arXiv subjects

Joost de Graaf

Publications and source records attributed to Joost de Graaf.

At least 37 records · Page 2Linked to original sources

arXiv2020

Autonomously Probing Viscoelasticity in Disordered Suspensions

Recent experiments show a strong rotational-diffusion enhancement for self-propelled microrheological probes in colloidal glasses. Here, we provide microscopic understanding using simulations with a frictional probe-medium coupling that converts active translation into rotation. Diffusive enhancement emerges from the medium's disordered structure and peaks at a second-order transition in the number of contacts. Our results reproduce the salient features of the colloidal glass experiment and support an effective description that is applicable to a broader class of viscoelastic suspensions.

cond-mat.soft↗

arXiv2020

An extensible lattice Boltzmann method for viscoelastic flows: complex and moving boundaries in Oldroyd-B fluids

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 literature. Our approach can readily be extended to constitutive equations other than Oldroyd-B. This flexibility and the handling of complex boundaries holds promise for the study of microswimmers in viscoelastic fluids.

physics.flu-dyn↗

arXiv2020

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.

cond-mat.soft↗

arXiv2019

Slip length dependent propulsion speed of catalytic colloidal swimmers near walls

Catalytic colloidal swimmers that propel due to self-generated fluid flows exhibit strong affinity for surfaces. We here report experimental measurements of significantly different velocities of such microswimmers in the vicinity of substrates made from different materials. We find that velocities scale with the solution contact angle $θ$ on the substrate, which in turn relates to the associated hydrodynamic substrate slip length, as $V\propto(\cosθ+1)^{-3/2}$. We show that such dependence can be attributed to osmotic coupling between swimmers and substrate. Our work points out that hydrodynamic slip at the wall, though often unconsidered, can significantly impact the self-propulsion of catalytic swimmers.

cond-mat.soft↗

arXiv2019

Hydrodynamic Mobility Reversal of Squirmers near Flat and Curved Surfaces

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.

cond-mat.soft↗

arXiv2019

Self-Thermoelectrophoresis at Low Salinity

A locally heated Janus colloid can achieve motion in a fluid through the coupling of dissolved ions and the medium's polarizibility to an imposed temperature gradient, an effect known as self-thermo(di)electrophoresis. We numerically study the self-propulsion of such a "hot swimmer" in a monovalent electrolyte solution using the finite-element method. The effect of electrostatic screening for intermediate and large Debye lengths is charted and we report on the fluid flow generated by self-thermoelectrophoresis. We obtain excellent agreement between our analytic theory and numerical calculations in the limit of high salinity, validating our approach. At low salt concentrations, we consider two analytic approaches and use Teubner's integral formalism to arrive at expressions for the speed. These expressions agree semi-quantitatively with our numerical results for conducting swimmers, providing further validation. Our numerical approach provides a solid framework against the strengths and weaknesses of analytic theory can be appreciated and which should benefit the realization and analysis of further experiments on hot swimming.

cond-mat.soft↗

arXiv2019

A Lattice Boltzmann Model for Squirmers

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 straight-forward, 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.

physics.flu-dyn↗

arXiv2018

Hydrodynamics strongly affect the dynamics of colloidal gelation but not gel structure

Colloidal particles with strong, short-ranged attractions can form a gel. We simulate this process without and with hydrodynamic interactions (HI), using the lattice-Boltzmann method to account for presence of a thermalized solvent. We show that HI speed up and slow down gelation at low and high volume fractions, respectively. The transition between these two regimes is linked to the existence of a percolating cluster shortly after quenching the system. However, when we compare gels at matched 'structural age', we find nearly indistinguishable structures with and without HI. Our result explains longstanding, unresolved conflicts in the literature.

cond-mat.soft↗

arXiv2018

Sedimentation of a rigid helix in viscous media

We consider sedimentation of a rigid helical filament in a viscous fluid under gravity. In the Stokes limit, the drag forces and torques on the filament are approximated within the resistive-force theory. We develop an analytic approximation to the exact equations of motion that works well in the limit of a sufficiently large number of turns in the helix (larger than two, typically). For a wide range of initial conditions, our approximation predicts that the centre of the helix itself follows a helical path with the symmetry axis of the trajectory being parallel to the direction of gravity. The radius and the pitch of the trajectory scale as non-trivial powers of the number of turns in the original helix. For the initial conditions corresponding to an almost horizontal orientation of the helix, we predict trajectories that are either attracted towards the horizontal orientation, in which case the helix sediments in a straight line along the direction of gravity, or trajectories that form a helical-like path with many temporal frequencies involved. Our results provide new insight into the sedimentation of chiral objects and might be used to develop new techniques for their spatial separation.

