Related papers: On Dynamics and Optimal Number of Replicas in Para…
We propose a new mathematical tool for the study of transport properties of models for lattice vibrations in crystalline solids. By replication of dynamical degrees of freedom, we aim at a new dynamical system where the "local" dynamics can…
Simulation models of critical systems often have parameters that need to be calibrated using observed data. For expensive simulation models, calibration is done using an emulator of the simulation model built on simulation output at…
Many parallel and distributed computing research results are obtained in simulation, using simulators that mimic real-world executions on some target system. Each such simulator is configured by picking values for parameters that define the…
The protein dynamics are common and important for their biological functions and properties, the study of which usually involves time-consuming molecular dynamics (MD) simulations in silico. Recently, generative models has been leveraged as…
The simulation of rare events is one of the key problems in atomistic simulations. Towards its solution a plethora of methods have been proposed. Here we combine two such methods metadynamics and inte-grated tempering sampling. In…
Parallel tempering (PT) is a class of Markov chain Monte Carlo algorithms that constructs a path of distributions annealing between a tractable reference and an intractable target, and then interchanges states along the path to improve…
Optimal (reversible) processes in thermodynamics can be modelled as step-by-step processes, where the system is successively thermalized with respect to different Hamiltonians by an external thermal bath. However, in practice interactions…
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…
If accepted, the paper will be available at http://pubs.acs.org/journals/jpcbfh/
This paper reports on continuing research into the modelling of an order picking process within a Crossdocking distribution centre using Simulation Optimisation. The aim of this project is to optimise a discrete event simulation model and…
The replica exchange method is a powerful tool for overcoming slow relaxation in molecular simulations, but its efficiency depends strongly on the choice of the number and interval of replicas and their exchange probabilities. Here, we…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information…
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…
We propose a new global optimization method ({\em Simulated Tempering}) for simulating effectively a system with a rough free energy landscape (i.e. many coexisting states) at finite non-zero temperature. This method is related to simulated…
This paper proposes a general formulation for temporal parallelisation of dynamic programming for optimal control problems. We derive the elements and associative operators to be able to use parallel scans to solve these problems with…
Competing phases or interactions in complex many-particle systems can result in free energy barriers that strongly suppress thermal equilibration. Here we discuss how extended ensemble Monte Carlo simulations can be used to study the…
Curve registration plays a major role in functional data analysis by separating amplitude and phase variation through warping functions and the accurate simulation of warping processes is essential for developing statistical methods that…
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…
Simulated and parallel tempering are families of Markov Chain Monte Carlo algorithms where a temperature parameter is varied during the simulation to overcome bottlenecks to convergence due to multimodality. In this work we introduce and…