arXiv subjects

Joost de Graaf

Publications and source records attributed to Joost de Graaf.

51 records · Page 3Linked to original sources

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.

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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.

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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.

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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.

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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.

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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.

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arXiv2015

Diffusiophoretic Self-Propulsion for Partially Catalytic Spherical Colloids

Colloidal spheres with a partial platinum surface coating perform auto-phoretic motion when suspended in hydrogen peroxide solution. We present a theoretical analysis of the self-propulsion velocity of these particles using a continuum multi-component, self-diffusiophoretic model. With this model as a basis, we show how the slip-layer approximation can be derived and in which limits it holds. First, we consider the differences between the full multi-component model and the slip-layer approximation. Then the slip model is used to demonstrate and explore the sensitive nature of the particle's velocity on the details of the molecule-surface interaction. We find a strong asymmetry in the dependence of the colloid's velocity as a function of the level of catalytic coating, when there is a different interaction between the solute and solvent molecules and the inert and catalytic part of the colloid, respectively. The direction of motion can even be reversed by varying the level of the catalytic coating. Finally, we investigate the robustness of these results with respect to variations in the reaction rate near the edge between the catalytic and inert parts of the particle. Our results are of significant interest to the interpretation of experimental results on the motion of self-propelled particles.

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arXiv2014

Phase Behavior of a Family of Truncated Hard Cubes

In continuation of our work in [A.P. Gantapara et al., Phys. Rev. Lett. 111, 015501 (2013)], we investigate here the thermodynamic phase behavior of a family of truncated hard cubes, for which the shape evolves smoothly from a cube via a cuboctahedron to an octahedron. We used Monte Carlo simulations and free-energy calculations to establish the full phase diagram. This phase diagram exhibits a remarkable richness in crystal and mesophase structures, depending sensitively on the precise particle shape. In addition, we examined in detail the nature of the plastic crystal (rotator) phases that appear for intermediate densities and levels of truncation. Our results allow us to probe the relation between phase behavior and building-block shape and to further the understanding of rotator phases. Furthermore, the phase diagram presented here should prove instrumental for guiding future experimental studies on similarly-haped nanoparticles and the creation of new materials.

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arXiv2012

Electrostatic Interactions between Janus Particles

In this paper we study the electrostatic properties of `Janus' spheres with unequal charge densities on both hemispheres. We introduce a method to compare primitive-model Monte Carlo simulations of the ionic double layer with predictions of (mean-field) nonlinear Poisson-Boltzmann theory. We also derive practical DLVO-like expressions that describe the Janus-particle pair interactions by mean-field theory. Using a large set of parameters, we are able to probe the range of validity of the Poisson-Boltzmann approximation, and thus of DLVO-like theories, for such particles. For homogeneously charged spheres this range corresponds well to the range that was predicted by field-theoretical studies of homogeneously charged flat surfaces. Moreover, we find similar ranges for colloids with a Janus-type charge distribution. The techniques and parameters we introduce show promise for future studies of an even wider class of charged-patterned particles.

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arXiv2012

Phase diagram of colloidal hard superballs: from cubes via spheres to octahedra

The phase diagram of colloidal hard superballs, of which the shape interpolates between cubes and octahedra via spheres, is determined by free-energy calculations in Monte Carlo simulations. We discover not only a stable face-centered cubic (fcc) plastic crystal phase for near-spherical particles, but also a stable body-centered cubic (bcc) plastic crystal close to the octahedron shape, and in fact even coexistence of these two plastic crystals with a substantial density gap. The plastic fcc and bcc crystals are, however, unstable in the cube and octahedron limit, suggesting that the rounded corners of superballs play an important role in stablizing the rotator phases. In addition, we observe a two-step melting phenomenon for hard octahedra, in which the Minkowski crystal melts into a metastable bcc plastic crystal before melting into the fluid phase.

