Related papers: Distribution Functions, Loop Formation Probabiliti…
The influence of correlations on the momentum distribution of nucleons in nuclei is evaluated starting from a realistic nucleon-nucleon interaction. The calculations are performed directly for the finite nucleus $\,^{16}$O making use of the…
We consider the distribution of free path lengths, or the distance between consecutive bounces of random particles, in an n-dimensional rectangular box. If each particle travels a distance R, then, as R tends to infinity the free path…
Distance distributions are a key building block in stochastic geometry modelling of wireless networks and in many other fields in mathematics and science. In this paper, we propose a novel framework for analytically computing the closed…
Recent measurements of resonance widths for low-energy neutron scattering off heavy nuclei show large deviations from the standard Porter-Thomas distribution. We propose a new resonance width distribution based on the random matrix theory…
In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
Recently many important biopolymers have been found to possess intrinsic curvature. Tubulin protofilaments in animal cells, FtsZ filaments in bacteria and double stranded DNA are examples. We examine how intrinsic curvature influence the…
In a recent experiment, a single DNA double helix is stretched and relaxed in the presence of spermidine, a short positive polyelectrolyte, and the pulling force is measured as a function of DNA extension. In a certain range of spermidine…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
Sequencing by synthesis is the underlying technology for many next-generation DNA sequencing platforms. We developed a new model, the fixed flow cycle model, to derive the distributions of sequence length for a given number of flow cycles…
We study the effect of electrostatic interactions on the distribution function of the end-to-end distance of a single polyelectrolyte chain in a rodlike configuration. We investigate the validity of the concept of electrostatic persistence…
The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without…
Localization property in the disordered few-chain DNA systems with a long-range correlation is numerically investigated. We apply the chain system with the correlated disorder in the interchain and/or intrachain hoppings to the simple model…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
From the per unit length free energy for DNA under tension, we have calculated an effective contour length dependent persistence length for short DNA. This effective persistence length results from the enhanced fluctuations in short DNA. It…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Super-diffusion, characterized by a spreading rate $t^{1/\alpha}$ of the probability density function $p(x,t) = t^{-1/\alpha} p \left( t^{-1/\alpha} x , 1 \right)$, where $t$ is time, may be modeled by space-fractional diffusion equations…
Recent experimental data on inclusive and exclusive lepton and hadron scattering off nuclei have renewed the interest in theoretical and experimental studies of Short Range Correlations (SRC), due to the relevant impact they may have not…