Related papers: Work Distribution for Unzipping Processes
The front dynamics in the Harper (or Aubry-Andr\'e) model (which has a localization transition) is investigated using two different settings, particle number front where the system is at zero temperature, and initially, the particle numbers…
The role of interchain hopping in quasi-one-dimensional (Q-1D) electron systems is investigated by extending the Kadanoff-Wilson renormalization group of one-dimensional (1D) systems to Q-1D systems. This scheme is applied to the extended…
We analyze how the amount of work dissipated by a fixed nonequilibrium process depends on the initial distribution over states. Specifically, we compare the amount of dissipation when the process is used with some specified initial…
We study the distribution of threshold forces at the depinning transition for an elastic system of finite size, driven by an external force in a disordered medium at zero temperature. Using the functional renormalization group (FRG)…
We consider overdamped Brownian particles with two degrees of freedom (DoF) that are confined in a time-varying quadratic potential and are in simultaneous contact with heat baths of different temperatures along the respective DoF. The…
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…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of basepairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base-sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase…
We study statistical properties of a zero-range process (ZRP) on random networks. We derive an analytic expression for the distribution of particles (also called node occupation distribution) in the steady state of the ZRP in the ensemble…
We propose and analyze a process that extracts useful work from a single active particle maintained at constant temperature in a harmonic potential by measuring the relative sign of the self-propulsion and the confining force and then…
Using a beta-hairpin protein as a representative example of two-state folders, we studied how the exploration of native-like states affects the folding kinetics. It has been found that the first-passage time (FPT) distributions are…
Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse…
We study the unzipping of a double stranded DNA (dsDNA) by applying an external force on a single strand while leaving the other strand free. We find that the dsDNA can be unzipped to two single strands if the external force exceeds a…
We analyze the statistics of work generated by a gradient flow to stretch a nonlinear polymer. We obtain the Large Deviation Function (LDF) of the work in the full range of appropriate parameters by combining analytical and numerical tools.…
The study of thermodynamic fluctuations allows one to relate the free energy difference between two equilibrium states with the work done on a system through processes far from equilibrium. This finding plays a crucial role in the quantum…
We show that the laws of Zipf and Benford, obeyed by scores of numerical data generated by many and diverse kinds of natural phenomena and human activity are related to the focal expression of a generalized thermodynamic structure. This…
An analytic formula for the density of states of Wako-Saito-Munoz-Eaton model, for a simple class of beta-hairpins, is obtained. Under certain simplifying assumptions on the structure of the native contacts and the values of local entropy,…
We propose a new and effective means for designing stable and fast-folding polypeptide sequences using a cumulant expansion of the molecular partition function. This method is unique in that $T_{Z}$, the ``cumulant design temperature''…