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.

A growing bacterial colony in two dimensions as an active nematic

How a single bacterium becomes a colony of many thousand cells is important in biomedicine and food safety. Much is known about the molecular and genetic bases of this process, but less about the underlying physical mechanisms. Here we study the growth of single-layer micro-colonies of rod-shaped Escherichiacoli bacteria confined to just under the surface of soft agarose by a glass slide. Analysing this system as a liquid crystal, we find that growth-induced activity fragments the colony into microdomains of well-defined size, whilst the associated flow orients it tangentially at the boundary. Topological defect pairs with charges \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\pm {\textstyle{1 \over 2}}$$\end{document}±12 are produced at a constant rate, with the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$+ {\textstyle{1 \over 2}}$$\end{document}+12 defects being propelled to the periphery. Theoretical modelling suggests that these phenomena have different physical origins from similar observations in other extensile active nematics, and a growing bacterial colony belongs to a new universality class, with features reminiscent of the expanding universe.

Rod-shaped bacteria are an example of active matter. Here the authors find that a growing bacterial colony harbours internal cellular flows affecting orientational ordering in its interior and at the boundary. Results suggest this system may belong to a new active matter universality class.

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.

Entropic elasticity and dynamics of the bacterial chromosome: A simulation study

We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the compressional elasticity of the bacterial nucleoid (DNA plus associated proteins), where DNA is confined into a cylindrical container and subjected to the action of a "piston"-a spherical bead to which an external force is applied. We quantify the effect of steric interactions (excluded volume) on the force-extension curves as the polymer is compressed. We find that non-DNA-binding proteins, even at low densities, exert an osmotic force which can be a lot larger than the entropic force exerted by the compressed DNA. The trends we observe are qualitatively robust with respect to changes in protein sizes and are similar for neutral and charged proteins (and DNA). We also quantify the dynamics of DNA expansion following removal of the "piston": while the expansion is well fitted by power laws, the apparent exponent depends on protein concentration and protein-DNA interaction in a significant way. We further highlight an interesting kinetic process which we observe during the expansion of DNA interacting with DNA-binding proteins when the interaction strength is intermediate: the proteins bind while the DNA is packaged by the compression force, but they "pop-off" one-by-one as the force is removed, leading to a slow unzipping kinetics. Finally, we quantify the importance of supercoiling, which is an important feature of bacterial DNA in vivo.

Boundaries Control Collective Dynamics of Inertial Self-Propelled Robots

Simple ingredients, such as well-defined interactions and couplings for the velocity and orientation of self-propelled objects, are sufficient to produce complex collective behavior in assemblies of such entities. Here, we use assemblies of rodlike robots made motile through self-vibration. When confined in circular arenas, dilute assemblies of these rods act as a gas. Increasing the surface fraction leads to a collective behavior near the boundaries: polar clusters emerge while, in the bulk, gaslike behavior is retained. The coexistence between a gas and surface clusters is a direct consequence of inertial effects as shown by our simulations. A theoretical model, based on surface mediated transport accounts for this coexistence and illustrates the exact role of the boundaries. Our study paves the way towards the control of collective behavior: By using deformable but free to move arenas, we demonstrate that the surface induced clusters can lead to directed motion, while the topology of the surface states can be controlled by biasing the motility of the particles.

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.

Switching hydrodynamics in liquid crystal devices: a simulation perspective

In liquid crystal devices it is important to understand the physics underlying their switching between different states, which is usually achieved by applying or removing an electric field. Flow is known to be a key determinant of the timescales and pathways of the switching kinetics. Incorporating hydrodynamic effects into theories for liquid crystal devices is therefore important; however this is also highly non-trivial, and typically requires the use of accurate numerical methods. Here, we review some recent advances in our theoretical understanding of the dynamics of switching in liquid crystal devices, mainly gained through computer simulations. These results, as we shall show, uncover interesting new physics, and may be important for future applications.

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.

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.

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.

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.

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.