Universality of Cluster Dynamics

We have studied the kinetics of cluster formation for dynamical systems of dimensions up to $n=8$ interacting through elastic collisions or coalescence. These systems could serve as possible models for gas kinetics, polymerization and self-assembly. In the case of elastic collisions, we found that the cluster size probability distribution undergoes a phase transition at a critical time which can be predicted from the average time between collisions. This enables forecasting of rare events based on limited statistical sampling of the collision dynamics over short time windows. The analysis was extended to L$^p$-normed spaces ($p=1,...,\infty$) to allow for some amount of interpenetration or volume exclusion. The results for the elastic collisions are consistent with previously published low-dimensional results in that a power law is observed for the empirical cluster size distribution at the critical time. We found that the same power law also exists for all dimensions $n=2,...,8$, 2D L$^p$ norms, and even for coalescing collisions in 2D. This broad universality in behavior may be indicative of a more fundamental process governing the growth of clusters

The Effect of the Third Dimension on Rough Surfaces Formed by Sedimenting Particles in Quasi-Two-Dimensions

The roughness exponent of surfaces obtained by dispersing silica spheres into a quasi-two-dimensional cell is examined. The cell consists of two glass plates separated by a gap, which is comparable in size to the diameter of the beads. Previous work has shown that the quasi-one-dimensional surfaces formed have two distinct roughness exponents in two well-defined length scales, which have a crossover length about 1cm. We have studied the effect of changing the gap between the plates to a limit of about twice the diameter of the beads.Comment: 4 pages, 4 figures, submitted to IJMP

The Equilibrium Distribution of Gas Molecules Adsorbed on an Active Surface

We evaluate the exact equilibrium distribution of gas molecules adsorbed on an active surface with an infinite number of attachment sites. Our result is a Poisson distribution having mean $X = {\mu P P_s \over P_e}$, with $\mu$ the mean gas density, $P_s$ the sticking probability, $P_e$ the evaporation probability in a time interval $\tau$, and $P$ Smoluchowski's exit probability in time interval $\tau$ for the surface in question. We then solve for the case of a finite number of attachment sites using the mean field approximation, recovering in this case the Langmuir isotherm.Comment: 14 pages done in late

Facilitated diffusion of DNA-binding proteins: Simulation of large systems

The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be calibrated in numerical simulations inside a test system of moderate size. Once this is done, reaction times of systems of arbitrary dimensions are derived by extrapolation, with an accuracy of 10 to 15 percent. The achieved speed up, when compared to explicit simulations of the reaction process, is increasing proportional to the extrapolated volume of the cell.Comment: 8 pages, 4 figures, submitted to J. Chem. Phy

Motion by Stopping: Rectifying Brownian Motion of Non-spherical Particles

We show that Brownian motion is spatially not symmetric for mesoscopic particles embedded in a fluid if the particle is not in thermal equilibrium and its shape is not spherical. In view of applications on molecular motors in biological cells, we sustain non-equilibrium by stopping a non-spherical particle at periodic sites along a filament. Molecular dynamics simulations in a Lennard-Jones fluid demonstrate that directed motion is possible without a ratchet potential or temperature gradients if the asymmetric non-equilibrium relaxation process is hindered by external stopping. Analytic calculations in the ideal gas limit show that motion even against a fluid drift is possible and that the direction of motion can be controlled by the shape of the particle, which is completely characterized by tensorial Minkowski functionals.Comment: 11 pages, 5 figure

Selection of the scaling solution in a cluster coalescence model

The scaling properties of the cluster size distribution of a system of diffusing clusters is studied in terms of a simple kinetic mean field model. It is shown that a one parameter family of mathematically valid scaling solutions exists. Despite this, the kinetics reaches a unique scaling solution independent of initial conditions. This selected scaling solution is marginally physical; i.e., it is the borderline solution between the unphysical and physical branches of the family of solutions.Comment: 4 pages, 5 figure

Mechanism of Deep-focus Earthquakes Anomalous Statistics

Analyzing the NEIC-data we have shown that the spatial deep-focus earthquake distribution in the Earth interior over the 1993-2006 is characterized by the clearly defined periodical fine discrete structure with period L=50 km, which is solely generated by earthquakes with magnitude M 3.9 to 5.3 and only on the convergent boundary of plates. To describe the formation of this structure we used the model of complex systems by A. Volynskii and S. Bazhenov. The key property of this model consists in the presence of a rigid coating on a soft substratum. It is shown that in subduction processes the role of a rigid coating plays the slab substance (lithosphere) and the upper mantle acts as a soft substratum. Within the framework of this model we have obtained the estimation of average values of stress in the upper mantle and Young's modulus for the oceanic slab (lithosphere) and upper mantle.Comment: 9 pages, 7 figure

The cosine law at the atomic scale: Toward realistic simulations of Knudsen diffusion

We propose to revisit the diffusion of atoms in the Knudsen regime in terms of a complex dynamical reflection process. By means of molecular dynamics simulation we emphasize the asymptotic nature of the cosine law of reflection at the atomic scale, and carefully analyze the resulting strong correlations in the reflection events. A dynamical interpretation of the accomodation coefficient associated to the slip at the wall interface is also proposed. Finally, we show that the first two moments of the stochastic process of reflection non uniformly depend on the incident angle

Kinetics of viral self-assembly: the role of ss RNA antenna

A big class of viruses self-assemble from a large number of identical capsid proteins with long flexible N-terminal tails and ss RNA. We study the role of the strong Coulomb interaction of positive N-terminal tails with ss RNA in the kinetics of the in vitro virus self-assembly. Capsid proteins stick to unassembled chain of ss RNA (which we call "antenna") and slide on it towards the assembly site. We show that at excess of capsid proteins such one-dimensional diffusion accelerates self-assembly more than ten times. On the other hand at excess of ss RNA, antenna slows self-assembly down. Several experiments are proposed to verify the role of ss RNA antenna.Comment: 4 pages, 3 figures, several experiments are proposed, a new idea of experiment is adde

Thermal ratchet effects in ferrofluids

Rotational Brownian motion of colloidal magnetic particles in ferrofluids under the influence of an oscillating external magnetic field is investigated. It is shown that for a suitable time dependence of the magnetic field, a noise induced rotation of the ferromagnetic particles due to rectification of thermal fluctuations takes place. Via viscous coupling, the associated angular momentum is transferred from the magnetic nano-particles to the carrier liquid and can then be measured as macroscopic torque on the fluid sample. A thorough theoretical analysis of the effect in terms of symmetry considerations, analytical approximations, and numerical solutions is given which is in accordance with recent experimental findings.Comment: 18 pages, 6 figure