Related papers: Dynamical reweighting for estimation of fluctuatio…
We consider a class of deterministic local collisional dynamics, showing how to approximate them by means of stochastic models and then studying the fluctuations of the current of energy. We show first that the variance of the…
Markov State Models (MSM) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations, for example…
In this work we elaborate on two recently discovered invariance principles, according to which transport coefficients are, to a large extent, independent of the microscopic definition of the densities and currents of the conserved…
The transport coefficient of shear viscosity is studied for a hadron matter through microscopic transport model, the Ultra--relativistic Quantum Molecular Dynamics (UrQMD), using the Green--Kubo formulas. Molecular--dynamical simulations…
We propose an adaptive importance sampling scheme for the simulation of rare events when the underlying dynamics is given by a diffusion. The scheme is based on a Gibbs variational principle that is used to determine the optimal (i.e.…
We show how to evaluate mobility profiles, characterizing the transport of confined fluids under a perturbation, from equilibrium molecular simulations. The correlation functions derived with the Green-Kubo formalism are difficult to sample…
The purpose of this study is to provide a reproducible framework in the use of the Green-Kubo formalism to extract transport coefficients. More specifically, in the case of shear viscosity, we investigate the limitations and technical…
Directly computing mass transport coefficients in stochastic models requires integrating over time the equilibrium correlations between atomic displacements. Here, we show how to accelerate the computations via \green{correlation splitting…
Thermal transport coefficients are independent of the specific microscopic expression for the energy density and current from which they can be derived through the Green-Kubo formula. We discuss this independence in terms of a kind of gauge…
Molecular dynamics (MD) simulations are used to calculate transport coefficients in a two-component plasma interacting through a repulsive Coulomb potential. The thermal conductivity, electrical conductivity, electrothermal coefficient,…
Near equilibrium, Green-Kubo relations provide microscopic expressions for macroscopic transport coefficients in terms of equilibrium correlation functions. At their core, they are based on the intimate relationship between response and…
Green-Kubo and Einstein expressions for the transport coefficients of a fluid in a nonequilibrium steady state can be derived using the Fluctuation Theorem and by assuming the probability distribution of the time-averaged dissipative flux…
We introduce $\pi$-Girsanov, a new method for constructing Markov state models from biased enhanced-sampling molecular dynamics simulations based on Girsanov reweighting. The key idea behind this new method is to separate the reweighting…
We present a microscopic derivation of the laws of continuum mechanics of nonideal ordered solids including dissipation, defect diffusion, and heat transport. Starting point is the classical many-body Hamiltonian. The approach relies on the…
Gribov quantization is a method to improve the infrared dynamics of Yang-Mills theory. We study the thermodynamics and transport properties of a plasma consisting of gluons whose propagator is improved by the Gribov prescription. We first…
We propose a first-principles method of efficiently evaluating electron-transport properties of very long systems. Implementing the recursive Green's function method and the shifted conjugate gradient method in the transport simulator based…
In Part I of this two-part series, the reverse perturbation method for shearing simple liquids [Phys. Rev. E 59, 4894 (1999)] was extended to systems of interacting particles with time-discrete stochastic dynamics. For verification, in this…
We commonly encounter the problem of identifying an optimally weight adjusted version of the empirical distribution of observed data, adhering to predefined constraints on the weights. Such constraints often manifest as restrictions on the…
Building upon recent developments of force-based estimators with a reduced variance for the computation of densities, radial distribution functions or local transport properties from molecular simulations, we show that the variance can be…
We implement, optimize, and validate the linear-scaling Kubo-Greenwood quantum transport simulation on graphics processing units by examining resonant scattering in graphene. We consider two practical representations of the Kubo-Greenwood…