Related papers: Thermostats for "slow" configurational modes
Stochastic thermodynamics is the field of study relating fluctuations in stochastic systems to thermodynamic quantities. The total entropy production (EP), is central to the thermodynamic classification of systems. Non-equilibrium systems…
We present a new dynamical approach for measuring the temperature of a Hamiltonian dynamical system in the micro canonical ensemble of thermodynamics. We show that under the hypothesis of ergodicity the temperature can be computed as a…
Ability of dynamical systems to relax to equilibrium has been investigated since the invention of statistical mechanics, which establishes the connection between dynamics of many-body Hamiltonian systems and phenomenological thermodynamics.…
We present a general formalism able to derive the kinetic equations of polymer dynamics. It is based on the application of nonequilibrium thermodynamics to analyze the irreversible processes taking place in the conformational space of the…
In these lecture notes, the basic principles of stochastic thermodynamics are developed starting with a closed system in contact with a heat bath. A trajectory undergoes Markovian transitions between observable meso-states that correspond…
A modeling framework for the internal conformational dynamics and external mechanical movement of single biological macromolecules in aqueous solution at constant temperature is developed. Both the internal dynamics and external movement…
The role of thermodynamics in continuum mechanics and the derivation of the proper constitutive relations is a discussed subject of Rational Mechanics. The classical literature did not use the accumulated knowledge of thermostatics and was…
We investigate the relation between the phase space structure of Hamiltonian and non-Hamiltonian deterministic thermostats. We show that phase space structures governing reaction dynamics in Hamiltonian systems map to the same type of phase…
We use molecular dynamics simulations to compute the Lyapunov spectra of many-particle systems resembling simple fluids in thermal equilibrium and in non-equilibrium stationary states. Here we review some of the most interesting results and…
Complex systems produce high-dimensional signals that lack macroscopic variables analogous to entropy, temperature, or free energy. This work introduces a thermoinformational formulation that derives entropy, internal energy, temperature,…
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…
This is our current research perspective on models providing insight into statistical mechanics. It is necessarily personal, emphasizing our own interest in simulation as it developed from the National Laboratories' work to the worldwide…
The stochastic thermodynamics provides a framework for the description of systems that are out of thermodynamic equilibrium. It is based on the assumption that the elementary constituents are acted by random forces that generate a…
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…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
We consider the modeling of the dynamics of the chemostat at its very source. The chemostat is classically represented as a system of ordinary differential equations. Our goal is to establish a stochastic model that is valid at the scale…
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…
A thermodynamics for systems at a stationary states is formulated. It is based upon the assumption of the existence of local equilibrium in phase space which enables one to interpret the probability density ans its conjugated nonequilibrium…
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.…
The numerical investigation of the statics and dynamics of systems in nonequilibrium in general, and under shear flow in particular, has become more and more common. However, not all the numerical methods developed to simulate equilibrium…