arXiv subjects

Christian Holm

Publications and source records attributed to Christian Holm.

At least 73 records · Page 4Linked to original sources

arXiv2017

Simulation of weak polyelectrolytes: A comparison between the constant pH and the reaction ensemble method

The reaction ensemble and the constant pH method are well-known chemical equilibrium approaches to simulate protonation and deprotonation reactions in classical molecular dynamics and Monte Carlo simulations. In this article, we show similarity between both methods {under certain conditions}. We perform molecular dynamics simulations of a weak polyelectrolyte in order to compare the titration curves obtained by both approaches. Our findings reveal a good agreement between the methods when the reaction ensemble is used to sweep the reaction constant. Pronounced differences between the reaction ensemble and the constant pH method can be observed for stronger acids and bases in terms of adaptive pH values. These deviations are due to the presence of explicit protons in the reaction ensemble method which induce a screening of electrostatic interactions between the charged titrable groups of the polyelectrolyte. The outcomes of our simulation hint to a better applicability of the reaction ensemble method for systems in confined geometries and titrable groups in polyelectrolytes with different pK$_\text{a}$ values.

cond-mat.soft↗

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↗

arXiv2016

Selective Trapping of DNA using Glass Microcapillaries

We show experimentally that a cheap glass microcapillary can accumulate λ-phage DNA at its tip and deliver the DNA into the capillary using a combination of electro-osmotic flow, pressure-driven flow, and electrophoresis. We develop an efficient simulation model for this phenomenon based on the electrokinetic equations and the finite-element method. Using our model, we explore the large parameter space of the trapping mechanism by varying the salt concentration, the capillary surface charge, the applied voltage, the pressure difference, and the mobility of the analyte molecules. Our simulation results show that this system can be tuned to capture a wide range of analyte molecules, such as DNA or proteins, based on their electrophoretic mobility. Our method for separation and pre-concentration of analytes has implications for the development of low-cost lab-on-a-chip devices.

cond-mat.soft↗

arXiv2016

Understanding the Onset of Oscillatory Swimming in Microchannels

Self-propelled colloids (swimmers) in confining geometries follow trajectories determined by hydrodynamic interactions with the bounding surfaces. However, typically these interactions are ignored or truncated to lowest order. We demonstrate that higher-order hydrodynamic moments cause rod-like swimmers to follow oscillatory trajectories in quiescent fluid between two parallel plates, using a combination of lattice-Boltzmann simulations and far-field calculations. This behavior occurs even far from the confining walls and does not require lubrication results. We show that a swimmer's hydrodynamic quadrupole moment is crucial to the onset of the oscillatory trajectories. This insight allows us to develop a simple model for the dynamics near the channel center based on these higher hydrodynamic moments, and suggests opportunities for trajectory-based experimental characterization of swimmers' hydrodynamic properties.

cond-mat.soft↗

arXiv2016

Limiting Spurious Flow in Simulations of Electrokinetic Phenomena

Electrokinetic transport phenomena can strongly influence the behaviour of macromolecules and colloidal particles in solution, with applications in, e.g., DNA translocation through nanopores, electro-osmotic flow in nanocapillaries, and electrophoresis of charged macromolecules. Numerical simulations are an important tool to investigate these electrokinetic phenomena, but are often plagued by spurious fluxes and spurious flows that can easily exceed physical fluxes and flows. Here, we present a method that reduces one of these spurious currents, spurious flow, by several orders of magnitude. We demonstrate the effectiveness and generality of our method for both electrokinetic lattice-Boltzmann and finite-element-method based algorithms by simulating a charged sphere in an electrolyte solution, and flow through a nanopore. We also show that previous attempts to suppress these spurious currents introduce other sources of error.

cond-mat.soft↗

arXiv2016

The Efficiency of Self-Phoretic Propulsion Mechanisms with Surface Reaction Heterogeneity

We consider the efficiency of self-phoretic colloidal particles (swimmers) as a function of the heterogeneity in the surface reaction rate. The set of fluid, species, and electrostatic continuity equations is solved analytically using a linearization and numerically using a finite-element method. To compare spherical swimmers of different size and with heterogeneous catalytic conversion rates, a 'swimmer efficiency' functional $η$ is introduced. It is proven, that in order to obtain maximum swimmer efficiency the reactivity has to be localized at the pole(s). Our results also shed light on the sensitivity of the propulsion speed to details of the surface reactivity, a property that is notoriously hard to measure. This insight can be utilized in the design of new self-phoretic swimmers.

