arXiv subjects

K. Stratford

Publications and source records attributed to K. Stratford.

At least 19 recordsLinked to original sources

arXiv2021

dlmontepython: A Python library for automation and analysis of Monte Carlo molecular simulations

We present an open source Python 3 library aimed at practitioners of molecular simulation, especially Monte Carlo simulation. The aims of the library are to facilitate the generation of simulation data for a wide range of problems; and to support data analysis methods which enable one to make the most of previously generated data. The library contains a framework for automating the task of measuring target physical properties (e.g. density) over a range of thermodynamic parameters (e.g. temperature) calculated using a molecular simulation program, in particular the Monte Carlo program DL_MONTE. The library also supports analysis methods including block averaging, equilibration detection and histogram reweighting. Here we describe the library and provide examples to demonstrate its key functionality: we use the library to automatically calculate isotherms to a specified precision; and to calculate the surface tension and liquid-vapour coexistence properties of methane.

physics.comp-ph↗

arXiv2019

Dynamic clustering and re-dispersion in concentrated colloid-active gel composites

We study the dynamics of quasi-two-dimensional concentrated suspensions of colloidal particles in active gels by computer simulations. Remarkably, we find that activity induces a dynamic clustering of colloids even in the absence of any preferential anchoring of the active nematic director at the particle surface. When such an anchoring is present, active stresses instead compete with elastic forces and re-disperse the aggregates observed in passive colloid-liquid crystal composites. Our quasi-two-dimensional "inverse" dispersions of passive particles in active fluids (as opposed to the more common "direct" suspensions of active particles in passive fluids) provide a promising route towards the self-assembly of new soft materials.

cond-mat.soft↗

arXiv2018

Mixtures of blue phase liquid crystal with simple liquids: elastic emulsions and cubic fluid cylinders

We investigate numerically the behaviour of a phase-separating mixture of a blue phase I liquid crystal with an isotropic fluid. The resulting morphology is primarily controlled by an inverse capillary number, $χ$, setting the balance between interfacial and elastic forces. When $χ$ and the concentration of the isotropic component are both low, the blue phase disclination lattice templates a cubic array of fluid cylinders. For larger $χ$, the isotropic phase arranges primarily into liquid emulsion droplets which coarsen very slowly, rewiring the blue phase disclination lines into an amorphous elastic network. Our blue phase/simple fluid composites can be externally manipulated: an electric field can trigger a morphological transition between cubic fluid cylinder phases with different topologies.

cond-mat.soft↗

arXiv2015

Self-assembly of colloid-cholesteric composites provides a possible route to switchable optical materials

Colloidal particles dispersed in liquid crystals can form new materials with tunable elastic and electro-optic properties. In a periodic `blue phase' host, particles should template into colloidal crystals with potential uses in photonics, metamaterials, and transformational optics. Here we show by computer simulation that colloid/cholesteric mixtures can give rise to regular crystals, glasses, percolating gels, isolated clusters, twisted rings and undulating colloidal ropes. This structure can be tuned via particle concentration, and by varying the surface interactions of the cholesteric host with both the particles and confining walls. Many of these new materials are metastable: two or more structures can arise under identical thermodynamic conditions. The observed structure depends not only on the formulation protocol, but also on the history of an applied electric field. This new class of soft materials should thus be relevant to design of switchable, multistable devices for optical technologies such as smart glass and e-paper.

cond-mat.soft↗

arXiv2013

Colloidal templating at a cholesteric - oil interface: Assembly guided by an array of disclination lines

We simulate colloids (radius $R \sim 1μ$m) trapped at the interface between a cholesteric liquid crystal and an immiscible oil, at which the helical order (pitch p) in the bulk conflicts with the orientation induced at the interface, stabilizing an ordered array of disclinations. For weak anchoring strength W of the director field at the colloidal surface, this creates a template, favoring particle positions eitheron top of or midway between defect lines, depending on $α= R/p$. For small $α$, optical microscopy experiments confirm this picture, but for larger $α$ no templating is seen. This may stem from the emergence at moderate W of a rugged energy landscape associated with defect reconnections.

