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The elastic properties of the double-stranded DNA handles used in optical tweezers experiments on biomolecules are customarily modeled by an extensible worm-like chain model. Fitting such model to experimental data however is no trivial…
Experimental work has shown that non-equilibrium concentration fluctuations arise during free diffusion in fluids and theoretical analysis has been carried on. The results show that, in usual three-dimensional fluids, the phenomenon is…
Inspired by recent experiments on the dynamics of particles and polymers in artificial cytoskeletons and in cells, we introduce a modified Langevin equation for a particle in an environment that is a viscoelastic medium and that is brought…
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…
We consider the dependence of the electron transfer in photosynthetic complexes on correlation properties of random fluctuations of the protein environment. The electron subsystem is modeled by a finite network of connected electron…
The fundamental insight into Brownian motion by Einstein is that all substances exhibit continual fluctuations due to thermal agitation balancing with the frictional resistance. However, even at thermal equilibrium, biological activity can…
Extracting the intrinsic kinetic information of biological molecule from its single-molecule kinetic data is of considerable biophysical interest. In this work, we theoretically investigate the feasibility of inferring single RNA's…
A polymer chain pinned in space exerts a fluctuating force on the pin point in thermal equilibrium. The average of such fluctuating force is well understood from statistical mechanics as an entropic force, but little is known about the…
Mechanical characteristics of single biological cells are used to identify and possibly leverage interesting differences among cells or cell populations. Fluidity---hysteresivity normalized to the extremes of an elastic solid or a viscous…
We present force-clamp data on the collapse of ubiquitin polyproteins in response to a quench in the force. These nonequilibrium trajectories are analyzed using a general method based on a diffusive assumption of the end-to-end length to…
We study large $n$ expansions for the partition function of a Coulomb gas $$Z_n=\frac 1 {\pi^n}\int_{\mathbb{C}^n}\prod_{1\le i<j\le n}|z_i-z_j|^2\prod_{i=1}^n e^{-nQ(z_i)}\, d^2 z_i,$$ where $Q$ is a radially symmetric confining potential…
Systems with many interacting stochastic constituents are fully characterized by their free energy. Computing this quantity is therefore the objective of various approaches, notably perturbative expansions, which are applied in problems…
There has been an increasing interest in the quantification of nearly deterministic work extraction from a finite number of copies of microscopic particles in finite time. This paradigm, so called single-shot epsilon-deterministic work…
The structural dynamics of a biopolymer is governed by a process of diffusion through its conformational energy landscape. In pulling experiments using optical tweezers, features of the energy landscape can be extracted from the probability…
We use the bond fluctuation model to study the contraction process of two polymer loops with $N$ segments that are connected each to the bottom and top part of a Feringa engine. The change in the size of the molecules as well as the folding…
In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non covalent bonding in drug receptor systems. I show that most of the pitfalls and entanglements for the…
This paper extends on a recent work where it was shown that forces dependent on the helical structure may cause two DNA molecules to spontaneously braid [R. Cortini et Al, Biophys. J. 101, 875 (2011)]. Here, bending fluctuations of DNA…
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…
In this work, I propose a statistical mechanical framework, for the evaluation of the free energy in molecular systems, by "deleting" all the molecules in a "single" step. The approach can be considered as the statistical mechanics…
The energy cost of computation has emerged as a central challenge at the intersection of physics and computer science. Recent advances in statistical physics -- particularly in stochastic thermodynamics -- enable precise characterizations…