Related papers: Efficiency analysis of reaction rate calculation m…
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…
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 family of algorithms for the fast determination of reaction paths and barriers in phase space and the computation of the corresponding rates. The method requires the reaction times be large compared to the microscopic time,…
We derive a novel efficient scheme to measure the rate constant of transitions between stable states separated by high free energy barriers in a complex environment within the framework of transition path sampling. The method is based on…
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.…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
We review two recently developed efficient methods for calculating rate constants of processes dominated by rare events in high-dimensional complex systems. The first is transition interface sampling (TIS), based on the measurement of…
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…
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…
Reaction rates are a complicated function of molecular interactions, which can be selected from vast chemical design spaces. Seeking the design that optimizes a rate is a particularly challenging problem since the rate calculation for any…
The efficiency of path sampling simulations can be improved considerably using the approach of path swapping. For this purpose, we have devised a new algorithmic procedure based on the transition interface sampling technique. In the same…
Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and…
We show how reaction coordinate path lengths affect the relaxation efficiency of a complex system. To this purpose, we consider the metric contributions to the transition rates. These metric contributions preserve informations about the…
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 propose an efficient novel path sampling-based framework designed to accelerate the investigation of rare events in complex molecular systems. A key innovation is the shift from sampling restricted path ensemble distributions, as in…
In the presence of multiscale dynamics in a reaction network, direct simulation methods become inefficient as they can only advance the system on the smallest scale. This work presents stochastic averaging techniques to accelerate…
We introduce a path sampling method for the computation of rate constants for systems with a highly diffusive character. Based on the recently developed algorithm of transition interface sampling (TIS) this procedure increases 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…
We propose a new Monte Carlo method for efficiently sampling trajectories with fixed initial and final conditions in a system with discrete degrees of freedom. The method can be applied to any stochastic process with local interactions,…
We introduce a path sampling method for obtaining statistical properties of an arbitrary stochastic dynamics. The method works by decomposing a trajectory in time, estimating the probability of satisfying a progress constraint, modifying…