cond-mat.soft↗

arXiv2012

Bulk rheology and microrheology of active fluids

We simulate macroscopic shear experiments in active nematics and compare them with microrheology simulations where a spherical probe particle is dragged through an active fluid. In both cases we define an effective viscosity: in the case of bulk shear simulations this is the ratio between shear stress and shear rate, whereas in the microrheology case it involves the ratio between the friction coefficient and the particle size. We show that this effective viscosity, rather than being solely a property of the active fluid, is affected by the way chosen to measure it, and strongly depends on details such as the anchoring conditions at the probe surface and on both the system size and the size of the probe particle.

cond-mat.soft↗

arXiv2012

Colloids in active fluids: Anomalous micro-rheology and negative drag

We simulate an experiment in which a colloidal probe is pulled through an active nematic fluid. We find that the drag on the particle is non-Stokesian (not proportional to its radius). Strikingly, a large enough particle in contractile fluid (such as an actomyosin gel) can show negative viscous drag in steady state: the particle moves in the opposite direction to the externally applied force. We explain this, and the qualitative trends seen in our simulations, in terms of the disruption of orientational order around the probe particle and the resulting modifications to the active stress.

cond-mat.soft↗

arXiv2012

Rheology of Lamellar Liquid Crystals in Two and Three Dimensions: A Simulation Study

We present large scale computer simulations of the nonlinear bulk rheology of lamellar phases (smectic liquid crystals) at moderate to large values of the shear rate (Peclet numbers 10-100), in both two and three dimensions. In two dimensions we find that modest shear rates align the system and stabilise an almost regular lamellar phase, but high shear rates induce the nucleation and proliferation of defects, which in steady state is balanced by the annihilation of defects of opposite sign. The critical shear rate at onset of this second regime is controlled by thermodynamic and kinetic parameters; we offer a scaling analysis that relates the critical shear rate to a critical "capillary number" involving those variables. Within the defect proliferation regime, the defects may be partially annealed by slowly decreasing the applied shear rate; this causes marked memory effects, and history-dependent rheology. Simulations in three dimensions show instead shear-induced ordering even at the highest shear rates studied here. This suggests that the critical shear rate shifts markedly upward on increasing dimensionality. This may in part reflect the reduced constraints on defect motion, allowing them to find and annihilate each other more easily. Residual edge defects in the 3D aligned state mostly point along the flow velocity, an orientation impossible in two dimensions.

cond-mat.soft↗

arXiv2012

Confined Cubic Blue Phases under Shear

We study the behaviour of confined cubic blue phases under shear flow via lattice Boltzmann simulations. We focus on the two experimentally observed phases, blue phase I and blue phase II. The disinclination network of blue phase II continuously breaks and reforms under shear, leading to an oscillatory stress response in time. The oscillations are only regular for very thin samples. For thicker samples, the shear leads to a "stick-slip" motion of part of the network along the vorticity direction. Blue phase I responds very differently: its defect network undergoes seemingly chaotic rearrangements under shear, irrespective of system size.

cond-mat.soft↗

arXiv2012

Self-Assembly and Nonlinear Dynamics of Dimeric Colloidal Rotors in Cholesterics

We study by simulation the physics of two colloidal particles in a cholesteric liquid crystal with tangential order parameter alignment at the particle surface. The effective force between the pair is attractive at short range and favors assembly of colloid dimers at specific orientations relative to the local director field. When pulled through the fluid by a constant force along the helical axis, we find that such a dimer rotates, either continuously or stepwise with phase-slip events. These cases are separated by a sharp dynamical transition and lead, respectively, to a constant or an ever-increasing phase lag between the dimer orientation and the local nematic director.

cond-mat.soft↗

arXiv2011

On the structure of blue phase III

We report large scale simulations of the blue phases of cholesteric liquid crystals. Our results suggest a structure for blue phase III, the blue fog, which has been the subject of a long debate in liquid crystal physics. We propose that blue phase III is an amorphous network of disclination lines, which is thermodynamically and kinetically stabilised over crystalline blue phases at intermediate chiralities}. This amorphous network becomes ordered under an applied electric field, as seen in experiments.

cond-mat.soft↗

arXiv2011

The MOLDY short-range molecular dynamics package

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy.

