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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, $\chi$, setting the balance between interfacial and elastic forces. When $\chi$ and the concentration of the isotropic component are both low, the blue phase disclination lattice templates a cubic array of fluid cylinders. For larger $\chi$, 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., Comment: 7 pages, 4 figures; contains Supplementary Material as Appendix. Supplementary Movies Movies can be found at https://www2.ph.ed.ac.uk/~dmarendu/BPMixtureSM.html

We report the exfoliation of layered Na2Ti3O7, a promising anode material for Na-ion batteries, and restacking using HNO3 and NaOH to form H-Ti3O7 and Na(x)-Ti3O7 compositions, respectively. The materials were characterised by a range of techniques (SEM, TEM, solid-state NMR, XRD, PDF). Although the formation of aggregated nanoparticles is favoured under acidic restacking conditions, the use of basic conditions can lead to control over the adherence between the exfoliated layers. Pair distribution function (PDF) analysis confirms that the local TiO6 connectivity of the pristine material is maintained. The lowest sodium-containing Na(1)-Ti3O7 phase, which is the stable product upon Na+ leaching after consecutive washing steps, displays the best performance among the compositions studied, affording a stable reversible capacity of about 200 mAh/g for 20 cycles at a C/20 rate. Washing removes the excess of free/reactive Na+, which otherwise forms inactive Na2CO3 in the insufficiently-washed compositions.

DL_MONTE is an open source, general-purpose software package for performing Monte Carlo simulations. It includes a wide variety of force fields and MC techniques, and thus is applicable to a broad range of problems in molecular simulation. Here we provide an overview of DL_MONTE, focusing on key features recently added to the package. These include the ability to treat systems confined to a planar pore (i.e. `slit' or `slab' boundary conditions); the lattice-switch Monte Carlo (LSMC) method for evaluating precise free energy differences between competing polymorphs; various commonly-used methods for evaluating free energy profiles along transition pathways (including umbrella sampling, Wang-Landau and transition matrix); and a supplementary Python toolkit for simulation management and application of the histogram reweighting analysis method. We provide two `real world' examples to elucidate the use of these methods in DL_MONTE. In particular, we apply umbrella sampling to calculate the free energy profile associated with the translocation of a lipid through a bilayer. Moreover we employ LSMC to examine the thermodynamic stability of two plastic crystal phases of water at high pressure. Beyond this, we provide instructions on how to access DL_MONTE, and point to additional information valuable to existing and prospective users.

We present a study of the hydrodynamics of an active particle, a model squirmer, in an envi- ronment with a broken rotational symmetry: a nematic liquid crystal. By combining simulations with analytic calculations, we show that the hydrodynamic coupling between the squirmer flow field and liquid crystalline director can lead to re-orientation of the swimmers. The preferred orientation depends on the exact details of the squirmer flow field. In a steady state, pushers are shown to swim parallel with the nematic director while pullers swim perpendicular to the nematic director. This behaviour arises solely from hydrodynamic coupling between the squirmer flow field and anisotropic viscosities of the host fluid. Our results suggest that an anisotropic swimming medium can be used to characterise and guide spherical microswimmers in the bulk., Comment: 10 (6 + 4) pages, 5 figures

Leading HPC systems achieve their status through use of highly parallel devices such as NVIDIA GPUs or Intel Xeon Phi many-core CPUs. The concept of performance portability across such architectures, as well as traditional CPUs, is vital for the application programmer. In this paper we describe targetDP, a lightweight abstraction layer which allows grid-based applications to target data parallel hardware in a platform agnostic manner. We demonstrate the effectiveness of our pragmatic approach by presenting performance results for a complex fluid application (with which the model was co-designed), plus a separate lattice QCD particle physics code. For each application, a single source code base is seen to achieve portable performance, as assessed within the context of the Roofline model. TargetDP can be combined with MPI to allow use on systems containing multiple nodes: we demonstrate this through provision of scaling results on traditional and GPU-accelerated large scale supercomputers., Comment: 11 pages, 5 figures, accepted to the International Journal of High Performance Computing Applications (IJHPCA), acceptance date 27th October 2016

