Related papers: Equilibrium sampling by re-weighting non-equilibri…
Joint Energy-based Model (JEM) is a recently proposed hybrid model that retains strong discriminative power of modern CNN classifiers, while generating samples rivaling the quality of GAN-based approaches. In this paper, we propose a…
Molecular relaxation, finding the equilibrium state of a non-equilibrium structure, is an essential component of computational chemistry to understand reactivity. Classical force field (FF) methods often rely on insufficient local energy…
Being able to effectively locate saddle (and other fixed) points in dynamical systems holds tremendous implications in a number of applications in engineering and science, among which the study of rare events in molecular simulations stands…
We introduce a straightforward, single-ensemble, path sampling approach to calculate free energy differences based on Jarzynski's relation. For a two-dimensional ``toy'' test system, the new (minimally optimized) method performs roughly one…
We propose a relative entropy gradient sampler (REGS) for sampling from unnormalized distributions. REGS is a particle method that seeks a sequence of simple nonlinear transforms iteratively pushing the initial samples from a reference…
We describe short-time kinetic and steady-state properties of the non--equilibrium phases, namely, solid, liquid and gas anisotropic phases in a driven Lennard-Jones fluid. This is a computationally-convenient two-dimensional model which…
Equilibrium quantum systems are often described by a gas of weakly-interacting normal modes. Bringing such systems far from equilibrium, however, can drastically enhance mode-to-mode interactions. Understanding the resulting liquid is a…
Processing sets or other unordered, potentially variable-sized inputs in neural networks is usually handled by aggregating a number of input tensors into a single representation. While a number of aggregation methods already exist from…
A nonequilibrium statistical operator method is developed for ensembles of particles obeying non-Hamiltonian equations of motion in classical phase space. The main consequences of non-zero compressibility of phase space are examined in…
Cryo-electron microscopy (cryo-EM) has recently become a premier method for obtaining high-resolution structures of biological macromolecules. However, it is limited to biomolecular samples with low conformational heterogeneity, where all…
Predictive simulations of complex systems are essential for applications ranging from weather forecasting to drug design. The veracity of these predictions hinges on their capacity to capture the effective system dynamics. Massively…
Non-equilibrium Monte Carlo simulations based on Jarzynski's equality are a well-understood method to compute differences in free energy and also to sample from a target probability distribution without the need to thermalize the system…
Nested sampling (NS) has emerged as a powerful tool for exploring thermodynamic properties in materials science. However, its efficiency is often hindered by the limitations of Markov chain Monte Carlo (MCMC) sampling. In strongly…
The Jarzynski estimator is a powerful tool that uses nonequilibrium statistical physics to numerically obtain partition functions of probability distributions. The estimator reconstructs partition functions with trajectories of the…
The weighted ensemble (WE) method, an enhanced sampling approach based on periodically replicating and pruning trajectories in a set of parallel simulations, has grown increasingly popular for computational biochemistry problems, due in…
The theoretical analysis of many problems in physics, astronomy and applied mathematics requires an efficient numerical exploration of multimodal parameter spaces that exhibit broken ergodicity. Monte Carlo methods are widely used to deal…
In the global framework of finding an axiomatic derivation of nonequilibrium Statistical Mechanics from fundamental principles, such as the maximum path entropy -- also known as Maximum Caliber principle -- , this work proposes an…
A method for adaptive model order reduction for nonsmooth discrete element simulation is developed and analysed in numerical experiments. Regions of the granular media that collectively move as rigid bodies are substituted with rigid bodies…
The convergence to equilibrium for renormalised solutions to nonlinear reaction-diffusion systems is studied. The considered reaction-diffusion systems arise from chemical reaction networks with mass action kinetics and satisfy the complex…
State estimation is key to both analyzing physical mechanisms and enabling real-time control of fluid flows. A common estimation approach is to relate sensor measurements to a reduced state governed by a reduced-order model (ROM). (When…