Related papers: Computing equilibrium free energies through a none…
We describe a method to explore the configurational phase space of chemical systems. It is based on the nested sampling algorithm recently proposed by Skilling [Skilling J. (2004) In AIP Conference Proceedings, vol. 735, p. 395.; Skilling…
Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when multiple parallel channels along the reaction coordinate or hidden barriers in directions…
This article describes nonequilibrium techniques for the calculation of free energies of solids using molecular dynamics (MD) simulations. These methods provide an alternative to standard equilibrium thermodynamic integration methods and…
Free energy perturbation (FEP) is frequently used to evaluate the free energy change of a biological process, e.g. the drug binding free energy or the ligand solvation free energy. Due to the sampling inefficiency, FEP is often employed…
Studies in atomic-scale modeling of surface phase equilibria often focus on temperatures near zero Kelvin due to the challenges in calculating the free energy of surfaces at finite temperatures. The Bayesian-inference-based nested sampling…
Biased sampling in molecular dynamics simulations overcomes timescale limitations and delivers free-energy landscapes, essential to understand complex atomistic phenomena. However, when applied across diverse systems and processes, biasing…
Sampling the free energy surface, namely, the distribution of collective variables (CVs), is a crucial problem in statistical physics, as it underpins a better understanding of chemical reactions and conformational transitions. Traditional…
The free energetics of water density fluctuations in bulk water, at interfaces, and in hydrophobic confinement inform the hydration of hydrophobic solutes as well as their interactions and assembly. The characterization of such free…
We present a new method to evaluate vibrational free energies of atomic systems without a priori specification of an interatomic potential. Our model-agnostic approach leverages descriptors, high-dimensional feature vectors of atomic…
Temperature Accelerated Sliced Sampling (TASS) is an efficient method to compute high dimensional free energy landscapes. The original TASS method employs the Weighted Histogram Analysis Method (WHAM) which is an iterative post-processing…
Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In…
Non-equilibrium thermodynamics provides a general framework for understanding non-equilibrium processes, particularly in small systems that are typically far from equilibrium and dominated by fluctuations. However, the experimental…
The computation of dynamical response functions is central to many problems in condensed matter physics. Owing to the rapid growth of quantum correlations following a quench, classical methods face significant challenges even if an…
Token sampling strategies critically influence text generation quality in large language models (LLMs). However, existing methods introduce additional hyperparameters, requiring extensive tuning and complicating deployment. We present…
This work develops a polygonal finite element method (PFEM) for the analysis of steady-state and transient thermal stresses in two dimensional continua. The method employs Wachspress rational basis functions to construct conforming…
Ensuring a satisfactory statistical convergence of anharmonic thermodynamic properties requires sampling of many atomic configurations, however the methods to obtain those necessarily produce correlated samples, thereby reducing the…
We develop a model based on the fractional exclusion statistics (FES) applicable to non-homogeneous interacting particle systems. Here the species represent elementary volumes in an (s+1)-dimensional space, formed by the direct product…
Simulating the nonequilibrium dynamics of thermal states is a fundamental problem across scales from high energy to condensed matter physics. Quantum computers may provide a way to solve this problem efficiently. Preparing a thermal state…
The recently introduced nested sampling algorithm allows the direct and efficient calculation of the partition function of atomistic systems. We demonstrate its applicability to condensed phase systems with periodic boundary conditions by…
Umbrella sampling efficiently yields equilibrium averages that depend on exploring rare states of a model by biasing simulations to windows of coordinate values and then combining the resulting data with physical weighting. Here, we…