the integration also provides a diffusion–advection–reaction solver coupled to electrostatics and lattice-Boltzmann for electrokinetic simulations. A key advantage of using waLBerla is its code generation infrastructure, which facilitates both the adaptation of algorithms and their optimisation for different hardware architectures. We demonstrate the scalability of coupled simulations with multi-GPU benchmarks on MareNostrum 5.

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.

Programming current supercomputers efficiently is a challenging task. Multiple levels of parallelism on the core, on the compute node, and between nodes need to be exploited to make full use of the system. Heterogeneous hardware architectures with accelerators further complicate the development process. waLBerla addresses these challenges by providing the user with highly efficient building blocks for developing simulations on block-structured grids. The block-structured domain partitioning is flexible enough to handle complex geometries, while the structured grid within each block allows for highly efficient implementations of stencil-based algorithms. We present several example applications realized with waLBerla, ranging from lattice Boltzmann methods to rigid particle simulations. Most importantly, these methods can be coupled together, enabling multiphysics simulations. The framework uses meta-programming techniques to generate highly efficient code for CPUs and GPUs from a symbolic method formulation.

Most biological fluids are viscoelastic, meaning that they have elastic properties in addition to the dissipative properties found in Newtonian fluids. Computational models can help us understand viscoelastic flow, but are often limited in how they deal with complex flow geometries and suspended particles. Here, we present a lattice Boltzmann solver for Oldroyd-B fluids that can handle arbitrarily shaped fixed and moving boundary conditions, which makes it ideally suited for the simulation of confined colloidal suspensions. We validate our method using several standard rheological setups and additionally study a single sedimenting colloid, also finding good agreement with the literature. Our approach can readily be extended to constitutive equations other than Oldroyd-B. This flexibility and the handling of complex boundaries hold promise for the study of microswimmers in viscoelastic fluids.

The US possesses the infrastructure and the technology to successfully offer digital care, and healthcare providers from different specialties have claimed that “healing at a distance” improves patient outcomes and captures the needs of vulnerable populations. Efforts to limit the spread of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with the implementation of lockdown measures have created an opportunity for mental health clinics to employ telemedicine— or, in the fi eld of psychiatry and mental health—telepsychiatry. Telepsychiatry, also referred to as “telepsych,” is a subset of telemedicine that includes remote services, such as psychiatric evaluations, therapy (individual, group, and family), patient education, and pharmacologic and nonpharmacologic management. The Nebraska Psychiatric Institute fi rst introduced telepsych in mental health practices in 1959, and this approach has since addressed several psychiatric disorders and problems. The adaptations necessitated by the COVID-19 pandemic, characterized by remote communications and services, are transforming mental health practices globally by expanding the availability of telepsych. Advanced practice registered nurses (APRNs) are equipped to contribute to the healthcare needs of the populations they serve. There are two types of APRN specialties that are trained specifi cally in psychopharmacology and psychotherapy to help patients across the lifespan: psychiatric-mental health nurse practitioners and psychiatricmental health clinical nurse specialists. Both of these APRN specialties are qualifi ed to provide telepsychiatry effectively and in many states have full-practice authority (FPA). There is increased accessibility to mental health services provided by a psychiatrist or APRN in states where APRNs have FPA. Telemedicine in psychiatry has observable effi cacy in diagnostic and management decisions. Virtual platforms are achieving greater popularity among mainstream healthcare services, and studies show that telepsych can overcome barriers to care associated with patient diffi culty in attending in-person sessions. However, while providers recognize the benefi ts of telepsych, they may be unaware of potential liability concerns as well as the clinical, technological, and ethical issues associated with this method. The purpose of this article is to describe the considerations impacting the use of telepsych in mental health and to enhance provider understanding of telepsych to enable more effi cient and cost-effective care amid this pandemic and beyond.

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.

The squirmer is a simple yet instructive model for microswimmers, which employs an effective slip velocity on the surface of a spherical swimmer to describe its self-propulsion. We solve the hydrodynamic flow problem with the lattice Boltzmann (LB) method, which is well-suited for time-dependent problems involving complex boundary conditions. Incorporating the squirmer into LB is relatively straightforward, but requires an unexpectedly fine grid resolution to capture the physical flow fields and behaviors accurately. We demonstrate this using four basic hydrodynamic tests: two for the far-field flow—accuracy of the hydrodynamic moments and squirmer-squirmer interactions—and two that require the near field to be accurately resolved—a squirmer confined to a tube and one scattering off a spherical obstacle—which LB is capable of doing down to the grid resolution. We find good agreement with (numerical) results obtained using other hydrodynamic solvers in the same geometries and identify a minimum required resolution to achieve this reproduction. We discuss our algorithm in the context of other hydrodynamic solvers and present an outlook on its application to multi-squirmer problems.

Self-propelled particles have been experimentally shown to orbit spherical obstacles and move along surfaces. Here, we theoretically and numerically investigate this behavior for a hydrodynamic squirmer interacting with spherical objects and flat walls using three different methods of approximately solving the Stokes equations: The method of reflections, which is accurate in the far field; lubrication theory, which describes the close-to-contact behavior; and a lattice Boltzmann solver that accurately accounts for near-field flows. The method of reflections predicts three distinct behaviors: orbiting/sliding, scattering, and hovering, with orbiting being favored for lower curvature as in the literature. Surprisingly, it also shows backward orbiting/sliding for sufficiently strong pushers, caused by fluid recirculation in the gap between the squirmer and the obstacle leading to strong forces opposing forward motion. Lubrication theory instead suggests that only hovering is a stable point for the dynamics. We therefore employ lattice Boltzmann to resolve this discrepancy and we qualitatively reproduce the richer far-field predictions. Our results thus provide insight into a possible mechanism of mobility reversal mediated solely through hydrodynamic interactions with a surface.

