相关论文: Configurational Temperature Control for Atomic and…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
The dynamics of short 1D nonlinear Hamiltonian chains is analyzed numerically at different temperatures (energy per particle). The boundary temperature $T_b$ separating the regular (quasiperiodic) and the stochastic (chaotic) chain motion…
The popular method of Nose and Hoover to create canonically distributed positions and momenta in classical molecular dynamics simulations is generalized to a genuine quantum system of infinite dimensionality. We show that for the quantum…
We propose a novel type of ergostats and thermostats for molecular dynamics simulations. A general class of active particle swarm models is considered, where any specific total energy (alternatively any specific temperature) can be provided…
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…
We present a general molecular-dynamics simulation scheme, based on the Nose' thermostat, for sampling according to arbitrary phase space distributions. We formulate numerical methods based on both Nose'-Hoover and Nose'-Poincare'…
A thermostat senses the temperature of a physical system and switches heating or cooling devices on or off, regulating the flow of heat to maintain the system's temperature near a desired setpoint. Taking advantage of recent advances in…
Nonequilibrium molecular dynamics (NEMD) has been extensively used to study thermal transport at various length scales in many materials. In this method, two local thermostats at different temperatures are used to generate a nonequilibrium…
We construct a new class of phenomenological equations of state for homogeneous matter for use in simulations of hot and dense matter in local thermodynamic equilibrium. We construct a functional form which respects experimental,…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
With this work we present two new methods for the generation of thermostated, manifestly Hamiltonian dynamics and provide corresponding illustrations. The basis for this new class of thermostats are the peculiar thermodynamics as exhibited…
Molecular dynamics simulations of a three dimensional relativistic gas with a soft potential are conducted with different interactions and particle masses. For all cases the velocity distribution agrees numerically with the J\"uttner…
Advanced thermostats for molecular dynamics are proposed on the base of the rigorous Langevin dynamics. Because the latter accounts for the subsystem-bath interactions in details, the bath anisotropy and nonuniformity are described via the…
We apply a recently proposed novel thermostating mechanism to an interacting many-particle system where the bulk particles are moving according to Hamiltonian dynamics. At the boundaries the system is thermalized by deterministic and…
We introduce a novel approach to sample the canonical ensemble at constant temperature and applied electric potential. Our approach can be straightforwardly implemented into any density-functional theory code. Using thermopotentiostat…
This paper suggests using the configurational temperature $\Tc$ for quantifying how far an active-matter system is from thermal equilibrium. We measure this ``distance'' by the ratio of the systemic temperature $\Ts$ to $\Tc$, where $\Ts$…
In this work we present a formalism to describe non equilibrium conditions in systems with a discretized energy spectrum, such as quantum systems. We develop a formalism based on a combination of Gibbs-Shannon entropy and information…
A fundamental challenge is to understand nonequilibrium statistical mechanics starting from microscopic chaos in the equations of motion of a many-particle system. In this review we summarize recent theoretical advances along these lines.…
The meaning of temperature in nonequilibrium thermodynamics is considered by using a forced harmonic oscillator in a heat bath, where we have two effective temperatures for the position and the momentum, respectively. We invent a concrete…
Recent laboratory experiments suggest an intrinsic asymmetry between heating and cooling, with heating occurring more efficiently. Two decades earlier, molecular dynamics (MD) simulations had examined a related setup - heating one side of a…