Related papers: Extrapolating molecular dynamics simulations to ze…
A minimal requirement for simulating multi-scale systems is to reproduce the statistical behavior of the slow variables. In particular, a good numerical method should accurately aproximate the probability density function of the…
Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by…
Common algorithms for computationally simulating Langevin dynamics must discretize the stochastic differential equations of motion. These resulting finite time step integrators necessarily have several practical issues in common:…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
Thermogenesis is a physiological activity of releasing heat that originates from intracellular biochemical reactions. Recent experimental studies discovered that externally applied heat changes intracellular signaling locally, resulting in…
A new simulation approach of field evaporation is presented. The model combines classical electrostatics with molecular dynamics (MD) simulations. Unlike previous atomic-level simulation approaches, our method does not rely on an…
A Gaussian operator basis provides a means to formulate phase-space simulations of the real- and imaginary-time evolution of quantum systems. Such simulations are guaranteed to be exact while the underlying distribution remains…
Accounting for geometry-induced changes in the electronic distribution in molecular simulation is important for capturing effects such as charge flow, charge anisotropy and polarization. Multipolar force fields have demonstrated their…
Phase-field simulations are a practical but also expensive tool to calculate microstructural evolution. This work aims to compare explicit time integrators for a broad class of phase-field models involving coupling between the phase-field…
This paper presents a molecular dynamics simulation of an inelastic gas, where collisions between molecules are characterized by a coefficient of restitution less than unity. The simulation employs an event-driven algorithm to efficiently…
Molecular dynamics algorithms are subject to some amount of error dependent on the size of the time step that is used. This error can be corrected by periodically updating the system with a Metropolis criteria, where the integration step is…
A combination of a steady-state preserving operator splitting method and a semi-implicit integration scheme is proposed for efficient time stepping in simulations of unsteady reacting flows, such as turbulent flames, using detailed chemical…
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
In this Letter, we investigate how changes in the system entropy influence the characteristic time scale of the system molecular dynamics near the glass transition. Independently of any model of thermodynamic evolution of the time scale,…
Using normalizing flows and reweighting, Boltzmann Generators enable equilibrium sampling from a Boltzmann distribution, defined by an energy function and thermodynamic state. In this work, we introduce Thermodynamic Interpolation (TI),…
Divertor plasma detachment is likely needed for the function of magnetically confined nuclear fusion. It greatly reduces the particle and heat flux incident on a target, and thus reduces the sputtering and heat loading on the target. It is…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
Sampling molecular conformations from the Boltzmann distribution is essential for computational chemistry, but iterative diffusion methods are prohibitively slow. Drifting Models offer one-step generation, yet their equilibrium matches the…
The oxidation of human sebum, a lipid mixture covering our skin, generates a range of volatile and semi-volatile carbonyl compounds that contribute largely to indoor air pollution in crowded environments. Kinetic models have been developed…