Related papers: Second generation wave-function thermostat for ab-…

We present a unique derivation of metadynamics. The starting point for the derivation is an on-the-fly reweighting scheme but through an approximation we recover the standard metadynamics and the well-tempered metadynamics in a general form…

A "minimal" generalization of Quantum Mechanics is proposed, where the Lagrangian or the action functional is a mapping from the (classical) states of a system to the Lie algebra of a general compact Lie group, and the wave function takes…

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…

An ab initio molecular dynamics study of femtosecond laser processing of germanium is presented in this paper. The method based on the finite temperature density functional theory is adopted to probe the structural change, thermal motion of…

Using the gauge-gravity duality, we argue that for a certain class of out-of-equilibrium steady-state systems in contact with a thermal background at a given temperature, the macroscopic physics can be captured by an effective thermodynamic…

We reformulate the algorithm of Gr{\o}nbech-Jensen and Farago (GJF) for Langevin dynamics simulations at constant temperature. The GJF algorithm has become increasingly popular in molecular dynamics simulations because it provides robust…

Microscopic thermal machines promise to play an important role in future quantum technologies. Making such devices widely applicable will require effective strategies to channel their output into easily accessible storage systems like…

Extending a previous single-temperature model, an electrostatic gyrofluid model that includes anisotropic temperatures (parallel and perpendicular) and can treat general nonlinear situations is constructed. The model is based on a…

We propose a new explicit pseudo-energy and momentum conserving scheme for the time integration of Hamiltonian systems. The scheme, which is formally second-order accurate, is based on two key ideas: the integration during the time-steps of…

We introduce a modified molecular dynamics algorithm that allows one to freeze the dynamics of parts of a physical system, and thus concentrate the simulation effort on selected, central degrees of freedom. This freezing, in contrast to…

We propose a generalization of quantum mechanical equations in the hydrodynamic form by introducing, into the Lagrangian density, terms taking into account the diffusion velocity at zero and finite temperatures and the diffusion pressure…

We report joint Lagrangian velocity and temperature measurements in turbulent thermal convection. Measurements are performed using an improved version (extended autonomy) of the neutrally-buoyant instrumented particle that was used by to…

First-principles molecular dynamics simulation based on a plane wave/pseudopotential implementation of density functional theory is adopted to investigate atomic scale energy transport for semiconductors (silicon and germanium). By imposing…

Chemical waves constitute a known class of dissipative structures emerging in reaction-diffusion systems. They play a crucial role in biology, spreading information rapidly to synchronize and coordinate biological events. We develop a…

In this work we describe a $\delta f$ particle simulation method where the bulk density is periodically remapped on a coarse spline grid using a Forward-Backward Lagrangian (FBL) approach. This method is designed to handle plasma regimes…

We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…

We investigate the influence of thermally activated internal molecular dynamics on the phase shifts of matter waves inside a molecule interferometer. While de Broglie physics generally describes only the center-of-mass motion of a quantum…

We present a new approach for the two-temperature molecular dynamics (MD) model for coupled simulations of electronic and phonon heat conduction in nanoscale systems. The proposed method uses a master equation to perform heat conduction of…

It has been shown recently that optimal control problems with the dynamical constraint given by a second order system admit a regular Lagrangian formulation. This implies that the optimality conditions can be obtained in a new form based on…

We consider continuously monitored quantum systems and introduce definitions of work and heat along individual quantum trajectories that are valid for coherent superpositions of energy eigenstates. We use these quantities to extend the…