Related papers: Efficient free energy profile reconstruction using…
We derive the differential equation describing the time evolution of the work probability distribution function of a stochastic system which is driven out of equilibrium by the manipulation of a parameter. We consider both systems described…
We present a method for determining the free energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting…
For a timely decarbonization of our economy, power systems need to accommodate increasing numbers of clean but stochastic resources. This requires new operational methods that internalize this stochasticity to ensure safety and efficiency.…
Almost 25 years ago, Jarzynski published a paper in which it was asserted: the work done, W, in driving a system from state A to state B, characterized by the Helmholtz free energies FA and FB, satisfies an equality in which an average over…
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 describe a strategy to improve the efficiency of free energy estimates by reducing dissipation in nonequilibrium Monte Carlo simulations. This strategy generalizes the targeted free energy perturbation approach [Phys. Rev. E. 65, 046122,…
Free energy differences are a central quantity of interest in physics, chemistry, and biology. We develop design principles that improve the precision and accuracy of free energy estimators, which has potential applications to screening for…
We reconsider a well-known relationship between the fluctuation theorem and the second law of thermodynamics by evaluating a probability measure-valued process. In order to establish a bridge between microscopic and macroscopic behaviors,…
Recently there has been growing interest in extending the thermodynamic method from static configurations to dynamical trajectories. In this approach, ensembles of trajectories are treated in an analogous manner to ensembles of…
We calculate and verify with simulations the ratio between the average translational and rotational energies of systems with rough, inelastic particles, either forced or freely cooling. The ratio shows non-equipartition of energy. In…
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 central endeavor of thermodynamics is the measurement of free energy changes. Regrettably, although we can measure the free energy of a system in thermodynamic equilibrium, typically all we can say about the free energy of a…
We derive and solve a differential equation satisfied by the probability distribution of the work done on a single biomolecule in a mechanical unzipping experiment. The unzipping is described as a thermally activated escape process in an…
The Jarzynski equality (JE) provides a nonequilibrium method to measure and calculate the free energy difference (FED). Note that if two systems share the same Hamiltonian at two equilibrium states, respectively, they share the same FED…
We derive a fluctuation theorem for generalized work distributions, related to bijective mappings of the phase spaces of two physical systems, and use it to derive a two-sided constraint maximum likelihood estimator of their free energy…
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…
The Jarzynski equality is generalized to situations in which nonequilibrium systems are subject to a feedback control. The new terms that arise as a consequence of the feedback describe the mutual information content obtained by measurement…
We analyze the perceptron model performing a Plefka-like expansion of the free energy. This model falls in the same universality class as hard spheres near jamming, allowing to get exact predictions in high dimensions for more complex…
A powerful and well-established tool for free-energy estimation is Bennett's acceptance ratio method. Central properties of this estimator, which employs samples of work values of a forward and its time reversed process, are known: for…
We develop a systematic procedure to approximate generalized free energy in out of equilibrium stochastic systems. The procedure only requires knowledge of the averages of macroscopic observables and uses quasi-equilibrium distribution to…