Related papers: A simple and accurate algorithm for path integral …
We present a method, based on a non-Markovian Langevin equation, to include quantum corrections to the classical dynamics of ions in a quasi-harmonic system. By properly fitting the correlation function of the noise, one can vary the…
We develop an algorithm for bosonic path integral molecular dynamics (PIMD) simulations with periodic boundary conditions (PBC) that scales quadratically with the number of particles. Path integral methods are a powerful tool to simulate…
We address the problem of constructing accurate mathematical models of the dynamics of molecular systems projected on a collective variable. To this aim we introduce an algorithm optimizing the parameters of a standard or generalized…
While gradient-based discrete samplers are effective in sampling from complex distributions, they are susceptible to getting trapped in local minima, particularly in high-dimensional, multimodal discrete distributions, owing to the…
The quantum harmonic oscillator is the fundamental building block to compute thermal properties of virtually any dielectric crystal at low temperatures in terms of phonons, extended further to cases with anharmonic couplings, or even…
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics…
Nuclear quantum effects (NQEs) play an essential role in many atomistic systems, yet their explicit inclusion in molecular simulations remains challenging. Path-integral molecular dynamics (PIMD) provides a rigorous framework for…
We review and compare numerical methods that simultaneously control temperature while preserving the momentum, a family of particle simulation methods commonly used for the modelling of complex fluids and polymers. The class of methods…
We study heat exchange in temperature-biased metal-molecule-metal molecular junctions by employing the LAMMPS atomic molecular dynamics simulator. Generating the nonequilibrium steady state with Langevin thermostats at the boundaries of the…
Traditionally, neural networks are parameterized using optimization procedures such as stochastic gradient descent, RMSProp and ADAM. These procedures tend to drive the parameters of the network toward a local minimum. In this article, we…
We investigate the continuum limit that the number of beads goes to infinity in the ring polymer representation of thermal averages. Studying the continuum limit of the trajectory sampling equation sheds light on possible preconditioning…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
We study numerical methods for dissipative particle dynamics (DPD), which is a system of stochastic differential equations and a popular stochastic momentum-conserving thermostat for simulating complex hydrodynamic behavior at mesoscales.…
We introduce a computational framework for generating realistic transition paths between distinct conformations of large bio-molecular systems. The method is built on a stochastic integro-differential formulation derived from the Langevin…
In light of the recently published complete set of statistically correct Gronbech-Jensen (GJ) methods for discrete-time thermodynamics, we revise a differential operator splitting method for the Langevin equation in order to comply with the…
Building on Paper I of this series, which introduced path integral Monte Carlo (PIMC) estimators for the derivative of the potential of mean force (PMF), we propose two path integral molecular dynamics (PIMD) integrators that can make use…
Bosonic exchange symmetry leads to fascinating quantum phenomena, from exciton condensation in quantum materials to the superfluidity of liquid Helium-4. Unfortunately, path integral molecular dynamics (PIMD) simulations of bosons are…
Given a particle system obeying overdamped Langevin dynamics, we demonstrate that it is always possible to construct a thermodynamically consistent macroscopic model which obeys a gradient flow with respect to its non-equilibrium free…
We introduce a variation of the dissipative particle dynamics (DPD) thermostat that allows for controlling transport properties of molecular fluids. The standard DPD thermostat acts only on a relative velocity along the interatomic axis.…
A formulation of Langevin dynamics for discrete systems is derived as a class of generic stochastic processes. The dynamics simplify for a two-state system and suggest a network architecture which is implemented by the Langevin machine. The…