The Raspberry model for hydrodynamic interactions revisited. II. The effect of confinement

Capture and translocation of a rod-like molecule by a nanopore: orientation, charge distribution and hydrodynamics

We investigate the translocation of rods with different charge distributions using hybrid Langevin dynamics and lattice Boltzmann (LD-LB) simulations. Electrostatic interactions are added to the system using the P³M algorithm to model the electrohydrodynamic interactions (EHI). We first examine the free-solution electrophoretic properties of rods with various charge distributions. Our translocation simulation results suggest that the order parameter is asymmetric during the capture and escape processes despite the symmetric electric field lines, while the impacts of the charge distribution on rod orientation are more significant during the capture process. The capture/threading/escape times are under the combined effects of charge screening, rod orientation, and charge distributions. We also show that the mean capture time of a rod is shorter when it is launched near the wall because rods tend to align along the wall and hence with the local field lines. Remarkably, the orientational capture radius we proposed previously for uniformly charged rods is still valid in the presence of EHI.

Flux and separation of magneto-active superballs in applied fields

The term "active matter" describes a class of out-of-equilibrium systems, whose ability to transform environmental to kinetic energy is sought after in multiple fields of science. A challenge that still remains is to craft nanometer-sized active particles, whose motion can be efficiently directed by externally applied bio-noninvasive stimuli. Adding a magnetic component and therefore being able to direct the motion of active nanoparticles with an applied magnetic field is one of the promising solutions in the field. In this study, we employ molecular dynamics simulations to predict an external field-induced flow that arises in mixtures of magneto-active nanosized cubic and spherical particles with distinct mutual orientations between magnetization and propulsion. We explain why the flux of the suspended particles in the field direction does not only depend on the angle between the active force, driving a particle forward, and the orientation of its magnetization, but also on particle shape and inter-particle interactions. Our results show that by tuning those parameters, one can achieve complete separation of particles according to their magnetization orientation. Based on our findings, along with optimizing the cargo properties of magneto-active nano-units, the actual composition of the magneto-active particle suspension can be characterized.

Diffusion-Based Height Analysis Reveals Robust Microswimmer-Wall Separation

Microswimmers typically move near walls, which can strongly influence their motion. However, direct experimental measurements of swimmer-wall separation remain elusive to date. Here, we determine this separation for model catalytic microswimmers from the height dependence of the passive component of their mean-squared displacement. We find that swimmers exhibit "ypsotaxis," a tendency to assume a fixed height above the wall for a range of salt concentrations, swimmer surface charges, and swimmer sizes. Our findings indicate that ypsotaxis is activity induced, posing restrictions on future modeling of their still-debated propulsion mechanism.

Lattice Boltzmann methods and active fluids

We review the state of the art of active fluids with particular attention to hydrodynamic continuous models and to the use of Lattice Boltzmann Methods (LBM) in this field. We present the thermodynamics of active fluids, in terms of liquid crystals modelling adapted to describe large-scale organization of active systems, as well as other effective phenomenological models. We discuss how LBM can be implemented to solve the hydrodynamics of active matter, starting from the case of a simple fluid, for which we explicitly recover the continuous equations by means of Chapman-Enskog expansion. Going beyond this simple case, we summarize how LBM can be used to treat complex and active fluids. We then review recent developments concerning some relevant topics in active matter that have been studied by means of LBM: spontaneous flow, self-propelled droplets, active emulsions, rheology, active turbulence, and active colloids.

A computational model for bacterial run-and-tumble motion

In this article we present a computational model for the simulation of self-propelled anisotropic bacteria. To this end we use a self-propelled particle model and augment it with a statistical algorithm for the run-and-tumble motion. We derive an equation for the distribution of reorientations of the bacteria that we use to analyze the statistics of the random walk and that allows us to tune the behavior of our model to the characteristics of an E. coli bacterium. We validate our implementation in terms of a single swimmer and demonstrate that our model is capable of reproducing E. coli's run-and-tumble motion with excellent accuracy.

Toward Understanding of Self-Electrophoretic Propulsion under Realistic Conditions: From Bulk Reactions to Confinement Effects

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.

Dissipative Coupling of Fluid and Immersed Objects for Modelling of Cells in Flow

Modelling of cell flow for biomedical applications relies in many cases on the correct description of fluid-structure interaction between the cell membrane and the surrounding fluid. We analyse the coupling of the lattice-Boltzmann method for the fluid and the spring network model for the cells. We investigate the bare friction parameter of fluid-structure interaction that is mediated via dissipative coupling. Such coupling mimics the no-slip boundary condition at the interface between the fluid and object. It is an alternative method to the immersed boundary method. Here, the fluid-structure coupling is provided by forces penalising local differences between velocities of the object's boundaries and the surrounding fluid. The method includes a phenomenological friction coefficient that determines the strength of the coupling. This work aims at determination of proper values of such friction coefficient. We derive an explicit formula for computation of this coefficient depending on the mesh density assuming a reference friction is known. We validate this formula on spherical and ellipsoidal objects. We also provide sensitivity analysis of the formula on all parameters entering the model. We conclude that such formula may be used also for objects with irregular shapes provided that the triangular mesh covering the object's surface is in some sense uniform. Our findings are justified by two computational experiments where we simulate motion of a red blood cell in a capillary and in a shear flow. Both experiments confirm our results presented in this work.

