Related papers: Partition function of a bubble formed in double st…
Correlation length exponent $\nu$ for long linear DNA molecules was determined by direct measurement of the average end-to-end distance as a function of the contour length $s$ by means of atomic force microscopy (AFM). Linear DNA, up to…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
Parton distributions can be defined in terms of the entropy of entanglement between the spatial region probed by deep inelastic scattering (DIS) and the rest of the proton. For very small $x$, the proton becomes a maximally entangled state.…
We calculate the entanglement entropy of a model proton wave function in coordinate space by integrating out degrees of freedom outside a small circular region $\bar A$ of radius $L$, where $L$ is much smaller than the size of the proton.…
The partitions of the integers can be expressed exactly in an iterative and closed-form expression. This equation is derived from distributing the partitions of a number in a network that locates each partition in a unique and orderly…
The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles respectively, when the strands of the DNA are subjected to a force along the same…
We compute the 1-loop partition function for strings in $AdS_4\times\mathbb{CP}^3$, whose worldsheets end along a line with small cusp angles in the boundary of AdS. We obtain these 1-loop results in terms of the vacuum energy for on-shell…
We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version…
Based on an estimate of the knot entropy of a worm-like chain we predict that the interplay of bending energy and confinement entropy will result in a compact metastable configuration of the knot that will diffuse, without spreading, along…
We compute the Coulomb branch partition function of the 4d $\mathcal{N}=2$ vector multiplet on closed simply-connected quasi-toric manifolds $B$. This includes a large class of theories, localising to either instantons or anti-instantons at…
We summarize recent work on the consistent calculation of bubble-nucleation rates. Our approach is based on the notion of a real coarse-grained potential. The bubble-nucleation rate is calculated through an expansion around the…
Motivated by the goal of understanding the evolution of populations undergoing selection, we consider branching Brownian motion in which particles independently move according to one-dimensional Brownian motion with drift, each particle may…
The probability distributions for bending angles in double helical DNA obtained in all-atom molecular dynamics simulations are compared with theoretical predictions. The computed distributions remarkably agree with the worm-like chain…
We study the order statistics of one dimensional branching Brownian motion in which particles either diffuse (with diffusion constant $D$), die (with rate $d$) or split into two particles (with rate $b$). At the critical point $b=d$ which…
The paper deals with the two-state (opening-closing of base pairs) model used to describe the fluctuation dynamics of a single bubble formation. We present an exact solution for the discrete and finite size version of the model that…
We present numerical results on the temperature dependence of the distribution of bubble lengths in DNA segments of various guanine-cytosine (GC) concentrations. Base-pair openings are described by the Peyrard-Bishop-Dauxois model and the…
We study theoretically the unzipping of a double stranded DNA from a condensed globule state by an external force. At constant force, we find that the double stranded DNA unzips an at critical force Fc and the number of unzipped monomers M…
We study various statistical properties of the double-dimer model, a generalization of the dimer model, on rectangular domains of the square lattice. We take advantage of the Grassmannian representation of the dimer model, first to…
The conjunction of insights from structural biology, solution biochemistry, genetics and single molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a…
We study the steady-state distribution function of a run-and-tumble particle evolving around a repulsive hard spherical obstacle. We show that the well-documented activity-induced attraction translates into a delta peak accumulation at the…