Effective run-and-tumble dynamics of bacteria baths

{\it E. coli} bacteria swim in straight runs interrupted by sudden reorientation events called tumbles. The resulting random walks give rise to density fluctuations that can be derived analytically in the limit of non interacting particles or equivalently of very low concentrations. However, in situations of practical interest, the concentration of bacteria is always large enough to make interactions an important factor. Using molecular dynamics simulations, we study the dynamic structure factor of a model bacterial bath for increasing values of densities. We show that it is possible to reproduce the dynamics of density fluctuations in the system using a free run-and-tumble model with effective fitting parameters. We discuss the dependence of these parameters, e.g., the tumbling rate, tumbling time and self-propulsion velocity, on the density of the bath

Directed transport of active particles over asymmetric energy barriers

We theoretically and numerically investigate the transport of active colloids to target regions, delimited by asymmetric energy barriers. We show that it is possible to introduce a generalized effective temperature that is related to the local variance of particle velocities. The stationary probability distributions can be derived from a simple diffusion equation in the presence of an inhomogeneous effective temperature resulting from the action of external force fields. In particular, transitions rates over asymmetric energy barriers can be unbalanced by having different effective temperatures over the two slopes of the barrier. By varying the type of active noise, we find that equal values of diffusivity and persistence time may produce strongly varied effective temperatures and thus stationary distributions

Aging under Shear: Structural Relaxation of a Non-Newtonian Fluid

The influence of an applied shear field on the dynamics of an aging colloidal suspension has been investigated by the dynamic light scattering determination of the density autocorrelation function. Though a stationary state is never observed, the slow dynamics crosses between two different non-equilibrium regimes as soon as the structural relaxation time approaches the inverse shear rate. In the shear dominated regime (at high shear rate values) the structural relaxation time is found to be strongly sensitive to shear rate while aging proceeds at a very slow rate. The effect of shear on the detailed shape of the density autocorrelation function is quantitatively described assuming that the structural relaxation process arises from the heterogeneous superposition of many relaxing units each one independently coupled to shear with a parallel composition rule for timescales.Comment: 5 pages, 5 figure

Run-and-tumble particles in speckle fields

The random energy landscapes developed by speckle fields can be used to confine and manipulate a large number of micro-particles with a single laser beam. By means of molecular dynamics simulations, we investigate the static and dynamic properties of an active suspension of swimming bacteria embedded into speckle patterns. Looking at the correlation of the density fluctuations and the equilibrium density profiles, we observe a crossover phenomenon when the forces exerted by the speckles are equal to the bacteria's propulsion

Polar features in the flagellar propulsion of E. coli bacteria

E. coli bacteria swim following a run and tumble pattern. In the run state all flagella join in a single helical bundle that propels the cell body along approximately straight paths. When one or more flagellar motors reverse direction the bundle unwinds and the cell randomizes its orientation. This basic picture represents an idealization of a much more complex dynamical problem. Although it has been shown that bundle formation can occur at either pole of the cell, it is still unclear whether this two run states correspond to asymmetric propulsion features. Using holographic microscopy we record the 3D motions of individual bacteria swimming in optical traps. We find that most cells possess two run states characterised by different propulsion forces, total torque and bundle conformations. We analyse the statistical properties of bundle reversal and compare the hydrodynamic features of forward and backward running states. Our method is naturally multi-particle and opens up the way towards controlled hydrodynamic studies of interacting swimming cells

Quasi-saddles as relevant points of the potential energy surface in the dynamics of supercooled liquids

The supercooled dynamics of a Lennard-Jones model liquid is numerically investigated studying relevant points of the potential energy surface, i.e. the minima of the square gradient of total potential energy $V$. The main findings are: ({\it i}) the number of negative curvatures $n$ of these sampled points appears to extrapolate to zero at the mode coupling critical temperature $T_c$; ({\it ii}) the temperature behavior of $n(T)$ has a close relationship with the temperature behavior of the diffusivity; ({\it iii}) the potential energy landscape shows an high regularity in the distances among the relevant points and in their energy location. Finally we discuss a model of the landscape, previously introduced by Madan and Keyes [J. Chem. Phys. {\bf 98}, 3342 (1993)], able to reproduce the previous findings.Comment: To be published in J. Chem. Phy

Holographic tracking and sizing of optically trapped microprobes in diamond anvil cells

We demonstrate that Digital Holographic Microscopy can be used for accurate 3D tracking and sizing of a colloidal probe trapped in a diamond anvil cell (DAC). Polystyrene beads were optically trapped in water up to Gigapascal pressures while simultaneously recording in-line holograms at 1 KHz frame rate. Using Lorenz-Mie scattering theory to fit interference patterns, we detected a 10% shrinking in the bead’s radius due to the high applied pressure. Accurate bead sizing is crucial for obtaining reliable viscosity measurements and provides a convenient optical tool for the determination of the bulk modulus of probe material. Our technique may provide a new method for pressure measurements inside a DAC

First-passage time of run-and-tumble particles

We solve the problem of first-passage time for run-and-tumble particles in one dimension. Exact expression is derived for the mean first-passage time in the general case, considering external force-fields and chemotactic-fields, giving rise to space dependent swim-speed and tumble rate. Agreement between theoretical formulae and numerical simulations is obtained in the analyzed case studies -- constant and sinusoidal force fields, constant gradient chemotactic field. Reported findings can be useful to get insights into very different phenomena involving active particles, such as bacterial motion in external fields, intracellular transport, cell migration, animal foraging