相关论文: Work probability distribution in single molecule e…
We investigate the work dissipated during the irreversible unfolding of single molecules by mechanical force, using the simplest model necessary to represent experimental data. The model consists of two levels (folded and unfolded states)…
A main goal of single-molecule experiments is to evaluate equilibrium free energy differences by applying fluctuation relations to repeated work measurements along irreversible processes. We quantify the error that is made in a free energy…
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 show that the rare events present in dissipated work that enters Jarzynski equality, when mapped appropriately to the phenomenon of large deviations found in a biased coin toss, are enough to yield a quantitative work probability…
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.…
We present a generalization of Jarzynski's Equality, applicable to quantum systems, relating discretized mechanical work and free-energy changes. The theory is based on a step-wise pulling protocol. We find that work distribution functions…
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…
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…
A simple zipper model is introduced, representing in a simplified way, e.g., the folded DNA double helix or hairpin structures in RNA. The double stranded hairpin is connected to a heat bath at temperature $T$ and subject to an external…
In the global framework of finding an axiomatic derivation of nonequilibrium Statistical Mechanics from fundamental principles, such as the maximum path entropy -- also known as Maximum Caliber principle -- , this work proposes an…
One particle in a classical perfect gas is driven out of equilibrium by changing its mass over a short time interval. The work done on the driven particle depends on its collisions with the other particles in the gas. This model thus…
We consider a mean-field system described by a general collective variable $M$, driven out of equilibrium by the manipulation of a parameter $\mu$. Given a general dynamics compatible with its equilibrium distribution, we derive the…
The validity of the Jarzynski equation for a very simple, exactly solvable quantum system is analyzed. The implications of two different definitions of work proposed in the literature are investigated. The first one derives from…
We investigate the dynamics of a single-ended N-state molecular zipper based on a model originally proposed by Kittel. The molecule is driven unidirectionally towards the completely unzipped state with increasing time t, where the driving…
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…
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 illustrate the Jarzynski equality on the exactly solvable model of a one-dimensional ideal gas in uniform expansion or compression. The analytical results for the probability density $P(W)$ of the work $W$ performed by the gas are…
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…
Jarzynski's nonequilibrium work relation can be understood as the realization of the (hidden) time-generator reciprocal symmetry satisfied for the conditional probability function. To show this, we introduce the reciprocal process where the…
We consider the relation between the microscopic and effective descriptions of the unfolding experiment on a model polypeptide. We evaluate the probability distribution function of the performed work by Monte Carlo simulations and compare…