Related papers: Reaction rate calculation by parallel path swappin…
We present a distilled multi-time-step (DMTS) strategy to accelerate molecular dynamics simulations using foundation neural network models. DMTS uses a dual-level neural network where the target accurate potential is coupled to a simpler…
Finding complex reaction and transformation pathways, involving many intermediate states, is in general not possible on the DFT level with existing simulation methods due to the very large number of required energy and force evaluations.…
In recent years, various means of efficiently detecting changepoints in the univariate setting have been proposed, with one popular approach involving minimising a penalised cost function using dynamic programming. In some situations, these…
We present results from our study of the Parallel Tempering algorithm. We examine the swapping acceptance rate of a twin subensemble PT system. We use action matching technology in an attempt to maximise the swap acceptance rate. We model…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…
In diffusion models, samples are generated through an iterative refinement process, requiring hundreds of sequential model evaluations. Several recent methods have introduced approximations (fewer discretization steps or distillation) to…
This article is concerned with the mathematical analysis of a family of adaptive importance sampling algorithms applied to diffusion processes. These methods, referred to as Adaptive Biasing Potential methods, are designed to efficiently…
In a dynamical system, the transition between reactants and products is typically mediated by an energy barrier whose properties determine the corresponding pathways and rates. The latter is the flux through a dividing surface (DS) between…
We introduce a method that ensures efficient computation of one-dimensional quantum systems with long-range interactions across all temperatures. Our algorithm operates within a quasi-polynomial runtime for inverse temperatures up to…
The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the…
In reaction path optimization, such as the calculation of a minimum energy path (MEP) between given reactant and product configurations of atoms, it is advantageous to start with an initial guess where close proximity of atoms is avoided…
An efficient algorithm for calculating radiative transfer on massively parallel computers using domain decomposition is presented. The integral formulation of the transfer equation is used to divide the problem into a local but…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
The computation of bounce action in a phase transition involves solving partial differential equations, inherently introducing non-negligible numerical uncertainty. Deriving characteristic temperatures and properties of this transition…
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an…
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 present a computational approach for solving reaction-diffusion equations on evolving surfaces which have been obtained from cell image data. It is based on finite element spaces defined on surface triangulations extracted from time…
Thermally coupled distillation is a new energy-saving method, but the traditional thermally coupled distillation simulation calculation process is complicated, and the optimization method based on the traditional simulation process is…
This paper proposes a new semi-analytical approach for online time-domain power system simulation. The approach applies the differential transformation method (DTM) to the power system differential equation model to offline derive a…
We introduce an alternative formulation of the exact stochastic simulation algorithm (SSA) for sampling trajectories of the chemical master equation for a well-stirred system of coupled chemical reactions. Our formulation is based on…