Active matter concerns itself with the study of particles that convert energy into work, typically motion of the particle itself. This field saw a surge of interest over the past decade, after the first micrometer-sized, man-made chemical motors were created. These particles served as a simple model system for studying in a well-controlled manner complex motion and cooperative behavior as known from biology. In addition, they have stimulated new efforts in understanding out-of-equilibrium statistical physics and started a revolution in microtechnology and robotics. Concentrated effort has gone into realizing these ambitions, and yet much remains unknown about the chemical motors themselves. The original designs for self-propelled particles relied on the conversion of the chemical energy of hydrogen peroxide into motion via catalytic decomposition taking place heterogeneously over the surface of the motor. This sets up gradients of chemical fields around the particle, which allow it to autophorese. That is, the interaction between the motor and the heterogeneously distributed solute species can drive fluid flow and the motor itself. There are two basic designs: the first relies on redox reactions taking place between the two sides of a bimetal, for example, a gold-platinum Janus sphere or nanorod. The second uses a catalytic layer of platinum inhomogeneously vapor-deposited onto a nonreactive particle. For convenience's sake, these can be referred to as redox motors and monometallic half-coated motors, respectively. To date, most researchers continue to rely on variations of these simple, yet elegant designs for their experiments. However, there is ongoing debate on the exact way chemical energy is transduced into motion in these motors. Many of the experimental observations on redox motors were successfully modeled via self-electrophoresis, while for half-coated motors there has been a strong focus on self-diffusiophoresis. Currently, there is mounting evidence that self-electrophoresis provides the dominant contribution to the observed speeds of half-coated motors, even if the vast majority of the reaction products are electroneutral. In this Account, we will summarize the most common electrophoretic propulsion model and discuss its strengths and weaknesses in relation to recent experiments. We will comment on the possible need to go beyond surface reactions and consider the entire medium as an "active fluid" that can create and annihilate charged species. This, together with confinement and collective effects, makes it difficult to gain a detailed understanding of these swimmers. The potentially dominant effect of confinement is highlighted on the basis of a recent study of an electro-osmotic pump that drives fluid along a substrate. Detailed analysis of this system allows for identification of the electro-osmotic driving mechanism, which is powered by micromolar salt concentrations. We will discuss how our latest numerical solver developments, based on the lattice Boltzmann method, should enable us to study collective behavior in systems comprised of these and other electrochemical motors in realistic environments. We conclude with an outlook on the future of modeling chemical motors that may facilitate the community's microtechnological ambitions.

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)

The motion of ionic solutes and charged particles under the influence of an electric field and the ensuing hydrodynamic flow of the underlying solvent is ubiquitous in aqueous colloidal suspensions. The physics of such systems is described by a coupled set of differential equations, along with boundary conditions, collectively referred to as the electrokinetic equations. Capuani et al. [J. Chem. Phys. 121, 973 (2004)] introduced a lattice-based method for solving this system of equations, which builds upon the lattice Boltzmann algorithm for the simulation of hydrodynamic flow and exploits computational locality. However, thus far, a description of how to incorporate moving boundary conditions into the Capuani scheme has been lacking. Moving boundary conditions are needed to simulate multiple arbitrarily moving colloids. In this paper, we detail how to introduce such a particle coupling scheme, based on an analogue to the moving boundary method for the pure lattice Boltzmann solver. The key ingredients in our method are mass and charge conservation for the solute species and a partial-volume smoothing of the solute fluxes to minimize discretization artifacts. We demonstrate our algorithm’s effectiveness by simulating the electrophoresis of charged spheres in an external field; for a single sphere we compare to the equivalent electro-osmotic (co-moving) problem. Our method’s efficiency and ease of implementation should prove beneficial to future simulations of the dynamics in a wide range of complex nanoscopic and colloidal systems that were previously inaccessible to lattice-based continuum algorithms.

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.

While the phenomenon of like-charge attraction of DNA is clearly observed experimentally and in simulations, mean-field theories fail to predict it. Kornyshev et al. argued that like-charge attraction is due to DNA's helical geometry and hydration forces. Strong-coupling (SC) theory shows that attraction of like-charged rods is possible through ion correlations alone at large coupling parameters, usually by multivalent counterions. However for SC theory to be applicable, counterion-counterion correlations perpendicular to the DNA strands need to be sufficiently small, which is not a priori the case for DNA even with trivalent counterions. We study a system containing infinitely long DNA strands and trivalent counterions by computer simulations employing varying degrees of coarse-graining. Our results show that there is always attraction between the strands, but its magnitude is indeed highly dependent on the specific shape of the strand. While discreteness of the charge distribution has little influence on the attractive forces, the role of the helical charge distribution is considerable: charged rods maintain a finite distance in equilibrium, while helices collapse to close contact with a phase shift of π, in full agreement with SC predictions. The SC limit is applicable because counterions strongly bind to the charged sites of the helices, so that helix-counterion interactions dominate over counterion-counterion interactions. Thus DNA's helical geometry is not crucial for like-charge DNA attraction, but strongly enhances it, and electrostatic interactions in the strong-coupling limit are sufficient to explain this attraction.