Related papers: Gamma Limit for Transition Paths of Maximal Probab…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
Reaction-diffusion equations deliver a versatile tool for the description of reactions in inhomogeneous systems under the assumption that the characteristic reaction scales and the scales of the inhomogeneities in the reactant…
An equilibrated model glass-forming liquid is studied by mapping successive configurations produced by molecular dynamics simulation onto a time series of inherent structures (local minima in the potential energy). Using this ``inherent…
Microorganisms often perform chemotaxis, (i.e., sensing and moving toward a region with a higher concentration of an attractive chemical) by changing the rate of tumbling for random walk. We studied several models with internal adaptive…
Chemical reaction networks offer a natural nonlinear generalisation of linear Markov jump processes on a finite state-space. In this paper, we analyse the dynamical large deviations of such models, starting from their microscopic version,…
Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…
Transition of a system between two states is an important but difficult problem in natural science. In this article we study the transition problem in the framework of transition path ensemble. Using the overdamped Langevin method, we…
We study switching between period-two states of an underdamped quantum oscillator modulated at nearly twice its natural frequency. For all temperatures and parameter values switching occurs via quantum activation: it is determined by…
In stochastic resonance, a periodically forced Brownian particle in a double-well potential jumps between minima at rare increments, the prediction of which poses a major theoretical challenge. Here, we use a path-integral method to find a…
A method to approximate transmission probabilities for a nonseparable multidimensional barrier is applied to a waveguide model. The method uses complex barrier-crossing orbits to represent reaction probabilities in phase space and is…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
A model is proposed for studying the reaction dynamics in complex quantum systems in which the complete mixing of states is hindered by an internal barrier. Such systems are often treated by the transition-state theory, also known in…
Transition states and minimum energy paths are essential to understand and predict chemical reactivity. Double-ended methods represent a standard approach for their determination. We introduce a new double-ended method that optimizes…
This article is a continuation of our previous works (see Yukhnovskii I.R. et al., J. Stat. Phys, 1995, 80, 405 and references therein), where we have described the behavior of a simple system of interacting particles in the region of…
For sampling multiple pathways in a rugged energy landscape, we propose a novel action-based path sampling method using the Onsager-Machlup action functional. Inspired by the Fourier-path integral simulation of a quantum mechanical system,…
We consider a reaction--diffusion equation in a domain consisting of two bulk regions connected via small channels periodically distributed within a thin layer. The height and the thickness of the channels are of order $\epsilon$, and the…
We study the problem of parameter estimation for the homogenization limit of multiscale systems involving fractional dynamics. In the case of stochastic multiscale systems driven by Brownian motion, it has been shown that in order for the…
We consider a nonlinear reaction--diffusion equation in a domain consisting of two bulk regions connected via small channels periodically distributed within a thin layer. The height and the thickness of the channels are of order $\epsilon$,…
We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where…
A path information is defined in connection with different possible paths of irregular dynamic systems moving in its phase space between two points. On the basis of the assumption that the paths are physically differentiated by their…