Related papers: Work Distribution for Unzipping Processes
We study a continuous time branching process where an individual splits into two daughters with rate b and dies with rate a, starting from a single individual at t=0. We show that the model can be mapped exactly to a random walk problem…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
The Metropolis Monte Carlo (MC) method is used to extract reaction kinetics from a given equilibrium distribution of states of a complex system. The approach is illustrated by the folding/unfolding reaction for two proteins - a model…
The Higgs RNA-Model is studied in regard to finite-time driving protocols with minimal-work requirement. In this paper, RNA sequences which at low temperature exhibits hairpins are considered, which are often cited as typical template…
Secondary structure formation of nucleic acids strongly depends on salt concentration and temperature. We develop a theory for RNA folding that correctly accounts for sequence effects, the entropic contributions associated with loop…
Pipeline-parallel distributed optimization is essential for large-scale machine learning but is challenged by significant communication overhead from transmitting high-dimensional activations and gradients between workers. Existing…
We revisit the classic thermodynamic problem of maximum work extraction from two arbitrary sized hot and cold reservoirs, modelled as perfect gases. Assuming ignorance about the extent to which the process has advanced, which implies an…
The forming and melting of complementary base pairs in RNA duplexes are conformational transitions required to accomplish a plethora of biological functions. Yet the dynamic steps of these transitions have not been quantitatively…
We study the low-temperature transport properties of out-of-equilibrium XXZ spin-$1/2$ chains. We consider the protocol where two semi-infinite chains are prepared in two thermal states at small but different temperatures and suddenly…
Distribution power systems (DPSs) are mostly unbalanced, and their loads may have notable static voltage characteristics (ZIP loads). Hence, despite abundant papers on linear single-phase power flow models, it is still necessary to study…
We develop a propagating front analysis, in terms of a local probability of zipping, for the helicase activity of opening up a double stranded DNA (dsDNA). In a fixed-distance ensemble (conjugate to the fixed-force ensemble) the front…
We study the Stochastic Thermodynamics of cell growth and division using a theoretical framework based on branching processes with resetting. Cell division may be split into two sub-processes: branching, by which a given cell gives birth to…
The force laws governing the extension behavior of homopolypeptides are obtained from a phenomenological free energy capable of describing the helix-coil transition. Just above the melting temperature of the free chains, T*, the plot of…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
We investigate the voltage-driven transport of hybridized DNA through membrane channels. As membrane channels are typically too narrow to accommodate hybridized DNA, the dehybridization of the DNA is the critical rate limiting step in the…
Many previous studies have demonstrated that work statistics can exhibit certain singular behaviors in the quantum critical regimes of many-body systems at zero or very low temperatures. However, as the temperature increases, it is commonly…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
Transfer-matrix methods are used to study the probability distributions of spin-spin correlation functions $G$ in the two-dimensional random-field Ising model, on long strips of width $L = 3 - 15$ sites, for binary field distributions at…