Related papers: Exact rate calculations by trajectory parallelizat…
This paper presents convergence acceleration, a method for computing efficiently the limit of numerical sequences as a typical application of streams and higher-order functions.
Chen [Ann. Appl. Probab. {\bf 11} (2001), 1242--1262] derived exact convergence rates in a central limit theorem and a local limit theorem for a supercritical branching Wiener process.We extend Chen's results to a branching random walk…
A massively parallel method to build large transition rate matrices from temperature accelerated molecular dynamics trajectories is presented. Bayesian Markov model analysis is used to estimate the expected residence time in the known state…
In this paper we consider the problem of estimating the parameters of a Poisson arrival process where the rate function is assumed to lie in the span of a known basis. Our goal is to estimate the basis expansions coefficients given a…
This paper is concerned with the development of rigorous approximations to various expectations associated with Markov chains and processes having non-stationary transition probabilities. Such non-stationary models arise naturally in…
We study fluctuations in diffusion-limited reaction systems driven out of their stationary state. Using a numerically exact method, we investigate fluctuation ratios in various systems which differ by their level of violation of microscopic…
We show that the steady-state entropy production rate of a stochastic process is inversely proportional to the minimal time needed to decide on the direction of the arrow of time. Here we apply Wald's sequential probability ratio test to…
Motivated by challenges arising in molecular simulation, we study reactive trajectories of the overdamped Langevin dynamics, i.e. trajectories observed as they pass from a set A corresponding to the reagents of a chemical reaction to a set…
The totally asymmetric simple exclusion process in discrete time is considered on finite rings with fixed number of particles. A translation-invariant version of the backward-ordered sequential update is defined for periodic boundary…
The time-dependent exchange-correlation potential has an unusual task in directing fictitious non-interacting electrons to move with exactly the same probability density as true interacting electrons. This has intriguing implications for…
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…
A modified method of functional constraints is used to construct the exact solutions of nonlinear equations of reaction-diffusion type with delay and which are associated with variable coefficients. This study considers a most generalized…
We calculate exact convergence times to reach random bipartite entanglement for various random protocols. The eigenproblem of a Markovian chain governing the process is mapped to a spin chain, thereby obtaining exact expression for the gap…
We present in a detailed manner the scaling theory of irreversible aggregation characterized by the set of reaction rates $K(k,l)=1/k+1/l$, as well as a minor generalisation thereof. In this case, it is possible to evaluate the scaling…
Under a complex technical condition, similar to such used in extreme value theory, we find the rate q(\epsilon)^{-1} at which a stochastic process with stationary increments \xi should be sampled, for the sampled process \xi(\lfloor\cdot…
Transition path theory computes statistics from ensembles of reactive trajectories. A common strategy for sampling reactive trajectories is to control the branching and pruning of trajectories so as to enhance the sampling of low…
Complex systems can convert energy imparted by nonequilibrium forces to regulate how quickly they transition between long lived states. While such behavior is ubiquitous in natural and synthetic systems, currently there is no general…
A discrete-time totally asymmetric simple exclusion process on a lattice with open boundaries is considered. There are particles of different types. The type of a particle is characterized by the probability that a particle moves to a…
Learning the structure of a network from time series data, in particular cyclostationary data, is of significant interest in many disciplines such as power grids, biology and finance. In this article, an algorithm is presented for…
A complete derivation, from first principles, of the reaction-rate formula for a generic process taking place in a heat bath of finite volume is given. It is shown that the formula involves no finite-volume correction. Through perturbative…