相关论文: Pseudo generators for under-resolved molecular dyn…
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…
Many cellular behaviors are regulated by gene regulation networks, kinetics of which is one of the main subjects in the study of systems biology. Because of the low number molecules in these reacting systems, stochastic effects are…
We propose a stochastic model for intracellular transport processes associated with the activity of molecular motors. This out-of-equilibrium model, based on a generalized Langevin equation, considers a particle immersed in a viscoelastic…
We explore situations in which certain stochastic and high-dimensional deterministic systems behave effectively as low-dimensional dynamical systems. We define and study moment maps, maps on spaces of low-order moments of evolving…
We consider an infinite locally finite system (configuration) $\gamma$ of particles distributed over a Euclidean space $X$. Each particle located at $x\in X$ carries an internal parameter (mark, or ``spin'') $\sigma_{x}\in S=\mathbb{R}.$…
A reduced chemical scheme involving a small number of variables is often sufficient to account for the deterministic evolution of the concentrations of the main species contributing to a reaction. However its predictions are questionable in…
We continue our study of the statistical properties of particles in equilibrium obeying Smoluchowski dynamics. We show that the system is governed by a kinetic equation of the memory function form and that the memory function is given by…
Modelling the evolution of a system using stochastic dynamics typically implies a greater subjective uncertainty in the adopted system coordinates as time progresses, and stochastic entropy production has been developed as a measure of this…
We develop a systematic approach to the linear-noise approximation for stochastic reaction systems with distributed delays. Unlike most existing work our formalism does not rely on a master equation, instead it is based upon a dynamical…
Phenotypical variability in the absence of genetic variation often reflects complex energetic landscapes associated with underlying gene regulatory networks (GRNs). In this view, different phenotypes are associated with alternative states…
Krylov subspace methods in quantum dynamics identify the minimal subspace in which a process unfolds. To date, their use is restricted to time evolutions governed by time-independent generators. We introduce a generalization valid for…
Given nonstationary data from molecular dynamics simulations, a Markovian Langevin model is constructed that aims to reproduce the time evolution of the underlying process. While at equilibrium the free energy landscape is sampled,…
We introduce a novel conditional stochastic interpolant framework for generative modeling of three-dimensional shapes. The method builds on a recent LDDMM-based registration approach to learn the conditional drift between geometries. By…
We numerically investigate stochastic dynamics in cosmology by solving Langevin equations for Infrared (IR) modes with stochastic noises generated by Ultraviolet (UV) modes at the coarse-graining scale. By construction, the stochastic…
The definition of metastable states is an ubiquitous task in the design and analysis of molecular simulations, and is a crucial input in a variety of acceleration methods for the sampling of long configurational trajectories. Although…
Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…
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 study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition path theory we…
An approach for the description of stochastic systems is derived. Some of the variables in the system are studied forward in time, others backward in time. The approach is based on a perturbation expansion in the strength of the coupling…
In this paper we introduce a new technique for depicting the phase portrait of stochastic differential equations. Following previous work for deterministic systems, we represent the phase space by means of a generalization of the method of…