Maximum in density heterogeneities of active swimmers

Suspensions of unicellular microswimmers such as flagellated bacteria or motile algae can exhibit spontaneous density heterogeneities at large enough concentrations. We introduce a novel model for biological microswimmers that creates the flow field of the corresponding microswimmers, and takes into account the shape anisotropy of the swimmer's body and stroke-averaged flagella. By employing multiparticle collision dynamics, we directly couple the swimmer's dynamics to the fluid's. We characterize the nonequilibrium phase diagram, as the filling fraction and Péclet number are varied, and find density heterogeneities in the distribution of both pullers and pushers, due to hydrodynamic instabilities. We find a maximum degree of clustering at intermediate filling fractions and at large Péclet numbers resulting from a competition of hydrodynamic and steric interactions between the swimmers. We develop an analytical theory that supports these results. This maximum might represent an optimum for the microorganisms' colonization of their environment.

Continuous electroosmotic sorting of particles in grooved microchannels

We propose a novel microfluidic fractionation concept suitable for neutrally buoyant micron-sized particles. This approach takes advantage of the ability of grooved channel walls oriented at an angle to the direction of an external electric field to generate a transverse electroosmotic flow. Using computer simulations, we first demonstrate that the velocity of this secondary transverse flow depends on the distance from the wall, so neutrally buoyant particles, depending on their size and initial location, will experience different lateral displacements. We then optimize the geometry and orientation of the surface texture of the channel walls to maximize the efficiency of particle fractionation. Our method is illustrated in a full scale computer experiment where we mimic the typical microchannel with a bottom grooved wall and a source of polydisperse particles that are carried along the channel by the forward electroosmotic flow. Our simulations show that the particle dispersion can be efficiently separated by size even in a channel that is only a few texture periods long. These results can guide the design of novel microfluidic devices for efficient sorting of microparticles.

A dsDNA model optimized for electrokinetic applications

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.

Lattice-Boltzmann simulations of microswimmer-tracer interactions

Hydrodynamic interactions in systems composed of self-propelled particles, such as swimming microorganisms and passive tracers, have a significant impact on the tracer dynamics compared to the equivalent "dry" sample. However, such interactions are often difficult to take into account in simulations due to their computational cost. Here, we perform a systematic investigation of swimmer-tracer interaction using an efficient force-counterforce-based lattice-Boltzmann (LB) algorithm [De Graaf et al., J. Chem. Phys. 144, 134106 (2016)JCPSA60021-960610.1063/1.4944962] in order to validate its ability to capture the relevant low-Reynolds-number physics. We show that the LB algorithm reproduces far-field theoretical results well, both in a system with periodic boundary conditions and in a spherical cavity with no-slip walls, for which we derive expressions here. The force-lattice coupling of the LB algorithm leads to a "smearing out" of the flow field, which strongly perturbs the tracer trajectories at close swimmer-tracer separations, and we analyze how this effect can be accurately captured using a simple renormalized hydrodynamic theory. Finally, we show that care must be taken when using LB algorithms to simulate systems of self-propelled particles, since its finite momentum transport time can lead to significant deviations from theoretical predictions based on Stokes flow. These insights should prove relevant to the future study of large-scale microswimmer suspensions using these methods.

The raspberry model for hydrodynamic interactions revisited. I. Periodic arrays of spheres and dumbbells

The so-called "raspberry" model refers to the hybrid lattice-Boltzmann and Langevin molecular dynamics scheme for simulating the dynamics of suspensions of colloidal particles, originally developed by Lobaskin and Dünweg [New J. Phys. 6, 54 (2004)], wherein discrete surface points are used to achieve fluid-particle coupling. This technique has been used in many simulation studies on the behavior of colloids. However, there are fundamental questions with regards to the use of this model. In this paper, we examine the accuracy with which the raspberry method is able to reproduce Stokes-level hydrodynamic interactions when compared to analytic expressions for solid spheres in simple-cubic crystals. To this end, we consider the quality of numerical experiments that are traditionally used to establish these properties and we discuss their shortcomings. We show that there is a discrepancy between the translational and rotational mobility reproduced by the simple raspberry model and present a way to numerically remedy this problem by adding internal coupling points. Finally, we examine a non-convex shape, namely, a colloidal dumbbell, and show that the filled raspberry model replicates the desired hydrodynamic behavior in bulk for this more complicated shape. Our investigation is continued in de Graaf et al. [J. Chem. Phys. 143, 084108 (2015)], wherein we consider the raspberry model in the confining geometry of two parallel plates.