Related papers: On Dynamics and Optimal Number of Replicas in Para…
Parallel tempering (PT), also known as replica exchange, is the go-to workhorse for simulations of multi-modal distributions. The key to the success of PT is to adopt efficient swap schemes. The popular deterministic even-odd (DEO) scheme…
In particle-in-cell simulations, excessive or even unfeasible computational demands can be caused by the growth of the number of particles in the course of prolific ionization or cascaded pair production due to the effects of quantum…
Mechanistic mathematical models of biological systems usually contain a number of unknown parameters whose values need to be estimated from available experimental data in order for the models to be validated and used to make quantitative…
This article proposes a new way to construct computationally efficient `wrappers' around fine scale, microscopic, detailed descriptions of dynamical systems, such as molecular dynamics, to make predictions at the macroscale `continuum'…
We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the…
Sampling complex potential energies is one of the most pressing challenges of contemporary computational science. Inspired by recent efforts that use quantum effects and discretized Feynman's path integrals to overcome large barriers we…
A common problem to all applications of linear finite dynamical systems is analyzing the dynamics without enumerating every possible state transition. Of particular interest is the long term dynamical behaviour. In this paper, we study the…
Computational methods in drug repositioning can help to conserve resources. In particular, methods based on biological networks are showing promise. Considering only the network topology and knowledge on drug target genes is not sufficient…
The method of tempered transitions was proposed by Neal (1996) for tackling the difficulties arising when using Markov chain Monte Carlo to sample from multimodal distributions. In common with methods such as simulated tempering and…
Controlling the evolution of nonequilibrium systems to minimize dissipated heat or work is a key goal for designing nanodevices, both in nanotechnology and biology. Progress in computing optimal protocols has thus far been limited to either…
We have introduced a variational method to improve the computation of integrated correlation times in the Parallel Tempering Dynamics, obtaining a better estimate (a lower bound, at least) of the exponential correlation time. Using this…
This letter compares the performance of four different, popular simulation environments for robotics and reinforcement learning (RL) through a series of benchmarks. The benchmarked scenarios are designed carefully with current industrial…
The process of calibrating computer models of natural phenomena is essential for applications in the physical sciences, where plenty of domain knowledge can be embedded into simulations and then calibrated against real observations. Current…
Optimization plays a significant role in many areas of science and technology. Most of the industrial optimization problems have inordinately complex structures that render finding their global minima a daunting task. Therefore, designing…
Several methods for density matrix propagation in distributed computing environments, such as clusters and graphics processing units, are proposed and evaluated. It is demonstrated that the large communication overhead associated with each…
We propose a novel method for fast and scalable evaluation of periodic solutions of systems of ordinary differential equations for a given set of parameter values and initial conditions. The equations governing the system dynamics are…
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…
The large demand for simulated data has made the reality gap a problem on the forefront of robotics. We propose a method to traverse the gap by tuning available simulation parameters. Through the optimisation of physics engine parameters,…
The sampling problem lies at the heart of atomistic simulations and over the years many different enhanced sampling methods have been suggested towards its solution. These methods are often grouped into two broad families. On the one hand…
The constant increase in parallelism available on large-scale distributed computers poses major scalability challenges to many scientific applications. A common strategy to improve scalability is to express the algorithm in terms of…