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A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
There has been substantial interest in developing Markov chain Monte Carlo algorithms based on piecewise-deterministic Markov processes. However existing algorithms can only be used if the target distribution of interest is differentiable…
We investigate ways of accurately simulating the propagation of energetic charged particles over small times where the standard Monte Carlo approximation to diffusive transport breaks down. We find that a small-angle scattering procedure…
The diffusion of molecules (penetrants) of variable size, shape, and chemistry through dense crosslinked polymer networks is a fundamental scientific problem that is broadly relevant in materials, polymer, physical and biological chemistry.…
We consider the speed of propagation of a {continuous-time continuous-space} branching random walk with the additional restriction that the birth rate at any spatial point cannot exceed $1$. The dispersion kernel is taken to have density…
The diffusion of a pulse of small grains in an horizontal rotating drum is studied through discrete elements methods simulations. We present a theoretical analysis of the diffusion process in a one-dimensional confined space in order to…
Diffusion can be conceptualized, at microscopic scales, as the random hopping of particles between neighboring lattice sites. In the case of diffusion in inhomogeneous media, distinct spatial domains in the system may yield distinct…
Mode separation, namely how sharply a distribution fragments into barrier-separated clusters, is a fundamental geometric property of densities, difficult to quantify in high dimensions. It is structurally distinct from dispersion, yet…
We consider the time dependent dispersion properties of overdamped tracer particles diffusing in a one dimensional periodic potential under the influence of an additional constant tilting force $F$. The system is studied in the region where…
We present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible…
We study the persistent random walk of photons on a one-dimensional lattice of random transmittances. Transmittances at different sites are assumed independent, distributed according to a given probability density $f(t)$. Depending on the…
Single-file diffusion is a one-dimensional interacting infinite-particle system in which the order of particles never changes. An intriguing feature of single-file diffusion is that the mean-square displacement of a tagged particle exhibits…
An investigation of the effect of surface diffusion in random deposition model is made by analytical methods and reasoning. For any given site, the extent to which a particle can diffuse is decided by the morphology in the immediate…
We study particle transport in a class of open channels of finite length, made of identical cells of connected open polygonal billiards with parallel boundaries. In these systems the Mean Square Displacement (MSD) grows in time faster than…
Many natural and industrial systems involve particle-laden interfaces. Because interfacial particles prevent the coalescence and coarsening of drops, they hold promise for various applications requiring stable emulsions. Despite their…
We use an off - lattice bead - spring model of a self - avoiding polymer chain immersed in a 3-dimensional quenched random medium to study chain dynamics by means of a Monte - Carlo (MC) simulation. The chain center of mass mean-squared…
A rapidly increasing number of systems is identified in which the stochastic motion of tracer particles follows the Brownian law $\langle\mathbf{r}^2(t) \rangle\simeq Dt$ yet the distribution of particle displacements is strongly…
Single-particle tracking allows to infer the motion of single molecules in living cells. When we observe a long trajectory (more than 100 points), it is possible that the particle switches mode of motion over time. Then, fitting a single…