Related papers: Reconstructing Equilibrium Entropy and Enthalpy Pr…
We introduce a straightforward, single-ensemble, path sampling approach to calculate free energy differences based on Jarzynski's relation. For a two-dimensional ``toy'' test system, the new (minimally optimized) method performs roughly one…
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…
We present in detail a Langevin formalism for constructing stochastic dynamical equations for active-matter systems coupled to a thermal bath. We apply the formalism to clarify issues of principle regarding the sources and signatures of…
Jarzynski's equality (JE) allows us to compute free energy differences from distributions of work. In molecular dynamics simulations, the traditional way of constructing work distributions is to perform as many pulling simulations as…
Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by…
The connection between work and changes in the Hamiltonian for a system with a time-dependent Hamiltonian has recently been called into question, casting doubt on the usefulness of the Jarzynski equality for calculating free energy changes.…
Entanglement entropy encodes important features of strongly interacting quantum many-body systems and gauge theories, but its analytical study is still limited to systems with high level of symmetry. This motivates the search for efficient…
When a system is driven out of equilibrium by a time-dependent protocol that modifies the Hamiltonian, it follows a nonequilibrium path. Samples of these paths can be used in nonequilibrium work theorems to estimate equilibrium quantities,…
We introduce a simple enhanced sampling approach for the calculation of free energy differences and barriers along a one-dimensional reaction coordinate. First, a small number of short nonequilibrium simulations are carried out along the…
Energy-based models (EBMs) are generative models inspired by statistical physics with a wide range of applications in unsupervised learning. Their performance is best measured by the cross-entropy (CE) of the model distribution relative 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…
On the basis of the balance equations for energy-momentum, spin, particle and entropy density, an approach is considered which represents a comparatively general framework for special- and general-relativistic continuum thermodynamics. In…
The nonequilibrium fluctuation theorems have paved the way for estimating equilibrium thermodynamic properties, such as free energy differences, using trajectories from driven nonequilibrium processes. While many statistical estimators may…
The nonequilibrium free energy theorems show how distributions of work along nonequilibrium paths are related to free energy differences between the equilibrium states at the end points of these paths. In this paper we develop a natural way…
Five different methods which can be used to analytically calculate entropies that are nonconcave as functions of the energy in the thermodynamic limit are discussed and compared. The five methods are based on the following ideas and…
The Jarzynski equality (JE) is known as an exact identity for nonequillibrium systems. The JE was originally formulated for isolated and isothermal systems, while Adib reported an JE extended to an isoenergetic process. In this paper, we…
Complex dissipative systems appear across science and engineering, from polymers and active matter to learning algorithms. These systems operate far from equilibrium, where energy dissipation and time irreversibility govern their behavior…
We use Newtonian and overdamped Langevin dynamics to study long flexible polymers dragged by an external force at a constant velocity $v$. The work $W$ by that force depends on the initial state of the polymer and the details of the…
In this paper, we consider Langevin processes with mechanical constraints. The latter are a fundamental tool in molecular dynamics simulation for sampling purposes and for the computation of free energy differences. The results of this…
A promising method for calculating free energy differences Delta F is to generate non-equilibrium data via ``fast-growth'' simulations or experiments -- and then use Jarzynski's equality. However, a difficulty with using Jarzynski's…