相关论文: Efficient stochastic thermostatting of path integr…

A wide variety of numerical methods are evaluated and compared for solving the stochastic differential equations encountered in molecular dynamics. The methods are based on the application of deterministic impulses, drifts, and Brownian…

Integrated tempering sampling (ITS) method is an approach to enhance the sampling over a broad range of energies and temperatures in computer simulations. In this paper, a new version of integrated tempering sampling method is proposed. In…

Parameter identification in pattern formation models from a single experimental snapshot is challenging, as traditional methods often require knowledge of initial conditions or transient dynamics -- data that are frequently unavailable in…

Many complex systems, ranging from migrating cells to animal groups, exhibit stochastic dynamics described by the underdamped Langevin equation. Inferring such an equation of motion from experimental data can provide profound insight into…

Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics like work, heat and entropy production to the level of individual trajectories of well-defined…

We propose a new method for computing the temperature dependence of the heat capacity in complex molecular systems. The proposed scheme is based on the use of the Langevin equation with low frequency color noise. We obtain the temperature…

Based on the quasiparticle model of the quark-gluon plasma (QGP), a color quantum path-integral Monte-Carlo (PIMC) method for calculation of thermodynamic properties and -- closely related to the latter -- a Wigner dynamics method for…

A thermostat of the Nose-Hoover type, based on relative velocities and a local definition of the temperature, is presented. The thermostat is momentum-conserving and Galilean-invariant, which should make it suitable for use in Dissipative…

We propose a novel Skew Gradient Embedding (SGE) framework for systematically reformulating thermodynamically consistent partial differential equation (PDE) models-capturing both reversible and irreversible processes-as generalized gradient…

Diffusion models achieve strong generation quality, diversity, and distribution coverage, but their performance often comes with expensive inference. In this work, we propose Stochastic Transition-Map Distillation (STMD), a teacher-free…

Integrals of the Liouville $1$-form, known as the first Poincar\'e integral invariant, provide a computable figure of merit for monitoring the conservation of symplecticity in the numerical integration of Hamiltonian systems. These…

We consider the class of stationary-increment harmonizable stable processes with infinite control measure, which most notably includes real harmonizable fractional stable motions. We give conditions for the integrability of the paths of…

Tissue biopsy evaluation in the clinic is in need of quantitative disease markers for diagnosis and, most importantly, prognosis. Among the new technologies, quantitative phase imaging (QPI) has demonstrated promise for histopathology…

Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…

A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…

The Generalized Langevin Equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general non-equilibrium processes. In this approach, a part of the whole system (an…

We present a new Partial Integral Equation (PIE) representation of Partial Differential Equations (PDEs) in which it is possible to use convex optimization to perform stability analysis with little or no conservatism. The first result gives…

The lack of a well-defined equilibrium reference configuration has long hindered a comprehensive atomic-level understanding of liquid dynamics and properties. The Instantaneous Normal Mode (INM) approach, which involves diagonalizing the…

We study a numerical method to compute probability density functions of solutions of stochastic differential equations. The method is sometimes called the numerical path integration method and has been shown to be fast and accurate in…

Thermodynamics of dissipative quantum systems with double-well potentials is studied by the path-integral Monte Carlo (PIMC) method without truncation to the two-state model. For efficient simulation at low temperatures, we develop a new…