Active Brownian particles (ABPs) and Run-and-Tumble particles (RTPs) both self-propel at fixed speed $v$ along a body-axis ${bf u}$ that reorients either through slow angular diffusion (ABPs) or sudden complete randomisation (RTPs). We compare the ph
ysics of these two model systems both at microscopic and macroscopic scales. Using exact results for their steady-state distribution in the presence of external potentials, we show that they both admit the same effective equilibrium regime perturbatively that breaks down for stronger external potentials, in a model-dependent way. In the presence of collisional repulsions such particles slow down at high density: their propulsive effort is unchanged, but their average speed along ${bf u}$ becomes $v(rho) < v$. A fruitful avenue is then to construct a mean-field description in which particles are ghost-like and have no collisions, but swim at a variable speed $v$ that is an explicit function or functional of the density $rho$. We give numerical evidence that the recently shown equivalence of the fluctuating hydrodynamics of ABPs and RTPs in this case, which we detail here, extends to microscopic models of ABPs and RTPs interacting with repulsive forces.
In bacteria, regulatory proteins search for a specific DNA binding target via facilitated diffusion: a series of rounds of 3D diffusion in the cytoplasm, and 1D linear diffusion along the DNA contour. Using large scale Brownian dynamics simulations w
e find that each of these steps is affected differently by crowding proteins, which can either be bound to the DNA acting as a road block to the 1D diffusion, or freely diffusing in the cytoplasm. Macromolecular crowding can strongly affect mechanistic features such as the balance between 3D and 1D diffusion, but leads to surprising robustness of the total search time.
Active Brownian particles (ABPs, such as self-phoretic colloids) swim at fixed speed $v$ along a body-axis ${bf u}$ that rotates by slow angular diffusion. Run-and-tumble particles (RTPs, such as motile bacteria) swim with constant $u$ until a random
tumble event suddenly decorrelates the orientation. We show that when the motility parameters depend on density $rho$ but not on ${bf u}$, the coarse-grained fluctuating hydrodynamics of interacting ABPs and RTPs can be mapped onto each other and are thus strictly equivalent. In both cases, a steeply enough decreasing $v(rho)$ causes phase separation in dimensions $d=2,3$, even when no attractive forces act between the particles. This points to a generic role for motility-induced phase separation in active matter. However, we show that the ABP/RTP equivalence does not automatically extend to the more general case of $u$-dependent motilities.
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.
We study a model of self propelled particles exhibiting run and tumble dynamics on lattice. This non-Brownian diffusion is characterised by a random walk with a finite persistence length between changes of direction, and is inspired by the motion of
bacteria such as E. coli. By defining a class of models with multiple species of particle and transmutation between species we can recreate such dynamics. These models admit exact analytical results whilst also forming a counterpart to previous continuum models of run and tumble dynamics. We solve the externally driven non-interacting and zero-rang
We consider self-propelled particles undergoing run-and-tumble dynamics (as exhibited by E. coli) in one dimension. Building on previous analyses at drift-diffusion level for the one-particle density, we add both interactions and noise, enabling disc
ussion of domain formation by self-trapping, and other collective phenomena. Mapping onto detailed-balance systems is possible in certain cases.
We study numerically the rheological properties of a slab of active gel close o the isotropic-nematic transition. The flow behavior shows strong dependence on sample size, boundary conditions, and on the bulk constitutive curve, which, on entering th
e nematic phase, acquires an activity-induced discontinuity at the origin. The precursor of this within the metastable isotropic phase for contractile systems ({em e.g.,} actomyosin gels) gives a viscosity divergence; its counterpart for extensile ({em e.g.,} {em B. subtilis}) suspensions admits instead a shear-banded flow with zero apparent viscosity.
We report hybrid lattice Boltzmann (HLB) simulations of the hydrodynamics of an active nematic liquid crystal sandwiched between confining walls with various anchoring conditions. We confirm the existence of a transition between a passive phase and a
n active phase, in which there is spontaneous flow in the steady state. This transition is attained for sufficiently ``extensile rods, in the case of flow-aligning liquid crystals, and for sufficiently ``contractile ones for flow-tumbling materials. In a quasi-1D geometry, deep in the active phase of flow-aligning materials, our simulations give evidence of hysteresis and history-dependent steady states, as well as of spontaneous banded flow. Flow-tumbling materials, in contrast, re-arrange themselves so that only the two boundary layers flow in steady state. Two-dimensional simulations, with periodic boundary conditions, show additional instabilities, with the spontaneous flow appearing as patterns made up of ``convection rolls. These results demonstrate a remarkable richness (including dependence on anchoring conditions) in the steady-state phase behaviour of active materials, even in the absence of external forcing; they have no counterpart for passive nematics. Our HLB methodology, which combines lattice Boltzmann for momentum transport with a finite difference scheme for the order parameter dynamics, offers a robust and efficient method for probing the complex hydrodynamic behaviour of active nematics.
We present a second-order accurate method to include arbitrary distributions of force densities in the lattice Boltzmann formulation of hydrodynamics. Our method may be used to represent singular force densities arising either from momentum-conservin
g internal forces or from external forces which do not conserve momentum. We validate our method with several examples involving point forces and find excellent agreement with analytical results. A minimal model for dilute sedimenting particles is presented using the method which promises a substantial gain in computational efficiency.
Active liquid crystals or active gels are soft materials which can be physically realised e.g. by preparing a solution of cytoskeletal filaments interacting with molecular motors. We study the hydrodynamics of an active liquid crystal in a slab-like
geometry with various boundary conditions, by solving numerically its equations of motion via lattice Boltzmann simulations. In all cases we find that active liquid crystals can sustain spontaneous flow in steady state contrarily to their passive counterparts, and in agreement with recent theoretical predictions. We further find that conflicting anchoring conditions at the boundaries lead to spontaneous flow for any value of the activity parameter, while with unfrustrated anchoring at all boundaries spontaneous flow only occurs when the activity exceeds a critical threshold. We finally discuss the dynamic pathway leading to steady state in a few selected cases.