We present a lattice Boltzmann study of the hydrodynamics of a fully resolved squirmer, radius R, confined in a slab of fluid between two no-slip walls. We show that the coupling between hydrodynamics and short-range repulsive interactions between the swimmer and the surface can lead to hydrodynamic trapping of both pushers and pullers at the wall, and to hydrodynamic oscillations in the case of a pusher. We further show that a pusher moves significantly faster when close to a surface than in the bulk, whereas a puller undergoes a transition between fast motion and a dynamical standstill according to the range of the repulsive interaction. Our results critically require near-field hydrodynamics; they further suggest that it should be possible to control density and speed of squirmers at a surface by tuning the range of steric and electrostatic swimmer-wall interactions., Comment: 5 + 8 pages, 4 + 4 Figures

We show that the plastic deformation of snow under uniaxial compression is characterized by complex spatio-temporal strain localization phenomena. Deformation is characterized by repeated nucleation and propagation of compaction bands. Compaction bands are also observed during the very first stage of compression of solid foams where a single band moves across the sample at approximately constant stress. However, snow differs from these materials as repeated nucleation and propagation of bands occurs throughout the subsequent hardening stage until the end of the deformation experiment. Band nucleation and/or reflection of bands at the sample boundaries are accompanied by stress drops which punctuate the stress strain curve. A constitutive model is proposed which quantitatively reproduces all features of this oscillatory deformation mode. To this end, a well-established compressive plasticity framework for solid foams is generalized to account for shear softening behavior, time dependence of microstructure (`rapid sintering') and non-locality of damage processes in snow.

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., Comment: Manuscript with 3 figures plus supporting text and figures

To achieve high performance on modern computers, it is vital to map algorithmic parallelism to that inherent in the hardware. From an application developer's perspective, it is also important that code can be maintained in a portable manner across a range of hardware. Here we present targetDP (target Data Parallel), a lightweight programming layer that allows the abstraction of data parallelism for applications that employ structured grids. A single source code may be used to target both thread level parallelism (TLP) and instruction level parallelism (ILP) on either SIMD multi-core CPUs or GPU-accelerated platforms. targetDP is implemented via standard C preprocessor macros and library functions, can be added to existing applications incrementally, and can be combined with higher-level paradigms such as MPI. We present CPU and GPU performance results for a benchmark taken from the lattice Boltzmann application that motivated this work. These demonstrate not only performance portability, but also the optimisation resulting from the intelligent exposure of ILP., Comment: 4 pages, 1 figure, to appear in proceedings of HPCC 2014 conference

We simulate colloids (radius $R \sim 1\mu$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 $\alpha = R/p$. For small $\alpha$, optical microscopy experiments confirm this picture, but for larger $\alpha$ no templating is seen. This may stem from the emergence at moderate W of a rugged energy landscape associated with defect reconnections., Comment: 5 pages, 4 figures

We study the behaviour of cubic blue phases under shear flow via lattice Boltzmann simulations. We focus on the two experimentally observed phases, Blue Phase I (BPI) and Blue Phase II (BPII). The disclination network of Blue Phase II continuously breaks and reforms under steady shear, leading to an oscillatory stress response in time. For larger shear rates, the structure breaks up into a Grandjean texture with a cholesteric helix lying along the flow gradient direction. Blue Phase I leads to a very different response. Here, oscillations are only possible for intermediate shear rates -- very slow flow causes a transition of the initially ordered structure into an amorphous network with an apparent yield stress. Larger shear rates lead to another amorphous state with different structure of the defect network. For even larger flow rates the same break-up into a Grandjean texture as for Blue Phase II is observed. At the highest imposed flow rates both cubic blue phases adopt a flow-aligned nematic state. Our results provide the first theoretical investigation of sheared blue phases in large systems, and are relevant to understanding the bulk rheology of these materials.

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., Comment: 12 pages, 10 figures

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., Comment: 5 pages, 3 figures

We simulate the response of a particle-stabilized emulsion droplet in an external force field, such as gravity, acting equally on all $N$ particles. We show that the field strength required for breakup (at fixed initial area fraction) decreases markedly with droplet size, because the forces act cumulatively, not individually, to detach the interfacial particles. The breakup mode involves the collective destabilization of a solidified particle raft occupying the lower part of the droplet, leading to a critical force per particle that scales approximately as $N^{-1/2}$., Comment: 4 pages, plus 3 pages of supplementary material

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., Comment: 4 + 5 pages

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., Comment: 18 pages, 12 figures

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., Comment: 10 pages, 5 figures, to be published in J. Phys. Condens. Matter (2012)

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., Comment: 9 pages, 6 figures

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.

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., Comment: 7 pages, 5 figures

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.

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., Comment: 4 pages, 4 figures