Related papers: Equilibrium sampling by re-weighting non-equilibri…
Nonequilibrium sampling is potentially much more versatile than its equilibrium counterpart, but it comes with challenges because the invariant distribution is not typically known when the dynamics breaks detailed balance. Here, we derive a…
Jarzynski Equality (JE) and the thermodynamic integration method are conventional methods to calculate free energy difference (FED) between two equilibrium states with constant temperature of a system. However, a number of ensemble samples…
We introduce an extension to the Weighted Ensemble (WE) path sampling method to restrict sampling to a one dimensional path through a high dimensional phase space. Our method, which is based on the finite-temperature string method, permits…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves trajectory accuracy at high temperatures, and thereby contributes to numerical stability. In addition, the…
We derive a general expression for the electron nonequilibrium (NE) distribution function in the context of steady state quantum transport through a two-terminal nanodevice with interaction. The central idea for the use of NE distributions…
I give an overview of rare event simulation techniques to generate dynamical pathways across high free energy barriers. The methods on which I will concentrate are the reactive flux approach, transition path sampling, (replica-exchange)…
Nonequilibrium experiments of single biomolecules such as force-induced unfolding reveal details about a few degrees of freedom of a complex system. Molecular dynamics simulations can provide complementary information, but exploration of…
Energy-Based Models (EBMs) provide a flexible framework for generative modeling, but their training remains theoretically challenging due to the need to approximate normalization constants and efficiently sample from complex, multi-modal…
The Jarzynski equality (JE), which connects the equilibrium free energy with non-equilibrium work statistics, plays a crucial role in quantum thermodynamics. Although practical quantum systems are usually multi-level systems, most tests of…
Energy-based models (EBMs) are generative models inspired by statistical physics with a wide range of applications in unsupervised learning. Their performance is best measured by the cross-entropy (CE) of the model distribution relative to…
We present a generic reweighting method for nonequilibrium Markov processes. With nonequilibrium Monte Carlo simulations at a single temperature, one calculates the time evolution of physical quantities at different temperatures, which…
According to the Jarzynski theorem, equilibrium free energy differences can be calculated from the statistics of work carried out during non-equilibrium transformations. Although exact, this approach can be plagued by large statistical…
The Jarzynski equality (JE) provides a nonequilibrium method to measure and calculate the free energy difference (FED). Note that if two systems share the same Hamiltonian at two equilibrium states, respectively, they share the same FED…
Although the reverse non-equilibrium molecular dynamics (RNEMD) simulation method has been widely employed, the range of applicability is yet to be discussed. In this study, for the first time, we systematically examine the method against…
The modern theory of rare events is grounded in near equilibrium ideas, however many systems of modern interest are sufficiently far from equilibrium that traditional approaches do not apply. Using the recently developed variational path…
To directly simulate rare events using atomistic molecular dynamics is a significant challenge in computational biophysics. Well-established enhanced-sampling techniques do exist to obtain the thermodynamic functions for such systems. But…
An issue for molecular dynamics simulations is that events of interest often involve timescales that are much longer than the simulation time step, which is set by the fastest timescales of the model. Because of this timescale separation,…
We extend the non-parametric framework of reaction coordinate optimization to non-equilibrium ensembles of (short) trajectories. For example, we show how, starting from such an ensemble, one can obtain an equilibrium free energy profile…
We review a dynamical approach to non-equilibrium MD (D-NEMD). We show how, using a proper simulation setup, is possible to treat interesting cases in which the initial condition is a stationary non-equilibrium state produced by a suitable…