cond-mat.mtrl-sci↗

arXiv2011

Colloids in liquid crystals: a lattice Boltzmann study

We propose a hybrid lattice Boltzmann algorithm to simulate the hydrodynamics of colloidal particles inside a liquid crystalline host. To validate our algorithm, we study the static and the microrheology of a colloid in a nematic, with tangential anchoring of the director field at the particle surface, and we confirm theories and experiments showing that the drag force in a nematic is markedly anisotropic. We then apply our method to consider the case of a colloid inside a cholesteric, and with normal anchoring at the surface. We show that by tuning the ratio between particle size and cholesteric pitch it is possible to control the defect configuration around the particle, and to stabilise novel figure-of-eight or highly twisted loops close to the colloid surface.

cond-mat.soft↗

arXiv2011

Bijels Containing Magnetic Particles: A Simulation Study

Bicontinuous, interfacially jammed emulsion gels (bijels) represent a class of soft solid materials in which interpenetrating domains of two immiscible fluids are stabilized by an interfacial colloidal monolayer. Such structures can be formed by arrested spinodal decomposition from an initially single-phase colloidal suspension. Here we explore by lattice Boltzmann simulation the possible effects of using magnetic colloids in bijels. This may allow additional control over the structure, during or after formation, by application of a magnetic field or field gradient. These effects are modest for typical parameters based on the magnetic nanoparticles used in conventional ferrofluids, although significantly larger particles might be appropriate here. Field gradient effects, which are cumulative across a sample, could then allow a route for controlled breakdown of bijels as they do for particle-stabilized droplet emulsions.

cond-mat.soft↗

arXiv2011

Colloids in Cholesterics: Size-Dependent Defects and Non-Stokesian Microrheology

We simulate a colloidal particle (radius R) in a cholesteric liquid crystal (pitch p) with tangential order parameter alignment at the particle surface. The local defect structure evolves from a dipolar pair of surface defects (boojums) at small R/p to a pair of twisted disclination lines wrapping around the particle at larger values. On dragging the colloid with small velocity v through the medium along the cholesteric helix axis (an active microrheology measurement), we find a hydrodynamic drag force that scales linearly with v but superlinearly with R-in striking violation of Stokes' law, as generally used to interpret such measurements.

cond-mat.soft↗

arXiv2010

Lattice Boltzmann simulations of liquid crystalline fluids: active gels and blue phases

Lattice Boltzmann simulations have become a method of choice to solve the hydrodynamic equations of motion of a number of complex fluids. Here we review some recent applications of lattice Boltzmann to study the hydrodynamics of liquid crystalline materials. In particular, we focus on the study of (a) the exotic blue phases of cholesteric liquid crystals, and (b) active gels - a model system for actin plus myosin solutions or bacterial suspensions. In both cases lattice Boltzmann studies have proved useful to provide new insights into these complex materials.

cond-mat.soft↗

arXiv2010

Ordering dynamics of blue phases entails kinetic stabilization of amorphous networks

The cubic blue phases of liquid crystals are fascinating and technologically promising examples of hierarchically structured soft materials, comprising ordered networks of defect lines (disclinations) within a liquid crystalline matrix. We present the first large-scale simulations of their domain growth, starting from a blue phase nucleus within a supercooled isotropic or cholesteric background. The nucleated phase is thermodynamically stable; one expects its slow orderly growth, creating a bulk cubic. Instead, we find that the strong propensity to form disclinations drives the rapid disorderly growth of a metastable amorphous defect network. During this process the original nucleus is destroyed; re-emergence of the stable phase may therefore require a second nucleation step. Our findings suggest that blue phases exhibit hierarchical behavior in their ordering dynamics, to match that in their structure.

cond-mat.soft↗

arXiv2010

Thermodynamics of Blue Phases In Electric Fields

We present extensive numerical studies to determine the phase diagrams of cubic and hexagonal blue phases in an electric field. We confirm the earlier prediction that hexagonal phases, both 2 and 3 dimensional, are stabilized by a field, but we significantly refine the phase boundaries, which were previously estimated by means of a semi-analytical approximation. In particular, our simulations show that the blue phase I -- blue phase II transition at fixed chirality is largely unaffected by electric field, as observed experimentally.

cond-mat.soft↗