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A free energy landscape estimation-method based on Bayesian inference is presented and used for comparing the efficiency of thermally enhanced sampling methods with respect to regular molecular dynamics, where the simulations are carried…
In this review we consider those processes in condensed matter that involve the irreversible flow of energy between electrons and nuclei that follows from a system being taken out of equilibrium. We survey some of the more important…
The Jarzynski equality allows the calculation of free-energy differences using values of work measured from nonequilibrium trajectories. The number of trajectories required to accurately estimate free-energy differences in this way grows…
Formation of the nonequilibrium subsystem in dynamical processes during defect generation is simulated by means of molecular dynamics. A particular process of dissipation of the low-frequency acoustic emission into high-frequency…
Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow…
The distributions of work for strongly non-equilibrium processes are studied using a very general form of a large-deviation approach, which allows one to study distributions of almost arbitrary quantities of interest for equilibrium,…
The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation…
Machine-learned interatomic potentials (MILPs) are rapidly gaining interest for molecular modeling, as they provide a balance between quantum-mechanical level descriptions of atomic interactions and reasonable computational efficiency.…
In this work we investigate the transient solidification of a Lennard-Jones liquid using non-equilibrium molecular dynamics simulations and continuum heat transfer theory. The simulations are performed in slab-shaped boxes, where a cold…
We present several equilibrium methods that allow to compute isentropic processes, either during the compression or the release of the material. These methods are applied to compute the isentropic release of a shocked monoatomic liquid at…
This thesis is devoted to the theoretical study of slow thermodynamic processes in non-equilibrium stochastic systems. Its main result is a physically and mathematically consistent construction of relevant thermodynamic quantities in the…
We use thermodynamic perturbation theory to calculate the free energies and resulting phase diagrams of binary systems of spherical colloidal particles and interacting polymer coils in good solvent within an effective one-component…
This is the first of three papers devoted to the nonequilibrium thermodynamics of amorphous materials. Our focus here is on the role of internal degrees of freedom in determining the dynamics of such systems. For illustrative purposes, we…
A hybrid lattice Boltzmann method (LBM) for binary mixtures based on the free-energy approach is proposed. Non-ideal terms of the pressure tensor are included as a body force in the LBM kinetic equations, used to simulate the continuity and…
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…
Thermodynamical arguments are known to be useful in the construction of physically motivated Lyapunov functionals for nonlinear stability analysis of spatially homogeneous equilibrium steady states in thermodynamically isolated systems.…
In this work a method is proposed for computing step free energies for faceted solid-liquid interfaces based on atomistic simulations. The method is demonstrated in an application to (111) interfaces in elemental Si, modeled with the…
Effective harmonic methods allow for calculating temperature dependent phonon frequencies by incorporating the anharmonic contributions into an effective harmonic Hamiltonian. The systematic errors arising from such an approximation are…
Multiparticle collision dynamics (MPC), a particle-based mesoscale simulation technique for com- plex fluid, is widely employed in non-equilibrium simulations of soft matter systems. To maintain a defined thermodynamic state, thermalization…
Large-scale atomistic simulations rely on interatomic potentials providing an efficient representation of atomic energies and forces. Modern machine-learning (ML) potentials provide the most precise representation compared to electronic…