Related papers: Distribution Functions, Loop Formation Probabiliti…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
A simple model of DNA based on two interacting polymers has been used to study the unzipping of a double stranded DNA subjected to a periodic force. We propose a dynamical transition, where without changing the physiological condition, it…
A simple zipper model is introduced, representing in a simplified way, e.g., the folded DNA double helix or hairpin structures in RNA. The double stranded hairpin is connected to a heat bath at temperature $T$ and subject to an external…
We propose a simple nonlinear scaler displacement model to calculate the distribution of effect created by a shear stress on a double stranded DNA (dsDNA) molecule and the value of shear force $F_c$ which is required to separate the two…
In this paper, the looping kinetics of a long polymer chain in solution has been investigated by using two state model, where one state represents open chain polymer molecule and the other represents closed chain polymer molecule. The…
The features of electromagnetic processes are considered which connected with finite size of space region in which final particles (photon, electron-positron pair) are formed. The longitudinal dimension of the region is known as the…
We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the…
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For…
We study a model describing the force-extension curves of modular proteins, nucleic acids, and other biomolecules made out of several single units or modules. At a mesoscopic level of description, the configuration of the system is given by…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We…
Power law potentials dictate interactions across scales and matter, controlling the structure and dynamics of inanimate, and living systems. Though the equilibrium distributions of particles with a power law repulsion were extensively…
We study the stationary states of an active Brownian particle (ABP) and run-and-tumble particle (RTP) in two dimensional power-law potentials, in the limit where translational diffusion is negligible. The potential energy of the particle…
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible…
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…
We study the distribution of sizes of erased loops for loop-erased random walks on regular and fractal lattices. We show that for arbitrary graphs the probability $P(l)$ of generating a loop of perimeter $l$ is expressible in terms of the…
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a…
The problem of diffusive bond-dissociation in a double well potential under application of an external force is scrutinized. We compute the probability distribution of rupture forces and present a detailed discussion of the influence of…
Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher…
Recent experimental progress in development of on-demand sources of electrons propagating along depleted quantum Hall edge channels has enabled creation and characterization of sufficiently compact single- and two-electron distributions…