Related papers: Efficiency analysis of reaction rate calculation m…
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…
Transition interface sampling (TIS) and replica exchange TIS (RETIS) are powerful methods for computing rates of rare events inaccessible to straightforward molecular dynamics (MD) simulations. Path reweighting extends their output,…
The time evolution of many physical, chemical, and biological systems can be modelled by stochastic transitions between the minima of the potential energy surface describing the system of interest. We show that in cases where there are two…
In comparison to numerous enhanced sampling methods for equilbrium thermodynamics, accelerating simulations for kinetics and nonequilibrium statistics are relatively rare and less effective. Here we derive a time-reversal path sampling…
The minimum energy path (MEP) describes the mechanism of reaction, and the energy barrier along the path can be used to calculate the reaction rate in thermal systems. The nudged elastic band (NEB) method is one of the most commonly used…
Two-phase sampling is commonly adopted for reducing cost and improving estimation efficiency. In many two-phase studies, the outcome and some cheap covariates are observed for a large sample in Phase I, and expensive covariates are obtained…
The primary emphasis of this work on kinetics is to illustrate the a posteriori approach to applications, where focus on data leads to novel outcomes, rather than the a priori tendencies of applied analysis which imposes constructs on the…
Ab initio instanton rate theory is a computational method for rigorously including tunnelling effects into calculations of chemical reaction rates based on a potential-energy surface computed on the fly from electronic-structure theory.…
When a chemical reaction is driven by an external field, the transition state that the system must pass through as it changes from reactant to product -for example, an energy barrier- becomes time-dependent. We show that for periodic…
This paper deals also with a problem of gas absorption accompanied by an instantaneous, irreversible reaction in the liquid layer. The well-known methods for calculating such processes are based usually on the certain amendments to…
In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance nucleation, protein folding, and chemical reactions. For these…
The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch…
We perform a systematic study of capture excitation functions by using an empirical coupled-channel model. In this model, a barrier distribution is used to take effectively into account the effects of couplings between the relative motion…
We present a one-way shooting algorithm for transition path sampling that accepts every proposed trajectory, yet samples the correct transition path ensemble for systems with overdamped stochastic dynamics. The method is based on two key…
Optimal designs minimize the number of experimental runs (samples) needed to accurately estimate model parameters, resulting in algorithms that, for instance, efficiently minimize parameter estimate variance. Governed by knowledge of past…
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…
We present a theory and accompanying importance sampling method for computing rate constants in spatially inhomogenious systems. Using the relationship between rate constants and path space partition functions, we illustrate that the…
Reaction rates of chemical reactions under nonequilibrium conditions can be determined through the construction of the normally hyperbolic invariant manifold (NHIM) [and moving dividing surface (DS)] associated with the transition state…
The random nature of traffic conditions on freeways can cause excessive congestions and irregularities in the traffic flow. Ramp metering is a proven effective method to maintain freeway efficiency under various traffic conditions. Creating…
In this work, we consider the problem of estimating summary statistics to characterise biochemical reaction networks of interest. Such networks are often described using the framework of the Chemical Master Equation (CME). For…