Dynamics and interactions of Quincke roller clusters: From orbits and flips to excited states

Active matter systems may be characterized by the conversion of energy into active motion, e.g., the self-propulsion of microorganisms. Artificial active colloids form models that exhibit essential properties of more complex biological systems but are amenable to laboratory experiments. While most experimental models consist of spheres, active particles of different shapes are less understood. Furthermore, interactions between these anisotropic active colloids are even less explored. Here, we investigate the motion of active colloidal clusters and the interactions between them. We focus on self-assembled dumbbells and trimers powered by an external dc electric field. For dumbbells, we observe an activity-dependent behavior of spinning, circular, and orbital motions. Moreover, collisions between dumbbells lead to the hierarchical self-assembly of tetramers and hexamers, both of which form rotational excited states. On the other hand, trimers exhibit flipping motion that leads to trajectories reminiscent of a honeycomb lattice.

Correction: Folding kinetics of a polymer

Correction for ‘Folding kinetics of a polymer’ by Štěpán Růžička et al., Phys. Chem. Chem. Phys., 2012, 14, 6044–6053.

Monte Carlo simulation of kinetically slowed down phase separation

Supercooled colloidal or molecular systems at low densities are known to form liquid, crystalline or glassy drops, which may remain isolated for a long time before they aggregate. This paper analyses the properties of this large time window, and how it can be tackled by computer simulation. We use single-particle and virtual move Monte Carlo simulations of short-range attractive spheres which are undercooled to the temperature region, where the spinodal intersects the attractive glass line. We study two different systems and we report the following kinetic behavior. A low-density system is shown to exhibit universal linear growth regimes under single-particle Monte Carlo correlating the growth rate to the local structure. These regimes are suppressed under collective motion, where droplets aggregate into a single large disordered domain. It is shown that the aggregation can be avoided and linear regimes recovered, if long-range repulsion is added to the short-range attraction. The results provide an insight into the behavior of the virtual move algorithm generating cluster moves according to the local forcefields. We show that different choices of maximum Monte Carlo displacement affect the dynamical trajectories but lead to the same kinetically slowed down or arrested states.

Propagating director bend fluctuations in nematic liquid crystals

We show, by molecular simulation, that for a range of standard, coarse-grained, nematic liquid crystal models, the director bend fluctuation is a propagating mode. This is in contrast to the generally accepted picture of nematic hydrodynamics, in which all the director modes (splay, twist, bend, and combinations thereof) are overdamped. By considering the various physical parameters that enter the equations of nematodynamics, we propose an explanation of this effect and conclude that propagating bend fluctuations may be observable in some experimental systems.

Testing the transferability of a coarse-grained model to intrinsically disordered proteins

The coarse-grained PLUM model is shown to capture structural and dimerization behaviour of the intrinsically disordered biomineralisation peptide n16N.

Collective translational and rotational Monte Carlo cluster move for general pairwise interaction

Virtual move Monte Carlo is a cluster algorithm which was originally developed for strongly attractive colloidal, molecular, or atomistic systems in order to both approximate the collective dynamics and avoid sampling of unphysical kinetic traps. In this paper, we present the algorithm in the form, which selects the moving cluster through a wider class of virtual states and which is applicable to general pairwise interactions, including hard-core repulsion. The newly proposed way of selecting the cluster increases the acceptance probability by up to several orders of magnitude, especially for rotational moves. The results have their applications in simulations of systems interacting via anisotropic potentials both to enhance the sampling of the phase space and to approximate the dynamics.

Collective translational and rotational Monte Carlo moves for attractive particles

Virtual move Monte Carlo is a Monte Carlo (MC) cluster algorithm forming clusters via local energy gradients and approximating the collective kinetic or dynamic motion of attractive colloidal particles. We carefully describe, analyze, and test the algorithm. To formally validate the algorithm through highlighting its symmetries, we present alternative and compact ways of selecting and accepting clusters which illustrate the formal use of abstract concepts in the design of biased MC techniques: the superdetailed balance and the early rejection scheme. A brief and comprehensive summary of the algorithms is presented, which makes them accessible without needing to understand the details of the derivation.

Selective adsorption of lattice peptides on patterned surfaces

To study the adsorption of individual peptides in implicit solvent, we propose a version of the Wang-Landau Monte Carlo algorithm that uses a single surface, with no need for a confining wall or grafting. Our "wall-free" method is both more efficient than the traditional ones and free of additional assumptions or approximations. We illustrate it by simulating an HP-model lattice peptide on planar surfaces with a variety of patterns of adsorption sites, discovering a temperature-induced switch of surface selection which is due to a balance of energetic and entropic effects.

Phase diagrams of knotted and unknotted ring polymers

The phase diagram for a lattice ring polymer under applied force, with variable solvent quality, for different topological knot states, is determined for the first time. In addition to eliminating pseudophases where the polymer is flattened into a single layer, it is found that nontrivial knots result in additional pseudophases under tensile force conditions.

