Related papers: Calculating the free energy difference by applying…
The accurate estimation of free energy differences between two states is a long-standing challenge in molecular simulations. Traditional approaches generally rely on sampling multiple intermediate states to ensure sufficient overlap in…
We introduce the Free Energy Manifold (FEM), a score-trained conditional energy model specialized for inference in hybrid Bayesian networks with discrete and continuous variables. FEM represents each conditional factor as an energy…
We combine the formalisms of diagonal entropy and Jarzynski Equality to study the thermodynamic properties of closed quantum systems. Applying this approach to a quantum harmonic oscillator, the diagonal entropy offers a notion of…
We derive a general information-theoretic equality for a system undergoing two projective measurements separated by a general temporal evolution. The equality implies the non-negativity of the mutual information between the measurement…
We used the atomic force microscope to manipulate and unfold individual molecules of the titin I27 domain and reconstructed its free energy surface using Jarzynski's equality. The free energy surface for both stretching and unfolding was…
It has recently been shown that the Helmholtz free energy difference between two equilibrium configurations of a system may be obtained from an ensemble of finite-time (nonequilibrium) measurements of the work performed in switching an…
Understanding and manipulating work fluctuations in microscale and nanoscale systems are of both fundamental and practical interest. For example, aspects of work fluctuations will be an important factor in designing nanoscale heat engines.…
The Free-Energy-Principle (FEP) is an influential and controversial theory which postulates a deep and powerful connection between the stochastic thermodynamics of self-organization and learning through variational inference. Specifically,…
Application of Jarzynski nonequilibrium work relation to free energy calculation is limited by the very slow convergence of the estimate when dissipation is high. We present a novel perturbation protocol able to improve the convergence of…
A methodology for calculating the contribution of charged defects to the configurational free energy of an ionic crystal is introduced. The temperature-independent Wang-Landau Monte Carlo technique is applied to a simple model of a solid…
We obtain the exact nonequilibrium work generating function (NEWGF), for a small system consisting of a massive Brownian particle connected to internal and external springs. The external work is provided to the system for a finite time…
Work is a process-based quantity, and its measurement typically requires interaction with a measuring device multiple times. While classical systems allow for non-invasive and accurate measurements, quantum systems present unique challenges…
A fluctuation relation, which is an extended form of the Jarzynski equality, is introduced and discussed. We show how to apply this relation in order to evaluate the free energy landscape of simple systems. These systems are manipulated by…
Let Delta F be the free energy difference between two equilibrium states of a system. An established method of numerically computing Delta F involves a single, long ``switching simulation'', during which the system is driven reversibly from…
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…
We show a practical application of the Jarzynski equality in quantum computation. Its implementation may open a way to solve combinatorial optimization problems, minimization of a real single-valued function, cost function, with many…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
Jarzynski equality and related fluctuation theorems can be formulated for various setups. Such an equality was recently derived for nonunitary quantum evolutions described by unital quantum operations, i.e., for completely positive,…
The free-energy difference $\Delta F$ between two high-dimensional systems is notoriously difficult to compute, but very important for many applications, such as drug discovery. We demonstrate that an unconventional definition of work…
Nonequilibrium processes of small systems such as molecular machines are ubiquitous in biology, chemistry and physics, but are often challenging to comprehend. In the past two decades, several exact thermodynamic relations of nonequilibrium…