相关论文: Maximum Flux Transition Paths of Conformational Ch…
Transition path theory (TPT) is a mathematical framework for quantifying rare transition events between a pair of selected metastable states $A$ and $B$. Central to TPT is the committor function, which describes the probability to hit the…
Many complex real world phenomena exhibit abrupt, intermittent or jumping behaviors, which are more suitable to be described by stochastic differential equations under non-Gaussian L\'evy noise. Among these complex phenomena, the most…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
The probability that a configuration of a physical system reacts, or transitions from one metastable state to another, is quantified by the committor function. This function contains richly detailed mechanistic information about transition…
Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the…
Chemical reactions can be modelled via diffusion processes conditioned to make a transition between specified molecular configurations representing the state of the system before and after the chemical reaction. In particular the model of…
This work is devoted to the investigation of the most probable transition time between metastable states for stochastic dynamical systems. Such a system is modeled by a stochastic differential equation with non-vanishing Brownian noise, and…
Transition Path Theory (TPT) provides a rigorous framework to investigate the dynamics of rare thermally activated transitions. In this theory, a central role is played by the forward committor function q^+(x), which provides the ideal…
The control flow graph (CFG) representation of a procedure used by virtually all flow-sensitive program analyses, admits a large number of infeasible control flow paths i.e., these paths do not occur in any execution of the program. Hence…
An asymmetric exclusion process with $N$ particles on $L$ sites is considered where particles can move one or two sites per infinitesimal time-step. An exact analysis for N=2 and a mean-field theory in comparison with simulations show…
Biological organisms are open, adaptve systems that can respond to changes in environment in specific ways. Adaptation and response can be posed as an optimization problem, with a tradeoff between the benefit obtained from a response and…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
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…
Determining the kinetic bottlenecks that make transitions between metastable states difficult is key to understanding important physical problems like crystallization, chemical reactions, or protein folding. In all these phenomena, the…
The committor function is a central object for quantifying the transitions between metastable states of dynamical systems. Recently, a number of computational methods based on deep neural networks have been developed for computing the…
As an optimal one-dimensional reaction coordinate, the committor function not only describes the probability of a trajectory initiated at a phase space point first reaching the product state before reaching the reactant state, but also…
Rare events such as conformational changes in biomolecules, phase transitions, and chemical reactions are central to the behavior of many physical systems, yet they are extremely difficult to study computationally because unbiased…
Stochastic systems often exhibit multiple viable metastable states that are long-lived. Over very long timescales, fluctuations may push the system to transition between them, drastically changing its macroscopic configuration. In realistic…
A solution to the optimal problem for determining vector fields which maximize (resp. minimize) the transition probabilities from one location to another for a class of reflecting diffusion processes is obtained in the present paper. The…
Many processes in chemistry, physics, and biology involve rare events in which the system escapes from a metastable state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation events…