Related papers: Work Distribution for Unzipping Processes
Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…
We summarize and extend some of the results obtained recently for the microscopic and macroscopic behavior of a pinned harmonic chain, with random velocity flips at Poissonian times, acted on by a periodic force {at one end} and in contact…
We develop a theoretical description of the critical zipping dynamics of a self-folding polymer. We use tension propagation theory and the formalism of the generalized Langevin equation applied to a polymer that contains two complementary…
We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and…
Using Monte Carlo simulations, we study the hysteresis in unzipping of a double stranded DNA whose ends are subjected to a time dependent periodic force with frequency ($\omega$) and amplitude ($G$). For the static force, i.e., $\omega \to…
Using molecular dynamics simulations, we report phase separation in a 50:50 mixture of hot(active) and cold(passive) dumbbells which interact by Lennard-Jones potential. The ratio of the temperature difference between hot and cold dumbbells…
The distributions of work for strongly non-equilibrium processes are studied using a very general form of a large-deviation approach, which allows one to study distributions of almost arbitrary quantities of interest for equilibrium,…
We review and discuss the equations governing the distribution of work done on a system which is driven out of equilibrium by external manipulation, as well as those governing the entropy flow to a reservoir in a nonequilibrium system. We…
Curve registration plays a major role in functional data analysis by separating amplitude and phase variation through warping functions and the accurate simulation of warping processes is essential for developing statistical methods that…
Work sharing and work stealing are two scheduling paradigms to redistribute work when performing distributed computations. In work sharing, processors attempt to migrate pending jobs to other processors in the hope of reducing response…
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 considered a dsDNA polymer in which distribution of bases are random at the base pair level but ordered at a length of 18 base pairs and calculated its force elongation behaviour in the constant extension ensemble. The unzipping force…
Using Monte Carlo simulations, we study the hysteresis in unzipping of a double stranded block copolymer DNA with $-A_n B_n-$ repeat units. Here $A$ and $B$ represent two different types of base pairs having two- and three-bonds,…
The asymptotic tails of the probability distributions of thermodynamic quantities convey important information about the physics of nanoscopic systems driven out of equilibrium. We apply a recently proposed method to analytically determine…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
We obtain a representation of the free energy of an XY model on a fully connected graph with spins subjected to a random crystal field of strength $D$ and with random orientation $\alpha$. Results are obtained for an arbitrary probability…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model. Phase diagrams and free energy landscapes are computed exactly and suggest a…
We study unzipping of a complementary RNA-DNA helix applied to an external force, focusing on the force-force correlations. While at the microscopic level these are given by the sequence, the experiment measures effective, macroscopic…
We suggest a new mean field method for studying the thermodynamic competition between magnetic and superconducting phases in a two-dimensional square lattice. A partition function is constructed by writing microscopic interactions that…