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.

Mixtures of Blue Phase Liquid Crystal with Simple Liquids: Elastic Emulsions and Cubic Fluid Cylinders.

We numerically investigate the behavior 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.

Hydrodynamics Defines the Stable Swimming Direction of Spherical Squirmers in a Nematic Liquid Crystal.

We present a study of the hydrodynamics of an active particle-a model squirmer-in an environment 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 reorientation 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 behavior 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 characterize and guide spherical microswimmers in the bulk.

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.

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

We simulate colloids (radius R ~ 1 µm) 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 a weak anchoring strength W of the director field at the colloidal surface, this creates a template, favoring particle positions either on 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.

Colloids in active fluids: anomalous microrheology 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.

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.

The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models.

Time-dependent light input is an important feature of computational models of the circadian clock. However, publicly available models encoded in standard representations such as the Systems Biology Markup Language (SBML) either do not encode this input or use different mechanisms to do so, which hinders reproducibility of published results as well as model reuse. The authors describe here a numerically continuous function suitable for use in SBML for models of circadian rhythms forced by periodic light-dark cycles. The Input Signal Step Function (ISSF) is broadly applicable to encoding experimental manipulations, such as drug treatments, temperature changes, or inducible transgene expression, which may be transient, periodic, or mixed. It is highly configurable and is able to reproduce a wide range of waveforms. The authors have implemented this function in SBML and demonstrated its ability to modify the behavior of publicly available models to accurately reproduce published results. The implementation of ISSF allows standard simulation software to reproduce specialized circadian protocols, such as the phase-response curve. To facilitate the reuse of this function in public models, the authors have developed software to configure its behavior without any specialist knowledge of SBML. A community-standard approach to represent the inputs that entrain circadian clock models could particularly facilitate research in chronobiology.

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 disclination 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.

Structure of blue phase III of cholesteric liquid crystals.

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 stabilized over crystalline blue phases at intermediate chiralities. This amorphous network becomes ordered under an applied electric field, as seen in experiments.

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.

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 two and three dimensional, are stabilized by a field, but we significantly refine the phase boundaries, which were previously estimated by means of a semianalytical 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.

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.

Arrest of fluid demixing by nanoparticles: a computer simulation study.

We use lattice Boltzmann simulations to investigate the formation of arrested structures upon demixing of a binary solvent containing neutrally wetting colloidal particles. Previous simulations for symmetric fluid quenches pointed to the formation of "bijels": bicontinuous interfacially jammed emulsion gels. These should be created when a glassy monolayer of particles forms at the fluid-fluid interface, arresting further demixing and rigidifying the structure. Experimental work has broadly confirmed this scenario, but it shows that bijels can also be formed in volumetrically asymmetric quenches. Here, we present new simulation results for such quenches, compare these to the symmetric case, and find a crossover to an arrested droplet phase at strong asymmetry. We then make extensive new analyses of the postarrest dynamics in our simulated bijel and droplet structures, on time scales comparable to the Brownian time for colloid motion. Our results suggest that, on these intermediate time scales, the effective activation barrier to ejection of particles from the fluid-fluid interface is smaller by at least 2 orders of magnitude than the corresponding barrier for an isolated particle on a flat interface.

Binary fluids under steady shear in three dimensions.

We simulate by the lattice Boltzmann method the steady shearing of a binary fluid mixture with full hydrodynamics in three dimensions. Contrary to some theoretical scenarios, a dynamical steady state is attained with finite correlation lengths in all three spatial directions. Using large simulations, we obtain at moderately high Reynolds numbers apparent scaling exponents comparable to those found by us previously in two dimensions (2D). However, in 3D there may be a crossover to different behavior at low Reynolds number: accessing this regime requires even larger computational resources than used here.

Nonequilibrium steady states in sheared binary fluids.

We simulate by lattice Boltzmann the steady shearing of a binary fluid mixture undergoing phase separation with full hydrodynamics in two dimensions. Contrary to some theoretical scenarios, a dynamical steady state is attained with finite domain lengths L(x,y) in the directions (x,y) of velocity and velocity gradient. Apparent scaling exponents are estimated as Lx approximately gamma (-2/3) and Ly approximately gamma(-3/4). We discuss the relative roles of diffusivity and hydrodynamics in attaining steady state.

Colloidal jamming at interfaces: a route to fluid-bicontinuous gels.