physics.flu-dyn↗

arXiv2018

ESPResSo 4.0 -- An Extensible Software Package for Simulating Soft Matter Systems

ESPResSo 4.0 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 3.1 Arnold et al., Meshfree Methods for Partial Differential 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.

cond-mat.soft↗

arXiv2017

Stirring by Periodic Arrays of Microswimmers

The interaction between swimming microorganisms or artificial self-propelled colloids and passive (tracer) particles in a fluid leads to enhanced diffusion of the tracers. This enhancement has attracted strong interest, as it could lead to new strategies to tackle the difficult problem of mixing on a microfluidic scale. Most of the theoretical work on this topic has focused on hydrodynamic interactions between the tracers and swimmers in a bulk fluid. However, in simulations, periodic boundary conditions (PBCs) are often imposed on the sample and the fluid. Here, we theoretically analyze the effect of PBCs on the hydrodynamic interactions between tracer particles and microswimmers. We formulate an Ewald sum for the leading-order stresslet singularity produced by a swimmer to probe the effect of PBCs on tracer trajectories. We find that introducing periodicity into the system has a surprisingly significant effect, even for relatively small swimmer-tracer separations. We also find that the bulk limit is only reached for very large system sizes, which are challenging to simulate with most hydrodynamic solvers.

cond-mat.soft↗

arXiv2017

Lattice-Boltzmann Simulations of Microswimmer-Tracer Interactions

Hydrodynamic interactions in systems comprised 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/counter-force based lattice-Boltzmann (LB) algorithm [J. de Graaf~\textit{et al.}, J. Chem. Phys.~\textbf{144}, 134106 (2016)] 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.

physics.flu-dyn↗

arXiv2017

Microfluidic Pumping by Micromolar Salt Concentrations

An ion-exchange-resin-based microfluidic pump is introduced that utilizes trace amounts of ions to generate fluid flows. We show experimentally that our pump operates in almost deionized water for periods exceeding 24h and induces fluid flows of um/s over hundreds of um. This flow displays a far-field, power-law decay which is characteristic of two-dimensional (2D) flow when the system is strongly confined and of three-dimensional (3D) flow when it is not. Using theory and numerical calculations we demonstrate that our observations are consistent with electroosmotic pumping driven by umol/L ion concentrations in the sample cell that serve as 'fuel' to the pump. Our study thus reveals that trace amounts of charge carriers can produce surprisingly strong fluid flows; an insight that should benefit the design of a new class of microfluidic pumps that operate at very low fuel concentrations.

cond-mat.soft↗

arXiv2016

Moving Charged Particles in Lattice Boltzmann-Based Electrokinetics

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 LB 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 was previously inaccessible to lattice-based continuum algorithms.

cond-mat.soft↗

arXiv2016

Clustering of Self-Propelled Triangles with Surface Roughness

Self-propelled particles can spontaneously form dense phases from a dilute suspension in a process referred to as motility-induced phase separation. The properties of the out-of-equilibrium structures that are formed are governed by the specifics of the particle interactions and the strength of the activity. Thus far, most studies into the formation of these structures have focused on spherical colloids, dumbbells, and rod-like particles endowed with various interaction potentials. Only a few studies have examined the collective behavior of more complex particle shapes. Here, we increase the geometric complexity and use Molecular Dynamics simulations to consider the structures formed by triangular self-propelled particles with surface roughness. These triangles either move towards their apex or towards their base, i.e., they possess a polarity. We find that apex-directed triangles cluster more readily, more stably, and have a smoother cluster interface than their base-directed counterparts. A difference between the two polarities is in line with the results of [H.H. Wensink, et al., Phys. Rev. E 89, 010302(R) (2014)], however, we obtain the reversed result when it comes to clustering, namely that apex-directed particles cluster more readily. We further show that reducing the surface roughness negatively impacts the stability of the base-directed structures, suggesting that their formation is in large part due to surface roughness. Our results lay a solid foundation for future experimental and computational studies into the effect of roughness on the collective dynamics of swimmers.