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arXiv2011

Dense Regular Packings of Irregular Non-Convex Particles

We present a new numerical scheme to study systems of non-convex, irregular, and punctured particles in an efficient manner. We employ this method to analyze regular packings of odd-shaped bodies, not only from a nanoparticle but also both from a computational geometry perspective. Besides determining close-packed structures for many shapes, we also discover a new denser configuration for Truncated Tetrahedra. Moreover, we consider recently synthesized nanoparticles and colloids, where we focus on the excluded volume interactions, to show the applicability of our method in the investigation of their crystal structures and phase behavior. Extensions to the presented scheme include the incorporation of soft particle-particle interactions, the study of quasicrystalline systems, and random packings.

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arXiv2009

A Triangular Tessellation Scheme for the Adsorption Free Energy at the Liquid-Liquid Interface: Towards Non-Convex Patterned Colloids

We introduce a new numerical technique, namely triangular tessellation, to calculate the free energy associated with the adsorption of a colloidal particle at a flat interface. The theory and numerical scheme presented here are sufficiently general to handle non-convex patchy colloids with arbitrary surface patterns characterized by a wetting angle, e.g., amphiphilicity. We ignore interfacial deformation due to capillary, electrostatic, or gravitational forces, but the method can be extended to take such effects into account. It is verified that the numerical method presented is accurate and sufficiently stable to be applied to more general situations than presented in this paper. The merits of the tessellation method prove to outweigh those of traditionally used semi-analytic approaches, especially when it comes to generality and applicability.

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arXiv2008

Stability of additive-free water-in-oil emulsions

We calculate ion distributions near a planar oil-water interface within non-linear Poisson-Boltzmann theory, taking into account the Born self-energy of the ions in the two media. For unequal self-energies of cations and anions, a spontaneous charge separation is found such that the water and oil phase become oppositely charged, in slabs with a typical thickness of the Debye screening length in the two media. From the analytical solutions, the corresponding interfacial charge density and the contribution to the interfacial tension is derived, together with an estimate for the Yukawa-potential between two spherical water droplets in oil. The parameter regime is explored where the plasma coupling parameter exceeds the crystallization threshold, i.e. where the droplets are expected to form crystalline structures due to a strong Yukawa repulsion, as recently observed experimentally. Extensions of the theory that we discuss briefly include numerical calculations on spherical water droplets in oil, and analytical calculations of the linear PB-equation for a finite oil-water interfacial width.

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arXiv2008

Curvature dependence of the electrolytic liquid-liquid interfacial tension

The interfacial tension of a liquid droplet surrounded by another liquid in the presence of microscopic ions is studied as a function of the droplet radius. An analytical expression for the interfacial tension is obtained within a linear Poisson-Boltzmann theory and compared with numerical results from non-linear Poisson-Boltzmann theory. The excess liquid-liquid interfacial tension with respect to the pure, salt-free liquid-liquid interfacial tension is found to decompose into a curvature-independent part due to short-ranged interfacial effects and a curvature-dependent electrostatic contribution. Several curvature-dependent regimes of different scaling of the electrostatic excess interfacial tension are identified. Symmetry relations of the interfacial tension upon swapping droplet and bulk liquid are found to hold in the low-curvature limit, which, e.g., lead to a sign change of the excess Tolman length. For some systems a low-curvature expansion up to second order turns out to be applicable if and only if the droplet size exceeds the Debye screening length in the droplet, independent of the Debye length in the bulk.

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arXiv2008

Spontaneous Charging and Crystallization of Water Droplets in Oil

We study the spontaneous charging and the crystallization of spherical micron-sized water-droplets dispersed in oil by numerically solving, within a Poisson-Boltzmann theory in the geometry of a spherical cell, for the density profiles of the cations and anions in the system. We take into account screening, ionic Born self-energy differences between oil and water, and partitioning of ions over the two media. We find that the surface charge density of the droplet as induced by the ion partitioning is significantly affected by the droplet curvature and by the finite density of the droplets. We also find that the salt concentration and the dielectric constant regime in which crystallization of the water droplets is predicted is enhanced substantially compared to results based on the planar oil-water interface, thereby improving quantitative agreement with recent experiments.

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