Related papers: A Parallel-pulling Protocol for Free-Energy Evalua…
Jarzynski's equality provides an elegant and powerful tool to directly compute differences in free energy in Monte Carlo simulations and it can be readily extended to lattice gauge theories to compute a large set of physically interesting…
In parallel iterative applications, computational efficiency is essential for addressing large problems. Load imbalance is one of the major performance degradation factors of parallel applications. Therefore, distributing, cleverly, and as…
Jarzynski's equality sets a strong bound on the probability of violating the second law of thermodynamics by extracting work beyond the free energy difference. We derive finite-time refinements to this bound for driven systems in contact…
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…
Parallel multiphysics simulations often suffer from load imbalances originating from the applied coupling of algorithms with spatially and temporally varying workloads. It is thus desirable to minimize these imbalances to reduce the time to…
Applying the method from recently developed fluctuation theorems to the stochastic dynamics of single macromolecules in ambient fluid at constant temperature, we establish two Jarzynski-type equalities: (1) between the log-mean-exponential…
This letter investigates parallelism approaches for equation and Jacobian evaluations in large-scale power flow calculation. Two levels of parallelism are proposed and analyzed: inter-model parallelism, which evaluates models in parallel,…
We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replica-exchange method; the latter is also referred to as parallel…
When a system is in equilibrium, external perturbations yield a time series of non-equilibrium distributions, and recent experimental techniques give access to the non-equilibrium data that may contain critical information. Jinwoo and…
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…
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
Recent developments in statistical mechanics have allowed the estimation of equilibrium free energies from the statistics of work measurements during processes that drive the system out of equilibrium. Here a different class of processes is…
The past two decades witnessed important developments in the field of non-equilibrium statistical mechanics. Among these developments, the Jarzynski equality, being a milestone following the landmark work of Clausius and Kelvin, stands out.…
We propose and analyze a process that extracts useful work from a single active particle maintained at constant temperature in a harmonic potential by measuring the relative sign of the self-propulsion and the confining force and then…
Jarzynski's theorem is a well-known equality in statistical mechanics, which relates fluctuations in the work performed during a non-equilibrium transformation of a system, to the free-energy difference between two equilibrium ensembles. In…
Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…
For systems in an externally controllable time-dependent potential, the optimal protocol minimizes the mean work spent in a finite-time transition between two given equilibrium states. For overdamped dynamics which ignores inertia effects,…
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,…
Two identities in statistical mechanics involving entropy differences (or ratios of density of states) at constant energy are derived. The first provides a nontrivial extension of the Jarzynski equality to the microcanonical ensemble [C.…
A quantum analogue of the Jarzynski equality is constructed. This equality connects an ensemble average of exponentiated work with the Helmholtz free-energy difference in a nonequilibrium switching process subject to a thermal heat bath. To…