相关论文: Predicting rare events in chemical reactions: appl…

Langevin equations are used to model many processes of physical interest, including low-energy nuclear collisions. In this paper we develop a general method for computing probabilities of very rare events (e.g. small fusion cross-sections)…

Single molecule chemical reactions yield new insight into fluctuation phenomena which are obscured in measurement of ensemble of molecules. Kramers escape problem is investigated here in a framework suitable for single molecule reactions.…

The escape rate of a Brownian particle over a potential barrier is accurately described by the Kramers theory. A quantitative theory explicitly taking the activity of Brownian particles into account has been lacking due to the inherently…

This paper is devoted to the development of a theoretical and computational framework to efficiently sample the statistically significant thermally activated reaction pathways, in multi-dimensional systems obeying Langevin dynamics. We show…

Rare events are processes that occur upon the emergence of unlikely fluctuations. Unlike what their name suggests, rare events are fairly ubiquitous in nature, as the occurrence of many structural transformations in biology and material…

Simulating rare events, such as the transformation of a reactant into a product in a chemical reaction typically requires enhanced sampling techniques that rely on heuristically chosen collective variables (CVs). We propose using…

We study chemical reaction networks with discrete state spaces, such as the standard continuous time Markov chain model, and present sufficient conditions on the structure of the network that guarantee the system exhibits an extinction…

Recent work of M.D. Johnston et al. has produced sufficient conditions on the structure of a chemical reaction network which guarantee that the corresponding discrete state space system exhibits an extinction event. The conditions consist…

Diffusion mediated reaction models are particularly ubiquitous in the description of physical, chemical or biological processes. The random walk schema is a useful tool for formulating these models. Recently, evanescent random walk models…

A recently proposed single progenitor cell model for skin cell proliferation [Clayton et al., Nature v446, 185 (2007)] is extended to incorporate homeostasis as a fixed point of the dynamics. Unlimited cell proliferation in such a model can…

We develop an efficient method to calculate probabilities of large deviations from the typical behavior (rare events) in reaction--diffusion systems. The method is based on a semiclassical treatment of underlying "quantum" Hamiltonian,…

We revise the encounter-based approach to imperfect diffusion-controlled reactions, which employs the statistics of encounters between a diffusing particle and the reactive region to implement surface reactions. We extend this approach to…

We develop a spectral formulation and a stationary WKB approximation for calculating the probabilities of rare events (large deviations from the mean) in systems of reacting particles with infinite-range interaction, describable by a master…

The efficient calculation of rare-event kinetics in complex dynamical systems, such as the rate and pathways of ligand dissociation from a protein, is a generally unsolved problem. Markov state models can systematically integrate ensembles…

This paper investigates optimal fluctuations for chemical reaction systems with N species, M reactions, and general rate law. In the limit of large volume, large fluctuations for such models occur with overwhelming probability in the…

Reaction prediction, a critical task in synthetic chemistry, is to predict the outcome of a reaction based on given reactants. Generative models like Transformer have typically been employed to predict the reaction product. However, these…

In Bhattacharya et al. (Science Advances, 2020), a set of chemical reactions involved in the dynamics of actin waves in cells was studied. Both at the microscopic level, where the individual chemical reactions are directly modelled using…

The escape problem is defined in the context of quantum field theory. The escape rate is explicitly derived for a scalar field governed by fluctuation-dissipation dynamics, through generalizing the standard Kramers problem. In the presence…

Chemical reaction networks are widely used to model stochastic dynamics in chemical kinetics, systems biology and epidemiology. Solving the chemical master equation that governs these systems poses a significant challenge due to the large…

Ordinary differential equations obtained as limits of Markov processes appear in many settings. They may arise by scaling large systems, or by averaging rapidly fluctuating systems, or in systems involving multiple time-scales, by a…