Related papers: Single-Sweep Methods for Free Energy Calculations
Finding and sampling multiple reaction channels for molecular transitions remains an important challenge in physical chemistry. Here we show that the weighted ensemble (WE) path sampling method can readily sample multiple channels. In a…
Computing accurate reaction rates is a central challenge in computational chemistry and biology because of the high cost of free energy estimation with unbiased molecular dynamics. In this work, a data-driven machine learning algorithm is…
We propose a new method for the problems of computing free energy and surface pressure for various statistical mechanics models on a lattice $\Z^d$. Our method is based on representing the free energy and surface pressure in terms of…
We present a complete prescription for the numerical calculation of surface Green's functions and self-energies of semi-infinite quasi-onedimensional systems. Our work extends the results of Sanvito et al. [1] generating a robust algorithm…
We describe a method for reconstructing spatially explicit maps of seasonal palaeoclimate variables from site-based reconstructions. Using a 3D-Variational technique, the method finds the best statistically unbiased, and spatially…
We propose a method to decompose the total energy of a supercell containing defects into contributions of individual atoms, using the energy density formalism within density functional theory. The spatial energy density is unique up to a…
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed…
The equilibrium free energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is…
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…
We present a simple model system with four hard disks moving in a circular region for which free energy landscapes can be directly calculated and visualized in two and three dimensions. We construct several energy landscapes for our system…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
Transition path sampling (TPS) is a powerful technique for investigating rare transitions, especially when the mechanism is unknown and one does not have access to the reaction coordinate. Straightforward application of TPS does not…
We report a novel Monte Carlo scheme that greatly enhances the power of parallel-tempering simulations. In this method, we boost the accumulation of statistical averages by including information about all potential parallel tempering trial…
Computing free energy is a fundamental problem in statistical physics. Recently, two distinct methods have been developed and have demonstrated remarkable success: the tensor-network-based contraction method and the neural-network-based…
We investigate relations between spatial properties of the free energy and the radius of Gaussian curvature of the underlying curved lattice geometries. For this purpose we derive recurrence relations for the analysis of the free energy…
Estimating free energy differences, an important problem in computational drug discovery and in a wide range of other application areas, commonly involves a computationally intensive process of sampling a family of high-dimensional…
We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined…
We develop a scalable, computationally efficient method for the task of energy disaggregation for home appliance monitoring. In this problem the goal is to estimate the energy consumption of each appliance over time based on the total…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
We present a methodology for accelerating the estimation of the free energy from path integral Monte Carlo simulations by considering an intermediate artificial reference system where interactions are inexpensive to evaluate numerically.…