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We study the probability of two Brownian particles to meet before one of them exits a finite interval. We obtain an explicit expression for the probability as a function of the initial distance of the two particles using the Weierstrass…
DNA double-strand breaks (DSBs) represent a serious source of damage for all living things and thus there have been many quantitative studies of DSBs both in vivo and in vitro. Despite this fact, the processes that lead to their production…
Encapsulation of dsDNA fragments (contour length 54 nm) by the cationic diblock copolymer poly(butadiene-b-N-methyl 4-vinyl pyridinium) [PBd-b-P4VPQ] has been studied with phase contrast, polarized light, and fluorescence microscopy, as…
We report in situ single-molecule measurements of proton-induced double-strand breaks (DSBs) in DNA immersed in water, using real-time fluorescence tracking along the entire proton path, including the Bragg peak region. By chemically…
We study the partition function of a two-dimensional Coulomb gas on a circle, in the presence of external pointlike charges, in a double scaling limit where both the external charges and the number of gas particles are large. Our original…
We study by using Monte Carlo simulations the hysteresis in unzipping and rezipping of a double stranded DNA (dsDNA) by pulling its strands in opposite directions in the fixed force ensemble. The force is increased, at a constant rate from…
RNA interference, particularly siRNA induced gene silencing is becoming an important avenue of modern therapeutics. The siRNA is delivered to the cells as short double helical RNA which becomes single stranded for forming the RISC complex.…
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…
DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel.…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
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…
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,…
We study escape dynamics of a double-stranded DNA (dsDNA) through an idealized double nanopore (DNP) geometry subject to two equal and opposite forces (tug-of-war) using Brownian dynamics (BD) simulation. In addition to the geometrical…
We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous…
Recent experiments demonstrated that knots in single DNA strands can be formed by hydrodynamic compression in a nanochannel. In this letter, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment…
We study the entropy function of two N =2 string compactifications obtained as freely acting orbifolds of N=4 theories : the STU model and the FHSV model. The Gauss-Bonnet term for these compactifications is known precisely. We apply the…
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…
The possibility that an unconventional depletion in the center of the charge density distribution of certain nuclei occurs due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. We…
The partition function and the one- and two-body distribution functions are evaluated for two hard spheres with different sizes constrained into a spherical pore. The equivalent problem for hard disks is addressed too. We establish a…
The block entanglement entropy and fluctuations are investigated in one dimension in finite size correlated electron systems using the Gutzwiller wave function as a prototype correlated electron state. Entanglement entropy shows logarithmic…