Related papers: Combining Metadynamics and Integrated Tempering Sa…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain…
We performed two-dimensional simulated tempering (ST) simulations of the two-dimensional Ising model with different lattice sizes in order to investigate the two-dimensional ST's applicability to dealing with phase transitions and to study…
Jamming is a common feature of out of equilibrium systems showing slow relaxation dynamics. Here we review our efforts in understanding jamming in granular materials using experiments and computer simulations. We first obtain an estimation…
We implement a standard Monte Carlo algorithm to study the slow, equilibrium dynamics of a silica melt in a wide temperature regime, from 6100 K down to 2750 K. We find that the average dynamical behaviour of the system is in quantitative…
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 scenario for systems with slow dynamics is characterised by stating that there are several temperatures coexisting in the sample, with a single temperature shared by all observables at each (widely separate) time-scale. In preparation for…
At fine lattice spacings, Markov chain Monte Carlo simulations of QCD and other gauge theories with or without fermions are plagued by slow modes that give rise to large autocorrelation times. This can lead to simulation runs that are…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
When approaching the continuum limit in lattice QCD or other theories in a setup with topological sectors, conventional update algorithms experience a particularly severe form of critical slowing down that is caused by high action barriers…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
Understanding the realization of thermal equilibrium through the thermalization process in a many-body system is a fundamental and complex scientific question, bridging thermodynamics and classical dynamics and connecting to a host of…
The study of controlled hybrid systems requires practical tools for approximation and comparison of system behaviors. Existing approaches to these problems impose undue restrictions on the system's continuous and discrete dynamics.…
In this paper, a hybrid quasi-static atomistic simulation method at finite temperature is developed, which combines the advantages of MD for thermal equilibrium and atomic-scale finite element method (AFEM) for efficient equilibration. Some…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
Simulated tempering is a widely used strategy for sampling from multimodal distributions. In this paper, we consider simulated tempering combined with an arbitrary local Markov chain Monte Carlo sampler and present a new decomposition…
Amplification (mitigation) is the increase (decrease) in the change of thermodynamic quantities when an initial thermal state is thermalized to a different temperature in the presence of constraints, studied thus far only for…
We show by means of experiments, theory and simulations, that the slow dynamics of coarsening systems displays dynamic heterogeneity similar to that observed in glass-forming systems. We measure dynamic heterogeneity via novel multi-point…
Addressing complex meteorological processes at a fine spatial resolution requires substantial computational resources. To accelerate meteorological simulations, researchers have utilized neural networks to downscale meteorological variables…