Related papers: Efficient multiple time scale molecular dynamics: …
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
The earliest molecular dynamics simulations relied on solving the Newtonian or equivalently the Hamiltonian equations of motion for a system. While pedagogically very important as the total energy is preserved in these simulations, they…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…
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…
We propose score dynamics (SD), a general framework for learning accelerated evolution operators with large timesteps from molecular-dynamics simulations. SD is centered around scores, or derivatives of the transition log-probability with…
A stochastic averaging technique based on energy-dependent frequency is extended to dynamical systems with triple-well potential driven by colored noise. The key procedure is the derivation of energy-dependent frequency according to the…
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations.…
Tipping in multistable systems occurs usually by varying the input slightly, resulting in the output switching to an often unsatisfactory state. This phenomenon is manifested in thermoacoustic systems. This thermoacoustic instability may…
The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
A single-step high-order implicit time integration scheme with controllable numerical dissipation at high frequencies is presented for the transient analysis of structural dynamic problems. The amount of numerical dissipation is controlled…
We investigate the dynamics of single microparticles immersed in water that are driven out of equilibrium in the presence of an additional external colored noise. As a case study, we trap a single polystyrene particle in water with optical…
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed…
Reliable dynamical properties from molecular dynamics simulations require careful control of thermostatting artifacts. We systematically assess how NVE, deterministic thermostats, velocity-rescale dynamics, and stochastic Langevin-type…
Many astrophysical simulations involve extreme dynamic range of timescales around 'special points' in the domain (e.g. black holes, stars, planets, disks, galaxies, shocks, mixing interfaces), where processes on small scales couple strongly…
Sensing via a mechanical frequency shift is a powerful measurement tool, and, therefore, understanding and mitigating frequency noise affecting mechanical resonators is imperative. Thermomechanical noise fundamentally limits mechanical…
Stochastic averaging allows for the reduction of the dimension and complexity of stochastic dynamical systems with multiple time scales, replacing fast variables with statistically equivalent stochastic processes in order to analyze…
We consider rare transitions induced by colored noise excitation in multistable systems. We show that undesirable transitions can be mitigated by a simple time-delay feedback control if the control parameters are judiciously chosen. We…
We propose a hybrid deterministic and stochastic approach to achieve extended time scales in atomistic simulations that combines the strengths of molecular dynamics (MD) and Monte Carlo (MC) simulations in an easy-to-implement way. The…