Related papers: Generating Generalized Distributions from Dynamica…
The concept of temperature is one of the key ideas in describing the thermodynamical properties of a physical system. In classical statistical mechanics of ideal gases, the notion of temperature can be described in two different ways, the…
The nested sampling algorithm has been shown to be a general method for calculating the pressure-temperature-composition phase diagrams of materials. While the previous implementation used single-particle Monte Carlo moves, these are…
We present a new method of conducting molecular dynamics simulation in isothermal-isobaric ensemble based on Langevin equations of motion. The stochastic coupling to all particle and cell degrees of freedoms is introduced in a correct way,…
We study the dynamics of an ensemble of non-interacting harmonic oscillators in a nonlinear dissipative environment described by the Nos\'e - Hoover model. Using numerical simulation we find the histogram for total energy, which agrees with…
We consider numerical methods for thermodynamic sampling, i.e. computing sequences of points distributed according to the Gibbs-Boltzmann distribution, using Langevin dynamics and overdamped Langevin dynamics (Brownian dynamics). A wide…
A general formalism is developed for constructing modified Hamiltonian dynamical systems which preserve a canonical equilibrium distribution by adding a time evolution equation for a single additional thermostat variable. When such systems…
We propose a new sampler that integrates the protocol of parallel tempering with the Nos\'e-Hoover (NH) dynamics. The proposed method can efficiently draw representative samples from complex posterior distributions with multiple isolated…
Using simulations or experiments performed at some set of temperatures to learn about the physics or chemistry at some other arbitrary temperature is a problem of immense practical and theoretical relevance. Here we develop a framework…
The present paper studies a large class of temperature dependent probability distributions and shows that entropy and energy can be defined in such a way that these probability distributions are the equilibrium states of a generalized…
Several different methods are regularly used to infer the properties of the neutral interstellar medium (ISM) using atomic hydrogen (H I) 21cm absorption and emission spectra. In this work, we study various techniques used for inferring ISM…
When a quantum field is in contact with a thermal bath, the vacuum state of the field may be generalized to a thermal vacuum state, which takes into account the thermal noise. In thermo field dynamics, this is realized by doubling the…
In this article, we focus on the sampling of the configurational Gibbs-Boltzmann distribution, that is, the calculation of averages of functions of the position coordinates of a molecular $N$-body system modelled at constant temperature. We…
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.…
We present a thermodynamic theory for a generic population of $M$ individuals distributed into $N$ groups (clusters). We construct the ensemble of all distributions with fixed $M$ and $N$, introduce a selection functional that embodies the…
We study the behavior of an assembly of $N$ granular particles contained in two compartments within a simple kinetic approach. The particles belonging to each compartment collide inelastically with each other and are driven by a stochastic…
A variety of enhanced statistical and numerical methods are now routinely used to extract comprehensible and relevant thermodynamic information from the vast amount of complex, high-dimensional data obtained from intensive molecular…
We develop a formulation for molecular dynamics, Langevin, and hybrid Monte Carlo algorithms in the recently proposed generalized ensemble that is based on a physically motivated realisation of Tsallis weights. The effectiveness of the…
In this article we study a fully relativistic model of a two dimensional hard-disk gas. This model avoids the general problems associated with relativistic particle collisions and is therefore an ideal system to study relativistic effects…
We show that a recently introduced stochastic thermostat [J. Chem. Phys. 126 (2007) 014101] can be considered as a global version of the Langevin thermostat. We compare the global scheme and the local one (Langevin) from a formal point of…
Employing a simple hydrophobic-polar heteropolymer model, we compare thermodynamic quantities obtained from Andersen and Nose-Hoover molecular dynamics as well as replica-exchange Monte Carlo methods. We find qualitative correspondence in…