Related papers: Statistically optimal analysis of samples from mul…
The multistate Bennett Acceptance Ratio is provably the lowest variance unbiased estimator of both free energies and ensemble averages, and has a number of important advantages over previous methods, such as WHAM. Despite its advantages,…
The multistate Bennett acceptance ratio (MBAR) method is a prevalent approach for computing free energies of thermodynamic states. In this work, we introduce BayesMBAR, a Bayesian generalization of the MBAR method. By integrating…
Free energy calculations based on atomistic Hamiltonians provide microscopic insight into the thermodynamic driving forces of biophysical or condensed matter systems. Many approaches use intermediate Hamiltonians interpolating between the…
The dynamics of molecules are governed by rare event transitions between long-lived (metastable) states. To explore these transitions efficiently, many enhanced sampling protocols have been introduced that involve using simulations with…
Computing the equilibrium properties of complex systems, such as free energy differences, is often hampered by rare events in the dynamics. Enhanced sampling methods may be used in order to speed up sampling by, for example, using high…
Multiple sampling strategies commonly used in molecular dynamics, such as umbrella sampling and alchemical free energy methods, involve sampling from multiple thermodynamic states. Commonly, the data are then recombined to construct…
Free energy difference calculations based on atomistic simulations generally improve in accuracy when sampling from a sequence of intermediate equilibrium thermodynamic states that bridge the configuration space between two states of…
We show how thermodynamic properties of molecular models can be computed over a large, multidimensional parameter space by combining multistate reweighting analysis with a linear basis function approach. This approach reduces the…
We introduce a method to compute the reweighted path ensemble by combining transition interface sampling simulations conditioned on different collective variables. The approach is based on the Multistate Bennett Acceptance Ratio (MBAR)…
Free energy calculations based on atomistic Hamiltonians and sampling are key to a first principles understanding of biomolecular processes, material properties, and macromolecular chemistry. Here, we generalize the Free Energy Perturbation…
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…
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…
Free energies are fundamental quantities governing phase behavior and thermodynamic stability in polymer systems, yet their accurate computation often requires extensive simulations and post-processing techniques such as the Bennett…
The nonequilibrium work fluctuation theorem provides the way for calculations of (equilibrium) free energy based on work measurements of nonequilibrium, finite-time processes and their reversed counterparts by applying Bennett's acceptance…
We consider the problem of estimating the energy of a quantum state preparation for a given Hamiltonian in Pauli decomposition. For various quantum algorithms, in particular in the context of quantum chemistry, it is crucial to have energy…
When studying high-dimensional dynamical systems such as macromolecules, quantum systems and polymers, a prime concern is the identification of the most probable states and their stationary probabilities or free energies. Often, these…
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…
Free energy of crystal phases is commonly evaluated by thermodynamic integration (TDI) along a reversible path that involves an external potential. A persistent problem in this method is that a significant hysteresis is observed due to…
This paper presents a consensus algorithm for a multi-agent system where each agent has access to its imperfect own state and neighboring state measurements. The measurements are subject to deterministic disturbances and the proposed…
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…