Related papers: Optimized free energies from bidirectional single-…
External biasing forces are often applied to enhance sampling in regions of phase space which would otherwise be rarely observed. While the typical goal of these experiments is to calculate the potential of mean force (PMF) along the…
According to the nonequilibrium work relations, path-ensembles generated by irreversible processes in which a system is driven out of equilibrium according to a predetermined protocol may be used to compute equilibrium free energy…
We present an approach to the estimate of the potential of mean force along a generic reaction coordinate based on maximum likelihood methods and path-ensemble averages in systems driven far from equilibrium. Following similar arguments,…
Recently discovered identities in statistical mechanics have enabled the calculation of equilibrium ensemble averages from realizations of driven nonequilibrium processes, including single-molecule pulling experiments and analogous computer…
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…
Existing optimal estimators of nonequilibrium path-ensemble averages are shown to fall within the framework of extended bridge sampling. Using this framework, we derive a general minimal-variance estimator that can combine nonequilibrium…
We present a detailed comparison of computational efficiency and precision for several free energy difference ($\Delta F$) methods. The analysis includes both equilibrium and non-equilibrium approaches, and distinguishes between…
We focus on an alignment-free method to estimate the underlying signal from a large number of noisy randomly shifted observations. Specifically, we estimate the mean, power spectrum, and bispectrum of the signal from the observations. Since…
Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently…
A vast array of phenomena, ranging from chemical reactions to phase transformations, are analysed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used,…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
This paper applies the Bayesian Model Averaging (BMA) statistical ensemble technique to estimate small molecule solvation free energies. There is a wide range of methods available for predicting solvation free energies, ranging from…
We present a new method to compute free energies at a quantum mechanical (QM) level of theory from molecular simulations using cheap reference potential energy functions, such as force fields. To overcome the poor overlap between the…
We derive the optimal estimates of the free energies of an arbitrary number of thermodynamic states from nonequilibrium work measurements; the work data are collected from forward and reverse switching processes and obey a fluctuation…
Chance-constrained optimization has emerged as a promising framework for managing uncertainties in power systems. This work advances its application to the DC Optimal Power Flow (DC-OPF) model, developing a novel approach to uncertainty…
We introduce a robust optimization method for flip-free distortion energies used, for example, in parametrization, deformation, and volume correspondence. This method can minimize a variety of distortion energies, such as the symmetric…
We derive the bias function that minimizes the statistical error of free energy differences calculated in work-biased fast-switching simulations. The optimum bias function is compared to other bias functions using a particle pulled through…
Quantifying the forces between and within macromolecules is a necessary first step in understanding the mechanics of molecular structure, protein folding, and enzyme function and performance. In such macromolecular settings, dynamic…
The estimation of advantage is crucial for a number of reinforcement learning algorithms, as it directly influences the choices of future paths. In this work, we propose a family of estimates based on the order statistics over the path…