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.

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.

Facilitated diffusion on confined DNA.

In living cells, proteins combine three-dimensional bulk diffusion and one-dimensional sliding along the DNA to reach a target faster. This process is known as facilitated diffusion and we investigate its dynamics in the physiologically relevant case of confined DNA. The confining geometry and DNA elasticity are key parameters: We find that facilitated diffusion is most efficient inside an isotropic volume and on a flexible polymer. By considering the typical copy numbers of proteins in vivo, we show that the speedup due to sliding becomes insensitive to fine tuning of parameters, rendering facilitated diffusion a robust mechanism to speed up intracellular diffusion-limited reactions. The parameter range we focus on is relevant for in vitro systems and for facilitated diffusion on yeast chromatin.