Elastic constants of hard thin platelets by Monte Carlo simulation and virial expansion

In this paper we present an investigation into the calculation of the Frank elastic constants of hard platelets via molecular simulation and virial expansion beyond second order. Monte Carlo simulations were carried out and director fluctuations measured as a function of wave vector k, giving the elastic constants through a fit in the low-k limit. Additionally, the virial expansion coefficients of the elastic constants up to sixth order were calculated, and the validity of the theory determined by comparison with the simulation results. The simulation results are also compared with experimental measurements on colloidal suspensions of platelike particles.

Structure and stability of isotropic states of hard platelet fluids

We study the thermodynamics and the pair structure of hard, infinitely thin, circular platelets in the isotropic phase. Monte Carlo simulation results indicate a rich spatial structure of the spherical expansion components of the direct correlation function, including nonmonotonical variation of some of the components with density. Integral equation theory is shown to reproduce the main features observed in simulations. The hypernetted chain closure, as well as its extended versions that include the bridge function up to second and third order in density, perform better than both the Percus-Yevick closure and Verlet bridge function approximation. Using a recent fundamental measure density functional theory, an analytic expression for the direct correlation function is obtained as the sum of the Mayer bond and a term proportional to the density and the intersection length of two platelets. This is shown to give a reasonable estimate of the structure found in simulations, but to fail to capture the nonmonotonic variation with density. We also carry out a density functional stability analysis of the isotropic phase with respect to nematic ordering and show that the limiting density is consistent with that where the Kerr coefficient vanishes. As a reference system, we compare to simulation results for hard oblate spheroids with small, but nonzero elongations, demonstrating that the case of vanishingly thin platelets is approached smoothly.

Tunable-slip boundaries for coarse-grained simulations of fluid flow

On the micro- and nanoscale, classical hydrodynamic boundary conditions such as the no-slip condition no longer apply. Instead, the flow profiles exhibit "slip" at the surface, which is characterized by a finite slip length (partial slip). We present a new, systematic way of implementing partial-slip boundary conditions with arbitrary slip length in coarse-grained computer simulations. The main idea is to represent the complex microscopic interface structure by a spatially varying effective viscous force. An analytical equation for the resulting slip length can be derived for planar and for curved surfaces. The comparison with computer simulations of a DPD (dissipative particle dynamics) fluid shows that this expression is valid from full slip to no slip.

Forces between cylindrical nanoparticles in a liquid crystal

Using classical density functional theory, the forces between two cylindrical nanoparticles in a liquid crystal solvent are calculated. Both the nematic and isotropic phases of the solvent are considered. In the nematic phase, the interaction is highly anisotropic. At short range, changes in the defect structure around the cylinders leads to a complex interaction between them. In the isotropic phase, an attractive interaction arises due to overlap between halos of ordered fluid adsorbed on the surfaces of the cylinders.

Structure of molecular liquids: hard rod-disk mixtures

The structure of hard rod-disk mixtures is studied using Monte Carlo simulations and integral equation theory, for a range of densities in the isotropic phase. By extension of methods used in single component fluids, the pair correlation functions of the molecules are calculated and comparisons between simulation and integral equation theory, using a number of different closure relations, are made. Comparison is also made for thermodynamic data and phase behavior.

Computer simulation of anisotropic polymer brushes

A polymer brush with chains consisting of anisotropic monomers, in a liquid consisting of free spherical particles, is studied by the molecular dynamics method. It is shown that, at some value of the concentration of spheres, a liquid-crystal or oriented-domain transition occurs in the brush. A densely-grafted brush and a sparsely-grafted brush are studied; for this system, the transition point seems not to depend strongly upon the grafting density. In the case of the densely-grafted brush, a liquid-crystal transition proceeds via an intermediate microphase segregated state. One microphase, located near the grafting surface, is characterized by high density and high degree of ordering of monomers. This part of the brush contains only a small concentration of spheres. On the periphery of the brush, a disordered microphase with low monomer density is located. This part of the brush is enriched with spherical particles. The two microphases are separated by a well-defined boundary. On increasing the sphere concentration, the boundary between microphases shifts towards the periphery, and eventually the ordered microphase extends through the whole brush volume. The monomers of the densely-grafted brush in their ordered state form different structures, namely, a smectic structure at relatively low values of sphere concentration, and a structure of orientationally ordered domains at the higher sphere densities.

Liquid-crystal-mediated force between a cylindrical nanoparticle and substrate

Using classical density functional theory, the structure of a molecular fluid around a cylindrical nanoparticle near a solid substrate is studied. The solvent-mediated force between the nanoparticle and the substrate is calculated in both the nematic and isotropic phases of the solvent. In the nematic phase, the force is short ranged and arises due to interaction between high-density regions near the substrate and nanoparticle. In the isotropic phase, the formation of a nematic bridge between the substrate and nanoparticle gives rise to an attractive force between them. The potential between the nanoparticle and substrate as a function of separation calculated numerically is compared to that calculated from the Derjaguin approximation. In the isotropic phase these are found to be in reasonable agreement at low separations, while the agreement is poorer in the nematic phase.