cond-mat.soft↗

arXiv2016

Lattice-Boltzmann Hydrodynamics of Anisotropic Active Matter

A plethora of active matter models exist that describe the behavior of self-propelled particles (or swimmers), both with and without hydrodynamics. However, there are few studies that consider shape-anisotropic swimmers and include hydrodynamic interactions. Here, we introduce a simple method to simulate self-propelled colloids interacting hydrodynamically in a viscous medium using the lattice-Boltzmann technique. Our model is based on raspberry-type viscous coupling and a force/counter-force formalism which ensures that the system is force free. We consider several anisotropic shapes and characterize their hydrodynamic multipolar flow field. We demonstrate that shape-anisotropy can lead to the presence of a strong quadrupole and octupole moments, in addition to the principle dipole moment. The ability to simulate and characterize these higher-order moments will prove crucial for understanding the behavior of model swimmers in confining geometries.

cond-mat.soft↗

arXiv2015

The influence of charged-induced variations in the local permittivity on the static and dynamic properties of polyelectrolyte solutions

There is a large body of literature investigating the static and dynamic properties of polyelectrolytes due both to their widespread application in industrial processes and their ubiquitous presence in biology. Because of their highly charged nature, polyelectrolytes tend to alter the local dielectric permittivity of the solution within a few nanometers of their backbone. This effect has, however, been almost entirely ignored in both simulations and theoretical work. In this article we apply our recently developed electrostatic solver based on Maxwell's equations to examine the effects of the permittivity reduction in the vicinity of the polyelectrolyte. We first verify our new approach by calculating and comparing ion distributions around a linear fixed polyelectrolyte and find both quantitative and qualitative changes in the ion distribution. Further simulations with an applied electric field show that the reduction in the local dielectric constant increases the mobility of the chains by approximately ten percent. More importantly, variations in the local dielectric constant lead to qualitatively different behavior of the conductivity.

cond-mat.soft↗

arXiv2015

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 [V. Lobaskin and B. 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 the 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 [J. de Graaf, et al., J. Chem. Phys. 143, 084107 (2015)], wherein we consider the raspberry model in the confining geometry of two parallel plates.

cond-mat.soft↗

arXiv2015

Importance of Varying Permittivity on the Conductivity of Polyelectrolyte Solutions

Dissolved ions can alter the local permittivity of water, nevertheless most theories and simulations ignore this fact. We present a novel algorithm for treating spatial and temporal variations in the permittivity and use it to measure the equivalent conductivity of a salt-free polyelectrolyte solution. Our new approach quantitatively reproduces experimental results unlike simulations with a constant permittivity that even qualitatively fail to describe the data. We can relate this success to a change in the ion distribution close to the polymer due to the built-up of a permittivity gradient.

cond-mat.soft↗

arXiv2015

Towards a scale-bridging description of ferrogels and magnetic elastomers

Ferrogels and magnetic elastomers differentiate themselves from other materials by their unique capability of reversibly changing shape and mechanical properties under the influence of an external magnetic field. A crucial issue in the study of these outstanding materials is the interaction between the mesoscopic magnetic particles and the polymer matrix in which they are embedded. Here we analyze interactions between two such particles connected by a polymer chain, a situation representative for particle-crosslinked magnetic gels. To make a first step towards a scale-bridging description of the materials, effective potentials for mesoscopic configurational changes are specified using microscopic input obtained from simulations. Furthermore, the impact of the presence of magnetic interactions on the probability distributions and thermodynamic quantities of the system is considered. The resulting mesoscopic model potentials can be used to economically model the system on the particle length scales. This first coarse-graining step is important to realize simplified but realistic scale-bridging models for these promising materials.

cond-mat.soft↗

arXiv2015

Ferrogels cross-linked by magnetic particles: Field-driven deformation and elasticity studied using computer simulations

Ferrogels, i.e. swollen polymer networks into which magnetic particles are immersed, can be considered as "smart materials" since their shape and elasticity can be controlled by an external magnetic field. Using molecular dynamics simulations on the coarse-grained level we study a ferrogel in which the magnetic particles act as the cross-linkers of the polymer network. In a homogeneous external magnetic field the direct coupling between the orientation of the magnetic moments and the polymers by means of covalent bonds gives rise to a deformation of the gel, independent of the interparticle dipole-dipole interaction. In this paper we report quantitative measurements of this deformation, the gel's elastic moduli and its magnetic response. Our results demonstrate that these properties depend significantly on the topology of the polymer network.

physics.chem-ph↗

arXiv2015

Buckling of paramagnetic chains in soft gels

We study the magneto-elastic coupling behavior of paramagnetic chains in soft polymer gels exposed to external magnetic fields. To this end, a laser scanning confocal microscope is used to observe the morphology of the paramagnetic chains together with the deformation field of the surrounding gel network. The paramagnetic chains in soft polymer gels show rich morphological shape changes under oblique magnetic fields, in particular a pronounced buckling deformation. The details of the resulting morphological shapes depend on the length of the chain, the strength of the external magnetic field, and the modulus of the gel. Based on the observation that the magnetic chains are strongly coupled to the surrounding polymer network, a simplified model is developed to describe their buckling behavior. A coarse-grained molecular dynamics simulation model featuring an increased matrix stiffness on the surfaces of the particles leads to morphologies in agreement with the experimentally observed buckling effects.

cond-mat.soft↗