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

Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…

Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie…

This article is about molecular simulation. However, the theoretical results apply for general overdamped Langevin dynamics simulations. Molecular simulation is often used for determining the stability of a complex (e.g., ligand-receptor).…

We propose a novel, tractable latent state inference scheme for Markov jump processes, for which exact inference is often intractable. Our approach is based on an entropic matching framework that can be embedded into the well-known…

We propose a non linear Langevin equation as a model for stock market fluctuations and crashes. This equation is based on an identification of the different processes influencing the demand and supply, and their mathematical transcription.…

It has been known that epidemic outbreaks in the SIR model on networks are described by phase transitions. Despite the similarity with percolation transitions, whether an epidemic outbreak occurs or not cannot be predicted with probability…

We discuss the use of tunneling electron current to control and catalyze chemical reactions. Assuming the separation of time scales for electronic and nuclear dynamics we employ the Langevin equation for the reaction coordinate. The…

We present a unified formalism for describing chemical reaction rates of trapped, ultracold molecules. This formalism reduces the scattering to its essential features, namely, a propagation of the reactant molecules through a gauntlet of…

We calculate the probabilities to find systems of reacting particles in states which largely deviate from typical behavior. The rare event statistics is obtained from the master equation which describes the dynamics of the probability…

In this paper an original interacting particle system approach is developed for studying Markov chains in rare event regimes. The proposed particle system is theoretically studied through a genealogical tree interpretation of Feynman--Kac…

The method of complex Langevin simulations is a tool that can be used to tackle the complex-action problem encountered, for instance, in finite-density lattice quantum chromodynamics or real-time lattice field theories. The method is based…

Chemical reactions can be described as the stepwise redistribution of electrons in molecules. As such, reactions are often depicted using `arrow-pushing' diagrams which show this movement as a sequence of arrows. We propose an electron path…

The transport and chemical reactions of solutes are modelled as a cellular automaton in which molecules of different species perform a random walk on a regular lattice and react according to a local probabilistic rule. The model describes…

This article focuses, in the context of epidemic models, on rare events that may possibly correspond to crisis situations from the perspective of Public Health. In general, no close analytic form for their occurrence probabilities is…

A detailed algorithmic explanation is required for how a network of chemical reactions can generate the sophisticated behavior displayed by living cells. Though several previous works have shown that reaction networks are computationally…

Estimating the likelihood, timing, and nature of events is a major goal of modeling stochastic dynamical systems. When the event is rare in comparison with the timescales of simulation and/or measurement needed to resolve the elemental…

The Brusselator model are used for the study of the intrinsic fluctuations of chemical reactions with different approaches. The equilibrium states of systems are assumed to be spirally stable in mean-field description, and two statistical…

The generalized Langevin mode analysis (GLMA) is applied to chemical reactions in biomolecules in solution. The theory sees a chemical reaction in solution as a barrier crossing process, similar to the Marcus theory. The barrier is defined…

For reaction-diffusion processes with at most bimolecular reactants, we derive well-behaved, numerically tractable, exact Langevin equations that govern a stochastic variable related to the response field in field theory. Using duality…

We study an instantaneous bimolecular chemical reaction in a two-dimensional chaotic, incompressible and closed Navier-Stokes flow. Areas of well mixed reactants are initially separated by infinite gradients. We focus on the initial regime,…