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

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

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

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

Partial synchronisation of stochastic oscillators through hydrodynamic coupling

Holographic optical tweezers are used to construct a static bistable optical potential energy landscape where a Brownian particle experiences restoring forces from two nearby optical traps and undergoes thermally activated transitions between the two energy minima. Hydrodynamic coupling between two such systems results in their partial synchronisation. This is interpreted as an emergence of higher mobility pathways, along which it is easier to overcome barriers to structural rearrangement.Comment: 4 pages, 4 figures, submitted to Phys. Rev. Let

Non-dynamic origin of the acoustic attenuation at high frequency in glasses

The sound attenuation in the THz region is studied down to T=16 K in glassy glycerol by inelastic x-ray scattering. At striking variance with the decrease found below 100 K in the GHz data, the attenuation in the THz range does not show any T dependence. This result i) indicates the presence of two different attenuation mechanisms, active respectively in the high and low frequency limits; ii) demonstrates the non-dynamic origin of the attenuation of THz sound waves, and confirms a similar conclusion obtained in SiO2 glass by molecular dynamics; and iii) supports the low frequency attenuation mechanism proposed by Fabian and Allen (Phys.Rev.Lett. 82, 1478 (1999)).Comment: 3 pages, 5 Figures, To be published in PR

A spectroscopic cell for fast pressure jumps across the glass transition line

We present a new experimental protocol for the spectroscopic study of the dynamics of glasses in the aging regime induced by sudden pressure jumps (crunches) across the glass transition line. The sample, initially in the liquid state, is suddenly brought in the glassy state, and therefore out of equilibrium, in a four-window optical crunch cell which is able to perform pressure jumps of 3 kbar in a time interval of ~10 ms. The main advantages of this setup with respect to previous pressure-jump systems is that the pressure jump is induced through a pressure transmitting fluid mechanically coupled to the sample stage through a deformable membrane, thus avoiding any flow of the sample itself in the pressure network and allowing to deal with highly viscous materials. The dynamics of the sample during the aging regime is investigated by Brillouin Light Scattering (BLS). For this purpose the crunch cell is used in conjunction with a high resolution double monochromator equipped with a CCD detector. This system is able to record a full spectrum of a typical glass forming material in a single 1 s shot. As an example we present the study of the evolution toward equilibrium of the infinite frequency longitudinal elastic modulus (M_infinity) of a low molecular weight polymer (Poly(bisphenol A-co-epichlorohydrin), glycidyl end capped). The observed time evolution of M_infinity, well represented by a single stretched exponential, is interpreted within the framework of the Tool-Narayanaswamy theory.Comment: 9 pages, 11 figure

Strategies against nonsense: oxadiazoles as translational readthrough-inducing drugs (TRIDs)

This review focuses on the use of oxadiazoles as translational readthrough-inducing drugs (TRIDs) to rescue the functional full-length protein expression in mendelian genetic diseases caused by nonsense mutations. These mutations in specific genes generate premature termination codons (PTCs) responsible for the translation of truncated proteins. After a brief introduction on nonsense mutations and their pathological effects, the features of various classes of TRIDs will be described discussing differences or similarities in their mechanisms of action. Strategies to correct the PTCs will be presented, particularly focusing on a new class of Ataluren-like oxadiazole derivatives in comparison to aminoglycosides. Additionally, recent results on the efficiency of new candidate TRIDs in restoring the production of the cystic fibrosis transmembrane regulator (CFTR) protein will be presented. Finally, a prospectus on complementary strategies to enhance the effect of TRIDs will be illustrated together with a conclusive paragraph about perspectives, opportunities, and caveats in developing small molecules as TRIDs