Colloidal particles or nanoparticles, with equal affinity for two fluids, are known to adsorb irreversibly to the fluid-fluid interface. We present large-scale computer simulations of the demixing of a binary solvent containing such particles. The newly formed interface sequesters the colloidal particles; as the interface coarsens, the particles are forced into close contact by interfacial tension. Coarsening is markedly curtailed, and the jammed colloidal layer seemingly enters a glassy state, creating a multiply connected, solidlike film in three dimensions. The resulting gel contains percolating domains of both fluids, with possible uses as, for example, a microreaction medium.

Physical and computational scaling issues in lattice Boltzmann simulations of binary fluid mixtures.

We describe some scaling issues that arise when using lattice Boltzmann (LB) methods to simulate binary fluid mixtures--both in the presence and absence of colloidal particles. Two types of scaling problem arise: physical and computational. Physical scaling concerns how to relate simulation parameters to those of the real world. To do this effectively requires careful physics, because (in common with other methods) LB cannot fully resolve the hierarchy of length, energy and time-scales that arise in typical flows of complex fluids. Care is needed in deciding what physics to resolve and what to leave unresolved, particularly when colloidal particles are present in one or both of two fluid phases. This influences steering of simulation parameters such as fluid viscosity and interfacial tension. When the physics is anisotropic (for example, in systems under shear) careful adaptation of the geometry of the simulation box may be needed; an example of this, relating to our study of the effect of colloidal particles on the Rayleigh-Plateau instability of a fluid cylinder, is described. The second and closely related set of scaling issues are computational in nature: how do you scale-up simulations to very large lattice sizes? The problem is acute for systems undergoing shear flow. Here one requires a set of blockwise co-moving frames to the fluid, each connected to the next by a Lees-Edwards like boundary condition. These matching planes lead to small numerical errors whose cumulative effects can become severe; strategies for minimizing such effects are discussed.

Intracortical excitation of spiny neurons in layer 4 of cat striate cortex in vitro.

Recordings were made from pairs of neurons in cat striate visual cortex in vitro to study the AMPA-channel-mediated components of intracortical excitatory synaptic connections between layer 4 spiny neurons and between layer 6 and layer 4 spiny neurons. Forty-six of the 72 cells recorded were identified morphologically. They consisted of spiny stellate and pyramidal cells in layer 4, and pyramidal cells in layer 6. Connections between layer 4 excitatory cells involve excitatory postsynaptic potentials (EPSPs) averaging 949 microV, with an average coefficient of variation of 0.21 (n = 30). The synapses operate at very high release probabilities (0.69-0.98). With repetitive stimulation these EPSPs show varying degrees of depression, largely mediated by presynaptic changes in release probability. Four pairs of layer 4 cells were reciprocally connected. The connections from layer 6 to layer 4 involve smaller, more variable EPSPs, with an average amplitude of 214 microV, and average coefficient of variation 0.72 (n = 7). These synapses operate at moderately high release probabilities (0.37-0.56). They show facilitation with repetitive stimulation, mediated largely by presynaptic changes in release probability. One excitatory connection from a layer 4 neuron to a layer 6 pyramidal cell was also detected. Thus, layer 4 spiny neurons receive effective excitation from two intracortical sources that have different synaptic dynamics and are likely to contribute significantly to the temporal properties of these cells in vivo.

Synaptic interactions between smooth and spiny neurones in layer 4 of cat visual cortex in vitro.

1. Dual intracellular recording was used to examine the interactions between neighbouring spiny (excitatory) and smooth (inhibitory) neurones in layer 4 of cat visual cortex in vitro. Synaptic connections were found in seventeen excitatory-inhibitory neurone pairs, along with one inhibitory-inhibitory connection. 2. Fast excitatory inputs onto smooth neurones (basket cells) from spiny cells (spiny stellate or pyramidal cells) (n = 6) produce large excitatory postsynaptic potentials (EPSPs) of up to 4 mV mean amplitude, whereas basket cells evoke slower inhibitory postsynaptic potentials (IPSPs) in their postsynaptic targets (n = 17), of smaller amplitude (up to 1.6 mV at membrane potentials of -60 mV). 3. Both types of PSP appear to be multiquantal, and both may exhibit depression of up to 60 % during short trains of presynaptic spikes. This depression can involve presynaptic and/or postsynaptic factors. 4. One-third (n = 5) of the spiny cell-smooth cell pairs tested were reciprocally connected, and in the one pair for which the suprathreshold interactions were comprehensively investigated, the pattern of basket cell firing was strongly influenced by the activity in the connected excitatory neurone. The basket cell was only effective in inhibiting spiny cell firing when the excitatory neurone was weakly driven.