Related papers: A Parallel-pulling Protocol for Free-Energy Evalua…
Single molecule pulling experiments provide information about interactions in biomolecules that cannot be obtained by any other method. However, the reconstruction of the molecule's free energy profile from the experimental data is still a…
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…
Extracting equilibrium information from nonequilibrium measurements is a challenge task of great importance in understanding the thermodynamic properties of physical, chemical, and biological systems. The discovery of the Jarzynski equality…
The Jarzynski Equality is a well-known and widely used identity, relating the free energy difference between two states of a system to the work done over some arbitrary, nonequilibrium transformation between the two states. Despite being…
The Jarzynski identity can be applied to instances when a microscopic system is pulled repeatedly but quickly along some coordinate, allowing the calculation of an equilibrium free energy profile along the pulling coordinate from a set of…
The well-known Jarzynski equality, often written in the form $e^{-\beta\Delta F}=\langle e^{-\beta W}\rangle$, provides a non-equilibrium means to measure the free energy difference $\Delta F$ of a system at the same inverse temperature…
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…
The computation of free energy differences through an exponential weighting of out of equilibrium paths (known as the Jarzynski equality) is often used for transitions between states described by an external parameter $\lambda$ in 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…
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.…
The equilibrium free energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is…
The excess free energy of a molecular cluster is a key quantity in models of the nucleation of droplets from a metastable vapour phase; it is often viewed as the free energy arising from the presence of an interface between the two phases.…
The existence of two types of internal friction wet and dry is revisited, and a simple protocol is proposed for distinguishing between the two types and extracting the appropriate internal friction coefficient. The scheme requires…
We study the non-equilibrium work in a pedagogical model of relativistic ideal gas. We obtain the exact work distribution and verify the Jarzynski's equality. In the non-relativistic limit, our results recover the non-relativistic results…
We suggest and discuss a simple model of an ideal gas under the piston to gain an insight into the workings of the Jarzynski identity connecting the average exponential of the work over the non-equilibrium trajectories with the equilibrium…
In thermodynamically characterizing a mixture comprising a finite number of molecules, we consider two kinds of protocol for producing a mixture from a pure substance. The first is a single alchemical operation, whereas the second is a…
According to the second law of thermodynamics, for every transformation performed on a system which is in contact with an environment of fixed temperature, the extracted work is bounded by the decrease of the free energy of the system.…
With the traditional equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space in complex systems, which are separated into some metastable conformational regions by high free energy…
Jarzynski's identity for the free energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase space mappings. Solving a system's equation of motion by approximate means…
We derive analytical expressions for the bias of the Jarzynski free-energy estimator from N nonequilibrium work measurements, for a generic work distribution. To achieve this, we map the estimator onto the Random Energy Model in a suitable…