Related papers: Stochastic approach to DNA breathing dynamics
In this paper, a physics-oriented stochastic kinetic scheme will be developed that includes random inputs from both flow and electromagnetic fields via a hybridization of stochastic Galerkin and collocation methods. Based on the BGK-type…
Synchronization with noise is important for understanding biophysical processes at nano- and micro-meter scales, such as neuronal firing and flagellar rotations. To understand the energetics of these processes, stochastic thermodynamics…
Using a field theory equivalent to a lattice version of the Poland-Scheraga (PS) model, the phase diagram for a long DNA molecule is derived in closed form. A one-loop renormalization group calculation for the generalized PS model with…
Based on the theory of stochastic chemical kinetics, the inherent randomness and stochasticity of biochemical reaction networks can be accurately described by discrete-state continuous-time Markov chains. The analysis of such processes is,…
We investigate stochastic predator-prey dynamics and their spatial phase synchronization using the Rosenzweig-MacArthur model coupled across multiple patches. Combining stochastic simulations based on the Gillespie algorithm with analytical…
An extension of the two-step staggered time discretization of linear elastodynamics in stress-velocity form to systems involving internal variables subjected to a possibly non-linear dissipative evolution is proposed. The original scheme is…
The effects of intrinsic noise on stochastic delay systems is studied within an expansion in the inverse system size. We show that the stochastic nature of the underlying dynamics may induce oscillatory behaviour in parameter ranges where…
We investigate the large population dynamics of a family of stochastic particle systems with three-state cyclic individual behaviour and parameter-dependent transition rates. On short time scales, the dynamics turns out to be approximated…
Let $\alpha=1/2$, $\theta>-1/2$, and $\nu_0$ be a probability measure on a type space $S$. In this paper, we investigate the stochastic dynamic model for the two-parameter Dirichlet process $\Pi_{\alpha,\theta,\nu_0}$. If $S=\mathbb{N}$, we…
We developed a low-energy model that can be used at any time to describe the dynamics of DNA bubbles at temperatures below the melting point. The Schr\"odinger equation associated with this problem is solved in imaginary time with a quantum…
We study experimentally the dissipative dynamics of ultracold bosonic gases in a dynamic disorder potential with tunable correlation time. First, we measure the heating rate of thermal clouds exposed to the dynamic potential and present a…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
We propose a parallel algorithm for the numerical solution of a class of second order semi-linear equations coming from stochastic optimal control problems, by means of a dynamic domain decomposition technique. The new method is an…
A relation between equilibrium, steady-state, and waiting-time dependent dynamical two-time correlation functions in dense glass-forming liquids subject to homogeneous steady shear flow is discussed. The systems under study show pronounced…
We propose a faster algorithm for individual based simulations for adaptive dynamics based on a simple modification to the standard Gillespie Algorithm for simulating stochastic birth-death processes. We provide an analytical explanation…
The non-equilibrium dynamic fluctuations of a stochastic version of the Gray-Scott (GS) model are studied analytically in leading order in perturbation theory by means of the dynamic renormalization group. There is an attracting stable…
Multiscale dynamics are frequently present in real-world processes, such as the atmosphere-ocean and climate science. Because of time scale separation between a small set of slowly evolving variables and much larger set of rapidly changing…
A modeling framework for the internal conformational dynamics and external mechanical movement of single biological macromolecules in aqueous solution at constant temperature is developed. Both the internal dynamics and external movement…
We investigate instabilities in a stochastic mathematical model of cochlear dynamics. The cochlea is modeled as a spatio-temporal dynamical system made up of a spatially distributed array of coupled oscillators, together with the cochlear…