相关论文: Fluctuations in the Ensemble of Reaction Pathways

We study the role of quantum fluctuations of atomic nuclei in the real-time dynamics of non-equilibrium macro-molecular transitions. To this goal we introduce an extension of the Dominant Reaction Pathways (DRP) formalism, in which the…

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…

We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…

We use the Dominant Reaction Pathway (DRP) approach to study the dynamics of the folding of a beta-hairpin, within a model which accounts for both native and non-native interactions. We compare the most probable folding pathways calculated…

We assess the reliability of the recently developed approach denominated Dominant Reaction Pathways (DRP) by studying the folding of a 16-residue beta-hairpin, within a coarse-grained Go-type model. We show that the DRP predictions are in…

Biological machines like molecular motors and enzymes operate in dynamic cycles representable as stochastic flows on networks. Current stochastic dynamics describes such flows on fixed networks. Here, we develop a scalable approach to…

Many chemical reactions can be formulated in terms of particle diffusion in a complex energy landscape. Transition path theory (TPT) is a theoretical framework for describing the direct (reaction) pathways from reactant to product states…

Ring-polymer instanton theory has been developed to simulate the quantum dynamics of molecular systems at low temperatures. Chemical reaction rates can be obtained by locating the dominant tunneling pathway and analyzing fluctuations around…

Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…

Fluctuations play an important role in the dynamics of stochastic systems. In particular, for small systems, the most probable thermodynamic quantities differ from their averages because of the fluctuations. Using the Onsager Machlup…

Large deviation theory (LDT) provides a mathematical framework to quantify the probabilities of rare events in stochastic systems. In this study, we applied LDT to model a chemical reaction system and demonstrated that the fluctuation…

In the past the study of reaction-diffusion systems has greatly contributed to our understanding of the behavior of many-body systems far from equilibrium. In this paper we aim at characterizing the properties of diffusion limited reactions…

Systems with interacting degrees of freedom play a prominent role in stochastic thermodynamics. Our aim is to use the concept of detached path probabilities and detached entropy production for bipartite Markov processes and elaborate on a…

We construct path integrals for stochastic hybrid reaction-diffusion (RD) processes, in which the reaction terms depend on the discrete state of a randomly switching environment. We proceed by spatially discretizing a given RD system and…

A rigorous derivation of nonequilibrium entropy production via the path-integral formalism is presented. Entropy production is defined as the entropy change piled in a heat reservoir as a result of a nonequilibrium thermodynamic process. It…

Using equilibrium fluctuations to understand the response of a physical system to an externally imposed perturbation is the basis for linear response theory, which is widely used to interpret experiments and shed light on microscopic…

Reaction-diffusion systems, which consist of the reacting particles subject to diffusion process, constitute one of the common examples of non-linear statistical systems. In low space dimensions $d \leq 2$ the usual description by means of…

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…

To explain day-to-day (DTD) route-choice behaviors and traffic dynamics observed in a series of lab experiments, Part I of this research proposed a discrete choice-based analytical dynamic model (Qi et al., 2023). Although the deterministic…

We propose an efficient method to compute reaction rate constants of thermally activated processes occurring in many-body systems at finite temperature. The method consists in two steps: first, paths are sampled using a transition path…