Related papers: Stochastic approach to DNA breathing dynamics
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
We consider a stochastic version of the Wilson-Cowan model which accommodates for discrete populations of excitatory and inhibitory neurons. The model assumes a finite carrying capacity with the two populations being constant in size. The…
We analyze the classical problem of the stochastic dynamics of a particle confined in a periodic potential, through the so called Il'in and Khasminskii model, with a novel semi-analytical approach. Our approach gives access to the transient…
We examined the Brownian motion of point defects in a two-dimensional hexagonal colloidal crystal, going beyond the conventional treatment that assumes constant diffusion coefficients. By extracting the spatially varying drift vector and…
We investigate a stochastic version of a simple enzymatic reaction which follows the generic Michaelis-Menten kinetics. At sufficiently high concentrations of reacting species, the molecular fluctuations can be approximated as a realization…
Many imaging techniques for biological systems -- like fixation of cells coupled with fluorescence microscopy -- provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics…
We introduce a classical stochastic field method that accounts for the quantum fluctuations responsible for spontaneous initiation of various atom optics processes. We assume a delta-correlated Gaussian noise in all initially empty modes of…
In this work we investigate the quantum dynamics of a model for two single-mode Bose--Einstein condensates which are coupled via Josephson tunneling. Using direct numerical diagonalisation of the Hamiltonian, we compute the time evolution…
We study the dynamics of overdamped Brownian particles diffusing in conservative force fields and undergoing stochastic resetting to a given location with a generic space-dependent rate of resetting. We present a systematic approach…
Turbulent suspensions of heavy particles in incompressible flows have gained much attention in recent years. A large amount of work focused on the impact that the inertia and the dissipative dynamics of the particles have on their dynamical…
We give an explicit stochastic Hamiltonian model of discontinuous unitary evolution for quantum spontaneous jumps like in a system of atoms in quantum optics, or in a system of quantum particles that interacts singularly with "bubbles"…
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
An important class of spatio-temporal models is constructed by leveraging the hierarchical structure of dynamical (or, state-space) models. This paper proposes a new statistical dynamical model for spatio-temporal processes motivated by…
We propose an extension of the Plefka expansion, which is well known for the dynamics of discrete spins, to stochastic differential equations with continuous degrees of freedom and exhibiting generic nonlinearities. The scenario is…
We present here a new stochastic modelling in the constitution of fluid flow reduced-order models. This framework introduces a spatially inhomogeneous random field to represent the unresolved small-scale velocity component. Such a…
We formulate a generalized self-consistent stochastic quantum kinetic theory for finite-temperature ultracold Bose gases interacting via a generic long-range interaction, applicable to a broad range of systems, by means of Keldysh…
A stochastic algorithm for simulation of fluctuation-induced kinetics of H$_2$ formation on grain surfaces is suggested as a generalization of the technique developed in our recent studies where this method was developed to describe the…
A stochastic field theory approach is applied to a coarse-grained polymer model that will enable studies of polymer behavior under non-equilibrium conditions. This article is focused on the validation of the new model in comparison to…
We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our…
We study the sensitivity of coupled condensate formation dynamics on the history of initial stochastic domain formation in the context of instantaneously quenched elongated harmonically-trapped immiscible two-component atomic Bose gases.…