Related papers: Augmented Transition Path Theory for Sequences of …
Mainstream flow matching methods typically focus on learning the local velocity field, which inherently requires multiple integration steps during generation. In contrast, Mean Velocity Flow models establish a relationship between the local…
A statistical-mechanical treatment of collision leads to a formal connection with transition-state theory, suggesting that collision theory and transition-state theory might be joined ultimately as a collision induced transition state…
We present a spatially-extended system of chemical reactions exhibiting adaptation to time-dependent influxes of reactants. Here adaptation is defined as improved reproductive success, namely the ability of one of the many locally stable…
Transition path sampling is a method for estimating the rates of rare events in molecular systems based on the gradual transformation of a path distribution containing a small fraction of reactive trajectories into a biased distribution in…
The chaotic scattering theory is here extended to obtain escape-rate expressions for the transport coefficients appropriate for a simple classical fluid, or for a chemically reacting system. This theory allows various transport coefficients…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
Complex systems are composed of many particles or agents that move and interact with one another. The underlying mathematical framework to model many of these systems must incorporate the spatial transport of particles and their…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
A set of analytical and computational tools based on transition path theory (TPT) is proposed to analyze flows in complex networks. Specifically, TPT is used to study the statistical properties of the reactive trajectories by which…
Chemical reactions subjected to time-varying external forces cannot generally be described through a fixed bottleneck near the transition state barrier or dividing surface. A naive dividing surface attached to the instantaneous, but moving,…
Motion of particles (bodies) in presence of random effects can be considered stochastic process. However, application of widely known stochastic processes used for description of particle motion is reduced to relatively small class of…
We present a real-time path integral theory for the rate of electron transfer reactions. Using graph theoretic techniques, the dynamics is expressed in a formally exact way as a set of integral equations. With a simple approximation for the…
We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a…
Thermodynamic conventions suffer from describing dynamical distinctions, especially when the structural and energetic changes induced by localized rare events are insignificant. By using the ensemble theory in the trajectory space, we…
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…
Many classic questions of structural theory concern discrete changes, such as the formation or dissolution of groups, role turnover, or faction realignment. Here, we consider a basic framework combining prior work on change paths and recent…
A description in terms of transition rates among cells is used to analyze self-diffusion of hard spheres in the fluid phase. Cell size is assumed much larger than the mean free path. Transition state theory is used to obtain an equation…
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…
In a physical system, changing parameters such as temperature can induce a phase transition: an abrupt change from one state of matter to another. Analogous phenomena have recently been observed in large language models. Typically, the task…
A recent article (D.A. Brown, et al., Phys. Rev. C98 024616 (2018)) rproposed a modification of the cross section formula used in practical calculations of compound nucleus reactions. We discuss the main concepts and approximations of…