Related papers: A Parallel-pulling Protocol for Free-Energy Evalua…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
The free-energy difference $\Delta F$ between two high-dimensional systems is notoriously difficult to compute, but very important for many applications, such as drug discovery. We demonstrate that an unconventional definition of work…
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…
The estimate of free energy changes based on Bennett's acceptance ratio method is examined in several limiting cases and compared with other estimates based on the Jarzynski equality and on the Crooks relation. While the absolute amount of…
We extend the Jarzynski equality, which is an exact identity between the equilibrium and nonequilibrium averages, to be useful to compute the value of the entropy difference by changing the Hamiltonian. To derive our result, we introduce…
Energy-Based Models (EBMs) provide a flexible framework for generative modeling, but their training remains theoretically challenging due to the need to approximate normalization constants and efficiently sample from complex, multi-modal…
Recent years have witnessed major advances in our understanding of nonequilibrium processes. The Jarzynski equality, for example, provides a link between equilibrium free energy differences and finite-time, nonequilibrium dynamics. We…
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…
Brownian dynamics simulations are used to study the detachment of a particle from a substrate. Although the model is simple and generic, we attempt to map its energy, length and time scales onto a specific experimental system, namely a bead…
We present a general scheme to obtain work distribution in closed systems under continuous quantum histories of corresponding "power" operator. The scheme is tested by analytically calculating the quantum work distribution for a prototype…
We discuss and qualify a previously unnoticed connection between two different phenomena in the physics of nanoscale friction, general in nature and also met in experiments including sliding emu- lations in optical lattices, and protein…
In this thesis we examine methodologies for determining free energy differences (FEDs) of phases via Monte Carlo simulation. We identify and address three generic issues that arise in FED calculations; the choice of representation, the…
Parallel replica dynamics is a method for accelerating the computation of processes characterized by a sequence of infrequent events. In this work, the processes are governed by the overdamped Langevin equation. Such processes spend much of…
Fluctuation relations allow for the computation of equilibrium properties, like free energy, from an ensemble of non-equilibrium dynamics simulations. Computing them for quantum systems, however, can be difficult, as performing dynamic…
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…
Recently discovered identities in statistical mechanics have enabled the calculation of equilibrium ensemble averages from realizations of driven nonequilibrium processes, including single-molecule pulling experiments and analogous computer…
This study investigates the use of the $J$-integral to compute the statistics of the energy release rate of a random elastic medium. The spatial variability of the elastic modulus is modeled as a homogeneous lognormal random field. Within…
We give a quantum version of the Jarzynski relation between the distribution of work done over a certain time-interval on a system and the difference of equilibrium free energies. The main new ingredient is the identification of work…
Five previously unknown inequalities relating equilibrium free energy differences and non-equilibrium work fluctuations are derived, and lucid path to derivation of many similar inequalities is presented. These results are based upon…
We propose a checking parameter utilizing the breaking of the Jarzynski equality in the simulated annealing method using the Monte Carlo method. This parameter is based on the Jarzynski equality. By using this parameter, to detect that the…