Related papers: Measurement of work in single-molecule experiments
We study the role of fluctuations in single molecule experimental measurements of force-extension curves. We use the Worm Like Chain (WLC) model to bring out the connection between the Helmholtz ensemble characterized by the Free Energy and…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Science students must deal with the errors inherent to all physical measurements and be conscious of the necessity to express their as a best estimate and a range of uncertainty. Errors are routinely classified as statistical or systematic.…
Exploiting the information provided by the molecular noise of a biological process has proven to be valuable in extracting knowledge about the underlying kinetic parameters and sources of variability from single cell measurements. However,…
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…
We present a practical scheme for performing error estimates for Density Functional Theory calculations. The approach which is based on ideas from Bayesian statistics involves creating an ensemble of exchange-correlation functionals by…
Due to their versatility in investigating phenomena in microscopic scales, optical tweezers have been an excellent platform for studying stochastic thermodynamics. In this context, this work presents experimental measurements of the…
The living cell uses a variety of molecular receptors to read and process chemical signals that vary in space and time. We model the dynamics of such molecular level measurements as Markov processes in steady state, with a coupling between…
Jarzynski equality and related fluctuation theorems can be formulated for various setups. Such an equality was recently derived for nonunitary quantum evolutions described by unital quantum operations, i.e., for completely positive,…
An expression is derived for the classical free energy difference between two configurations of a system, in terms of an ensemble of finite-time measurements of the work performed in parametrically switching from one configuration to the…
We consider work extraction from $N$ copies of a quantum system. When the same work-extraction process is implemented on each copy, the relative size of fluctuations is expected to decay as $1/\sqrt{N}$. Here, we consider protocols where…
Jarzynski's equality sets a strong bound on the probability of violating the second law of thermodynamics by extracting work beyond the free energy difference. We derive finite-time refinements to this bound for driven systems in contact…
A simple model featuring a double well potential is used to represent a liquid that is quenched from an ergodic state into a history dependent glassy state. Issues surrounding the application of the Jarzynski Equality to glass formation are…
In this paper we give a pedagogical introduction to the ideas of quantum thermodynamics and work fluctuations, using only basic concepts from quantum and statistical mechanics. After reviewing the concept of work, as usually taught in…
We investigate the connection between recent results in quantum thermodynamics and fluctuation relations by adopting a fully quantum mechanical description of thermodynamics. By including a work system whose energy is allowed to fluctuate,…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
We develop a mathematical approach to the nonequilibrium work theorem which is traditionally referred to in statistical mechanics as Jarzynski's identity. We suggest a mathematically rigorous formulation and proof of the identity.
A quantum analogue of the Jarzynski equality is constructed. This equality connects an ensemble average of exponentiated work with the Helmholtz free-energy difference in a nonequilibrium switching process subject to a thermal heat bath. To…
The result of a physical measurement depends on the timescale of the experimental probe. In solid-state systems, this simple quantum mechanical principle has far-reaching consequences: the interplay of several degrees of freedom close to…
We derive exact fluctuation equalities for open systems that recover free energy differences between two equilibrium endpoints connected by nonequilibrium processes with arbitrary dynamics and coupling. The exponential of the free energy…