Related papers: Distribution Functions, Loop Formation Probabiliti…
We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to…
Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
This study reports on the evolution of the probability distribution in the configuration space of the two-dimensional Toda system. The distribution is characterized by singularities, which predominantly take two forms: double-cusped…
Single molecule experiments on single- and double stranded DNA have sparked a renewed interest in the force-extension of polymers. The extensible Freely Jointed Chain (FJC) model is frequently invoked to explain the observed behavior of…
Brownian diffusion of rod-like polymers in the presence of randomly distributed spherical obstacles is studied using molecular dynamics (MD) simulations. It is observed that dependence of the reduced diffusion coefficient of these…
The unzipping of a double stranded DNA whose ends are subjected to a time dependent periodic force with frequency $\omega$ and amplitude $G$ is studied using Monte Carlo simulations. We obtain the dynamical order parameter, $Q$, defined as…
The formation of bubble defects of the double stranded DNA is treated according to the Lifshits theory of disordered chains. A molecule of the DNA is modelled on a harmonic lattice with nearest neighbour interaction, elastic constants being…
We study the effect of random forces on a double stranded DNA in unzipping the two strands, analogous to the problem of an adsorbed polymer under a random force. The ground state develops bubbles of various lengths as the random force…
We study a one-dimensional particles system, in the overdamped limit, where nearest particles attract with a force inversely proportional to a power of their distance and coalesce upon encounter. The detailed shape of the distribution…
Employing molecular dynamics simulations of jammed soft particles, we study microscopic responses of force-chain networks to quasi-static isotropic (de)compressions. We show that not only contacts but also interparticle gaps between the…
Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…
While analyzing the persistence length of DNA atomistic simulations Wu et al. [J. Chem. Phys. 142, 125103 (2015)] introduced an empirical formula to account for the observed length-dependence. In particular they found that the persistence…
We present a study of the bend angle distribution of semiflexible polymers of short and intermediate lengths within the wormlike chain model. This enables us to calculate the elastic response of a stiff molecule to a bending moment. Our…
Using the Langevin Dynamics simulation, we have studied the effects of the shear force on the rupture of short double stranded DNA at different temperatures. We show that the rupture force increases linearly with the chain length and…
The dynamics of loop formation by linear polymer chains has been a topic of several theoretical/experimental studies. Formation of loops and their opening are key processes in many important biological processes. Loop formation in flexible…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a…
Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
The relation between the jump length probability distribution function and the spectral line profile in resonance atomic radiation trapping is considered for Partial Frequency Redistribution (PFR) between absorbed and reemitted radiation.…