Structure of molecular liquids: closure relations for hard spheroids

We present the results of Monte Carlo simulations of hard spheroids of revolution of different elongations. Both prolate and oblate shapes are examined. A systematic study of the bridge function b(1,2), and direct comparison with the indirect correlation function gamma(1,2)=h(1,2)-c(1,2) at densities spanning the isotropic fluid range, allow us to evaluate the accuracy of various proposed closure relations for integral equations.

Structure of a liquid crystalline fluid around a macroparticle: Density functional theory

The structure of a molecular liquid, in both the nematic liquid crystalline and isotropic phases, around a cylindrical macroparticle, is studied using density functional theory. In the nematic phase the structure of the fluid is highly anisotropic with respect to the director, in agreement with results from simulation and phenomenological theories. On going into the isotropic phase the structure becomes rotationally invariant around the macroparticle with an oriented layer at the surface.

Evaluation of pressure tensor in constant-volume simulations of hard and soft convex bodies

A method for calculating the pressure tensor in constant-volume Monte Carlo simulations of convex bodies is presented. In contrast to other approaches, the method requires only an isotropic scaling of the simulation box and the counting of simple geometric quantities characterizing overlapping pairs. Nonsphericity presents no special difficulties. The result is expressed as a sum of pairwise contributions and can therefore be used to compute pressure tensor profiles in a conventional way.

Structure of molecular liquids: cavity and bridge functions of the hard spheroid fluid

We present methodologies for calculating the direct correlation function c(1,2), the cavity function y(1,2), and the bridge function b(1,2), for molecular liquids, from Monte Carlo simulations. As an example we present results for the isotropic hard spheroid fluid with elongation e = 3. The simulation data are compared with the results from integral equation theory. In particular, we solve the Percus-Yevick and hypernetted chain equations. In addition, we calculate the first two terms in the virial expansion of the bridge function and incorporate this into the closure. At low densities, the bridge functions calculated by theory and from simulation are in good agreement, lending support to the correctness of our numerical procedures. At higher densities, the hypernetted chain results are brought into closer agreement with simulation by incorporating the approximate bridge function, but significant discrepancies remain.

Configurational Temperature in Membrane Simulations Using Dissipative Particle Dynamics

The use of excessively long time steps in dissipative particle dynamics simulations may produce simulation artifacts due to the generation of configurations which are not representative of the desired canonical ensemble. The configurational temperature, among other quantities, may be used to assess the extent of the deviation from equilibrium. This paper presents results for simulations of models of water and lipid bilayer membranes to illustrate the nature of the problems.

Spin dynamics for the Lebwohl-Lasher model

A spin dynamics algorithm, combining checkerboard updating and a rotation algorithm based on the local second-rank ordering field, is developed for the Lebwohl-Lasher model of liquid crystals. The method is shown to conserve energy well and to generate simulation averages that are consistent with those obtained by Monte Carlo simulation. However, care must be taken to avoid the undesirable effects of director rotation, and a method for doing this is proposed.

Forces between elongated particles in a nematic colloid

Using molecular dynamics simulations we study the interactions between elongated colloidal particles (length to breath ratio >>1) in a nematic host. The simulation results are compared to the results of a Landau-de Gennes elastic free energy. We find that depletion forces dominate for the sizes of the colloidal particles studied. The tangential component of the force, however, allows us to resolve the elastic contribution to the total interaction. We find that this contribution differs from the quadrupolar interaction predicted at large separations. The difference is due to the presence of nonlinear effects, namely, the change in the positions and structure of the defects and their annihilation at small separations.

Drag on particles in a nematic suspension by a moving nematic-isotropic interface

We report a clear demonstration of drag on colloidal particles by a moving nematic-isotropic interface. The balance of forces explains our observation of periodic, striplike structures that are produced by the movement of these particles.

Dynamical precursor of nematic order in a dense fluid of hard ellipsoids of revolution

We investigate hard ellipsoids of revolution in a parameter regime where no long range nematic order is present but already finite-size domains are formed which show orientational order. Domain formation leads to a substantial slowing down of a collective rotational mode which separates well from the usual microscopic frequency regime. A dynamic coupling of this particular mode into all other modes provides a general mechanism which explains an excess peak in spectra of molecular fluids. Using molecular dynamics simulation on up to 4096 particles and on solving the molecular mode coupling equation we investigate dynamic properties of the peak and prove its orientational origin.

Defect structures and torque on an elongated colloidal particle immersed in a liquid crystal host

Combining molecular dynamics and Monte Carlo simulation, we study defect structures around an elongated colloidal particle embedded in a nematic liquid crystal host. By studying nematic ordering near the particle and the disclination core region, we are able to examine the defect core structure and the difference between two simulation techniques. In addition, we also study the torque on a particle tilted with respect to the director, and modification of this torque when the particle is close to the cell wall.