Related papers: Multi-scale time-stepping in molecular dynamics
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
Recent experiments have demonstrated single-site resolved observation of cold atoms in optical lattices. Thus, in the future it may be possible to take repeated snapshots of an interacting quantum many-body system during the course of its…
Quantum computing has the potential to reduce the computational cost required for quantum dynamics simulations. However, existing quantum algorithms for coupled electron-nuclear dynamics simulation either require fault-tolerant devices, or…
In this paper we develop a dynamic form of Bayesian optimization for machine learning models with the goal of rapidly finding good hyperparameter settings. Our method uses the partial information gained during the training of a machine…
A new symplectic time-reversible algorithm for numerical integration of the equations of motion in magnetic liquids is proposed. It is tested and applied to molecular dynamics simulations of a Heisenberg spin fluid. We show that the…
The Metropolis implementation of the Monte Carlo algorithm has been developed to study the equilibrium thermodynamics of many-body systems. Choosing small trial moves, the trajectories obtained applying this algorithm agree with those…
We present a framework for simulating relaxation dynamics through a conical intersection of an open quantum system that combines methods to approximate the motion of degrees of freedom with disparate time and energy scales. In the vicinity…
Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as…
We present a non-isothermal mesoscopic model for investigation of the phase transition dynamics of thermoresponsive polymers. Since this model conserves energy in the simulations, it is able to correctly capture not only the transient…
A recent reformulation [1] of the problem of Coulomb gases in the presence of a dynamical dielectric medium showed that finite temperature simulations of such systems can be accomplished on the basis of completely local Hamiltonians on a…
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…
Systems subject to a high-frequency drive can spend an exponentially long time in a prethermal regime, in which novel phases of matter with no equilibrium counterpart can be realized. Due to the notorious computational challenges of quantum…
In the study of the thermalization of closed quantum systems, the role of kinetic constraints on the temporal dynamics and the eventual thermalization is attracting significant interest. Kinetic constraints typically lead to long-lived…
We use computer simulations to study the dynamics of a physical gel at high densities where gelation and the glass transition interfere. We report and provide detailed physical understanding of complex relaxation patterns for time…
We report new statistical time-series analysis tools providing significant improvements in the rapid, precision extraction of discrete state dynamics from large databases of experimental observations of molecular machines. By building…
It is shown that the translational degrees of freedom of a large variety of molecules, from light diatomic to heavy organic ones, can be cooled sympathetically and brought to rest (crystallized) in a linear Paul trap. The method relies on…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
In traditional thermodynamical and statistical-mechanical approaches one has (some) detailed knowledge of the principles governing the microdynamics of a system. However in many instances we may not have a Hamiltonian or good information…
We develop algorithms built around properties of the transfer operator and Koopman operator which 1) test for possible multiscale dynamics in a given dynamical system, 2) estimate the magnitude of the time-scale separation, and finally 3)…
Cloud droplets containing ice-nucleating particles (INPs) may freeze at temperatures above the homogeneous freezing threshold temperature. This process, referred to as immersion freezing, is one of the modulators of aerosol-cloud…