Related papers: Reaction Pathways Based on the Gradient of the Mea…
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for…
We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…
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…
Confined nanoscale spaces, electric fields and tunneling currents make the molecular electronic junction an experimental device for the discovery of new, out-of-equilibrium chemical reactions. Reaction-rate theory for current-activated…
A variety of natural phenomena comprises a huge number of competing reactions and short-lived intermediates. Any study of such processes requires the discovery and accurate modeling of their underlying reaction network. However, this task…
Due to the time scale problem, rare events are not accessible by straight forward molecular dynamics. The presence of multiple reaction channels complicates the problem even further. The feasibility of the standard free energy based methods…
How much time does it take two molecules to react? If a reaction occurs upon contact, the answer to this question boils down to the classic first-passage time problem: find the time it takes the two molecules to meet. However, this is not…
Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from an initial to a final state. The committor is the ideal…
Mapping reaction pathways and transition states (TS) is fundamental to chemistry but computationally expensive at scale. The minimum energy pathway (MEP) dictates reaction rates and mechanisms, yet recovering it via electronic-structure…
We present an exact calculation of the mean first-passage time to a target on the surface of a 2D or 3D spherical domain, for a molecule alternating phases of surface diffusion on the domain boundary and phases of bulk diffusion. The…
The identification of trajectories that contribute to the reaction rate is the crucial dynamical ingredient in any classical chemical reactivity calculation. This problem often requires a full scale numerical simulation of the dynamics, in…
Using the crystallization transition in a Lennard-Jones fluid as example, we show that mean first-passage time based methods may underestimate the reaction rates. We trace the reason of this deficiency back to the non-Markovian character of…
Discrete-state stochastic models have become a well-established approach to describe biochemical reaction networks that are influenced by the inherent randomness of cellular events. In the last years severalmethods for accurately…
Traditional stochastic modeling of reactive systems limits the domain of applicability of the associated path thermodynamics to systems involving a single elementary reaction at the origin of each observed change in composition. An…
We study the efficiency of a two-channel reaction between two walkers on a finite one-dimensional periodic lattice. The walkers perform a combination of synchronous and asynchronous jumps on the lattice and react instantaneously when they…
We present a time dependent variational method to learn the mechanisms of equilibrium reactive processes and efficiently evaluate their rates within a transition path ensemble. This approach builds off variational path sampling methodology…
The dominant reaction pathway (DRP) is a rigorous framework to microscopically compute the most probable trajectories, in non-equilibrium transitions. In the low-temperature regime, such dominant pathways encode the information about the…
Simulation of surface processes is a key part of computational chemistry that offers atomic-scale insights into mechanisms of heterogeneous catalysis, diffusion dynamics, as well as quantum tunneling phenomena. The most common theoretical…
Pathways-reduced analysis is one of the techniques used by the Fispact-II nuclear activation and transmutation software to study the sensitivity of the computed inventories to uncertainties in reaction cross-sections. Although deciding…
We introduce a reaction-path statistical mechanics formalism based on the principle of large deviations to quantify the kinetics of single-molecule enzymatic reaction processes under the Michaelis-Menten mechanism, which exemplifies an…