Attempts to detect retrotransposition and de novo deletion of Alus and other dispersed repeats at specific loci in the human genome

Dispersed repeat elements contribute to genome instability by de novo insertion and unequal recombination between repeats. To study the dynamics of these processes, we have developed single DNA molecule approaches to detect de novo insertions at a single locus and Alu-mediated deletions at two different loci in human genomic DNA. Validation experiments showed these approaches could detect insertions and deletions at frequencies below 10(-6) per cell. However, bulk analysis of germline (sperm) and somatic DNA showed no evidence for genuine mutant molecules, placing an upper limit of insertion and deletion rates of 2 x 10(-7) and 3 x 10(-7), respectively, in the individuals tested. Such re-arrangements at these loci therefore occur at a rate lower than that detectable by the most sensitive methods currently available

Velocity distribution of fluidized granular gases in presence of gravity

The velocity distribution of a fluidized dilute granular gas in the direction perpendicular to the gravitational field is investigated by means of Molecular Dynamics simulations. The results indicate that the velocity distribution can be exactly described neither by a Gaussian nor by a stretched exponential law. Moreover, it does not exhibit any kind of scaling. In fact, the actual shape of the distribution depends on the number of monolayers at rest, on the restitution coefficient and on the height at what it is measured. The role played by the number of particle-particle collisions as compared with the number of particle-wall collisions is discussed

Energy fluctuations in vibrated and driven granular gases

We investigate the behavior of energy fluctuations in several models of granular gases maintained in a non-equilibrium steady state. In the case of a gas heated from a boundary, the inhomogeneities of the system play a predominant role. Interpreting the total kinetic energy as a sum of independent but not identically distributed random variables, it is possible to compute the probability density function (pdf) of the total energy. Neglecting correlations and using the analytical expression for the inhomogeneous temperature profile obtained from the granular hydrodynamic equations, we recover results which have been previously observed numerically and which had been attributed to the presence of correlations. In order to separate the effects of spatial inhomogeneities from those ascribable to velocity correlations, we have also considered two models of homogeneously thermostated gases: in this framework it is possible to reveal the presence of non-trivial effects due to velocity correlations between particles. Such correlations stem from the inelasticity of collisions. Moreover, the observation that the pdf of the total energy tends to a Gaussian in the large system limit, suggests that they are also due to the finite size of the system.Comment: 13 pages, 10 figure

Permeability of a bubble assembly: From the very dry to the wet limit

We measure the permeability of a fluidized bed of monodispersed bubbles with soap solution characteristic of mobile and non-mobile interfaces. These experimental data extend the permeability curves previously published for foam in the dry limit. In the wet limit, these data join the permeability curves of a hard sphere suspension at porosity equal to 0.4 and 0.6 in the cases of mobile and non-mobile interfaces respectively. We show that the model of permeability proposed by Kozeny and Carman and originally validated for packed beds of spheres (with porosity around 0.4) can be successfully applied with no adjustable parameters to liquid fractions from 0.001 up to 0.85 for systems made of monodisperse and deformable entities with non-mobile interfaces

Self-Similarity in Random Collision Processes

Kinetics of collision processes with linear mixing rules are investigated analytically. The velocity distribution becomes self-similar in the long time limit and the similarity functions have algebraic or stretched exponential tails. The characteristic exponents are roots of transcendental equations and vary continuously with the mixing parameters. In the presence of conservation laws, the velocity distributions become universal.Comment: 4 pages, 4 figure

Entropic Tightening of Vibrated Chains

We investigate experimentally the distribution of configurations of a ring with an elementary topological constraint, a ``figure-8'' twist. Using vibrated granular chains, which permit controlled preparation and direct observation of such a constraint, we show that configurations where one of the loops is tight and the second is large are strongly preferred. This agrees with recent predictions for equilibrium properties of topologically-constrained polymers. However, the dynamics of the tightening process weakly violate detailed balance, a signature of the nonequilibrium nature of this system.Comment: 4 pages, 4 figure

An elastic, plastic, viscous model for slow shear of a liquid foam

We suggest a scalar model for deformation and flow of an amorphous material such as a foam or an emulsion. To describe elastic, plastic and viscous behaviours, we use three scalar variables: elastic deformation, plastic deformation rate and total deformation rate; and three material specific parameters: shear modulus, yield deformation and viscosity. We obtain equations valid for different types of deformations and flows slower than the relaxation rate towards mechanical equilibrium. In particular, they are valid both in transient or steady flow regimes, even at large elastic deformation. We discuss why viscosity can be relevant even in this slow shear (often called "quasi-static") limit. Predictions of the storage and loss moduli agree with the experimental literature, and explain with simple arguments the non-linear large amplitude trends

Velocity Fluctuations in Electrostatically Driven Granular Media

We study experimentally the particle velocity fluctuations in an electrostatically driven dilute granular gas. The experimentally obtained velocity distribution functions have strong deviations from Maxwellian form in a wide range of parameters. We have found that the tails of the distribution functions are consistent with a stretched exponential law with typical exponents of the order 3/2. Molecular dynamic simulations shows qualitative agreement with experimental data. Our results suggest that this non-Gaussian behavior is typical for most inelastic gases with both short and long range interactions.Comment: 4 pages, 4 figure

Velocity correlations in dense granular gases

We report the statistical properties of spherical steel particles rolling on an inclined surface being driven by an oscillating wall. Strong dissipation occurs due to collisions between the particles and rolling and can be tuned by changing the number density. The velocities of the particles are observed to be correlated over large distances comparable to the system size. The distribution of velocities deviates strongly from a Gaussian. The degree of the deviation, as measured by the kurtosis of the distribution, is observed to be as much as four times the value corresponding to a Gaussian, signaling a significant breakdown of the assumption of negligible velocity correlations in a granular system.Comment: 4 pages, 4 Figure

Dynamics of electrostatically-driven granular media. Effects of Humidity

We performed experimental studies of the effect of humidity on the dynamics of electrostatically-driven granular materials. Both conducting and dielectric particles undergo a phase transition from an immobile state (granular solid) to a fluidized state (granular gas) with increasing applied field. Spontaneous precipitation of solid clusters from the gas phase occurs as the external driving is decreased. The clustering dynamics in conducting particles is primarily controlled by screening of the electric field but is aided by cohesion due to humidity. It is shown that humidity effects dominate the clustering process with dielectric particles.Comment: 4 pages, 4 fig