cond-mat.soft↗

arXiv2016

Ionic Screening and Dissociation are Crucial for Understanding Chemical Self-Propulsion in Water

Water is a polar solvent and hence supports the bulk dissociation of itself and its solutes into ions, and the re-association of these ions into neutral molecules in a dynamic equilibrium, e.g., ${\rm H_2O_2}\leftrightharpoons {\rm H^+~+~HO_2^-}$. Using continuum theory, we study the influence of these reactions on the self-propulsion of colloids driven by surface chemical reactions (chemical swimmers) in aqueous solution. The association-dissociation reactions are here shown to have a strong influence on the swimmers' behaviour, and must therefore be included in future modelling. In particular, such bulk reactions permit charged swimmers to propel electrophoretically even if all species involved in the surface reactions are neutral. The bulk reactions also significantly modify the predicted speed of chemical swimmers propelled by ionic currents, by up to an order of magnitude. For swimmers whose surface reactions produce both anions and cations (ionic self-diffusiophoresis), the bulk reactions produce an additional reactive screening length, analogous to the Debye length in electrostatics. This in turn leads to an inverse relationship between swimmer radius and swimming speed, which could provide an alternative explanation for recent experimental observations on Pt-polystyrene Janus swimmers [S. Ebbens et al., Phys. Rev. E 85, 020401 (2012)]. We also use our continuum theory to investigate the effect of the Debye screening length itself, going beyond the infinitely thin limit approximation used by previous analytical theories. We identify significant departures from this limiting behavior for micron-sized swimmers under typical experimental conditions, and find that the limiting behavior fails entirely for nanoscale swimmers.

cond-mat.soft↗

arXiv2016

The Raspberry Model for Hydrodynamic Interactions Revisited. II. The Effect of Confinement

The so-called 'raspberry' model refers to the hybrid lattice-Boltzmann (LB) and Langevin molecular dynamics scheme for simulating the dynamics of suspensions of colloidal particles, originally developed by [V. Lobaskin and B. Dünweg, New J. Phys. 6, 54 (2004)], wherein discrete surface points are used to achieve fluid-particle coupling. In this paper, we present a follow up to our study of the effectiveness of the raspberry model in reproducing hydrodynamic interactions in the Stokes regime for spheres arranged in a simple-cubic crystal [L. Fischer, et al., J. Chem. Phys. 143, 084108 (2015)]. Here, we consider the accuracy with which the raspberry model is able to reproduce such interactions for particles confined between two parallel plates. To this end, we compare our LB simulation results to established theoretical expressions and finite-element calculations. We show that there is a discrepancy between the translational and rotational mobility when only surface coupling points are used, as also found in Part I of our joint publication. We demonstrate that adding internal coupling points to the raspberry, can be used to correct said discrepancy in confining geometries as well. Finally, we show that the raspberry model accurately reproduces hydrodynamic interactions between a spherical colloid and planar walls up to roughly one LB lattice spacing.

cond-mat.soft↗

arXiv2016

Nanoparticle Translocation through Conical Nanopores: A Finite Element Study of Electrokinetic Transport

Recent years have seen a surge of interest in nanopores because such structures show a strong potential for characterizing nanoparticles, proteins, DNA, and even single molecules. These systems have been extensively studied in experiment as well as by all-atom and coarse-grained simulations, with a strong focus on DNA translocation. However, the equally interesting problem of particle characterization using nanopores has received far less attention. Here, we theoretically investigate the translocation of a nanoparticle through a conical nanocapillary. We use a model based on numerically solving the coupled system of electrokinetic continuum equations, which we introduce in detail. Based on our findings, we formulate basic guidelines for obtaining the maximum current signal during the translocation event, which should be transferable to other nanopore geometries. In addition, the dependence of the signal strength on particle properties, such as surface charge and size, is evaluated. Finally, we identify conditions under which the translocation is prevented by the formation of a strong electro-osmotic barrier and show that the particle may even become trapped at the pore orifice, without imposing an external hydrostatic pressure difference.

cond-mat.soft↗