Related papers: Reaction Pathways Based on the Gradient of the Mea…
The approach the first-passage time (FPT) of a random process to a certain level is applied to the description of radiation-enhanced diffusion. This is an integral approach to describing the problem of radiation-enhanced diffusion, which…
We develop numerical and analytical approaches to calculate mutual information between complete paths of two molecular components embedded into a larger reaction network. In particular, we focus on a continuous-time Markov chain formalism,…
Trimolecular reaction models are investigated in the compartment-based (lattice-based) framework for stochastic reaction-diffusion modelling. The formulae for the first collision time and the mean reaction time are derived for the case…
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…
The first passage time (FPT) is a generic measure that quantifies when a random quantity reaches a specific state. We consider the FTP distribution in nonlinear stochastic biochemical networks, where obtaining exact solutions of the…
Transition states and minimum energy paths are essential to understand and predict chemical reactivity. Double-ended methods represent a standard approach for their determination. We introduce a new double-ended method that optimizes…
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure, which requires no initial pathway guess, is capable of…
Identifying minimum-energy paths (MEPs) is crucial for understanding chemical reaction mechanisms but remains computationally demanding. We introduce MEPIN, a scalable machine-learning method for efficiently predicting MEPs from reactant…
We propose a unifying theoretical framework for the analysis of first-passage time distributions in two important classes of stochastic processes in which the diffusivity of a particle evolves randomly in time. In the first class of…
Finding optimal reaction coordinates and predicting accurate kinetic rates for activated processes are two of the foremost challenges of molecular simulations. We introduce an algorithm that tackles the two problems at once: starting from a…
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…
We consider the problem of computing first-passage time distributions for reaction processes modelled by master equations. We show that this generally intractable class of problems is equivalent to a sequential Bayesian inference problem…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
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 present a new method for the numerical calculation of canonical reaction rate constants in complex molecular systems, which is based on a path integral formulation of the flux-flux correlation function. Central is the partitioning of the…
Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…
We present the statistical method as a direct extension of the mean first-passage time concept to the analysis of molecular dynamics simulation data of a phase transformation. According to the method, the mean first-passage time…
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…
All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…
Probability generating functions for first passage times of Markov chains are found using the method of collective marks. A system of equations is found which can be used to obtain moments of the first passage times.