Related papers: Jarzynski matrix equality: calculating free energy…
Free energies of molecules can be calculated by quantum computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic…
Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…
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.…
Exchange energy statistics between two bodies at different thermal equilibrium obey the Jarzynski-W\'ojcik fluctuation theorem. The corresponding energy scale factor is the difference of the inverse temperatures associated to the bodies at…
We define common thermodynamic concepts purely within the framework of general Markov chains and derive Jarzynski's equality and Crooks' fluctuation theorem in this setup. In particular, we regard the discrete time case that leads to an…
Bridging equilibrium and nonequilibrium statistical physics attracts sustained interest. Hallmarks of nonequilibrium systems include a breakdown of detailed balance, and an absence of a priori potential function corresponding to the…
Accurate free-energy estimation is essential in molecular simulation, yet the periodic boundary conditions (PBC) commonly used in computer simulations have rarely been explicitly exploited. Equilibrium methods such as umbrella sampling,…
Fast and accurate evaluation of free energy has broad applications from drug design to material engineering. Computing the absolute free energy is of particular interest since it allows the assessment of the relative stability between…
Systematic inaccuracy is inherent in any computational estimate of a non-linear average, due to the availability of only a finite number of data values, N. Free energy differences (DF) between two states or systems are critically important…
The fluctuation theorems, and in particular, the Jarzynski equality, are the most important pillars of modern non-equilibrium statistical mechanics. We extend the quantum Jarzynski equality together with the Two-Time Measurement Formalism…
We compute the large-scale limit of the free energy associated with the problem of inference of a finite-rank matrix. The method follows the principle put forward in arXiv:1811.01432 which consists in identifying a suitable Hamilton-Jacobi…
We propose a method to evaluate general thermodynamic fluctuations in open quantum systems, based on performing a two-point measurement scheme on the system using dynamics-dependent thermodynamic observables. Our approach allows one to…
This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how…
Motivated by the design question of additional fuel needed to complete a task in an uncertain environment, this paper introduces metrics to quantify the maximal additional energy used by a control system in the presence of bounded…
The Jarzynski identity can describe small-scale nonequilibrium systems through stochastic thermodynamics. The identity considers fluctuating trajectories in a phase space. The complexity geometry frames the discussions on quantum…
We extend the non-parametric framework of reaction coordinate optimization to non-equilibrium ensembles of (short) trajectories. For example, we show how, starting from such an ensemble, one can obtain an equilibrium free energy profile…
The quantum Jarzynski equality and the Crooks relation are fundamental laws connecting equilibrium processes with nonequilibrium fluctuations. They are promising tools to benchmark quantum devices and measure free energy differences. While…
Energy distance is a statistical distance between the distributions of random variables, which characterizes the equality of the distributions. Utilizing the energy distance, we develop a nonparametric test for the diagonal symmetry, which…
We present the diagrammatic technique for calculating the free energy of the matrix eigenvalue model (the model with arbitrary power $\beta$ by the Vandermonde determinant) to all orders of 1/N expansion in the case where the limiting…
The gain of free energy upon unmixing is determined via application of Markov state modeling (MSM), using an Ising model with a fixed number of up- and down-spins. MSM yields reasonable estimates of the free energies. However, a closer look…