Related papers: Partition function of a bubble formed in double st…
Using analytical approach and Monte-Carlo (MC) simulations, we study the elastic behaviour of the intrinsically twisted elastic ribbons with bending anisotropy, such as double-stranded DNA (dsDNA), in two-dimensional (2D) confinement. We…
In previous work, we constructed a statistical framework for estimating the rate of clustered ionization from charged particle radiation in DNA. This model is extended to include contributions from secondary electrons. Using a simple…
Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics as well as biological research. The charge migration rate is controlled by the…
For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…
We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop…
We investigate the disk partition function for the open string. This is a subtle problem because of the presence of a residual gauge group $\mathrm{PSL}(2,\mathbb{R})$ on the worldsheet even after fixing the conformal gauge. It naively has…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…
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…
We consider voltage-driving DNA translocation through a nanopore in the present study. By assuming the DNA is coaxial with the cylindrical nanopore, a hydrodynamic model for determining effective force on a single DNA molecule in a nanopore…
Purpose: Auger emitters exhibit interesting features due to their emission of a cascade of short-range Auger electrons. Maximum DNA breakage efficacy is achieved when decays occur near DNA. Studies of double-strand breaks (DSBs) yields in…
We introduce the two-particle probability density $X(x)$ of $x=\bm{r}_{12}\cdot\bm{p}_{12}=\left(\bm{r}_1-\bm{r}_2\right) \cdot \left(\bm{p}_1-\bm{p}_2\right)$. We show how to derive $X(x)$, which we call the Posmom intracule, from the…
The large $N$ asymptotic expansion of the partition function for the normal matrix model is predicted to have special features inherited from its interpretation as a two-dimensional Coulomb gas. However for the latter, it is most natural to…
We study the entanglement entropy of gauged internal degrees of freedom in a two dimensional symmetric product orbifold CFT, whose configurations consist of $N$ strands sewn together into "long" strings, with wavefunctions symmetrized under…
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…
The damping effect to the DNA bubble is investigated within the Peyrard-Bishop model. In the continuum limit, the dynamics of the bubble of DNA is described by the damped nonlinear Schrodinger equation and studied by means of variational…
The 1-loop partition function of the handle-body solutions in the AdS$_3$ gravity have been derived some years ago using the heat-kernel and the method of images. In the semiclassical limit, such partition function should correspond 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 investigate the coalescence of two DNA-bubbles initially located at weak domains and separated by a more stable barrier region in a designed construct of double-stranded DNA. In a continuum Fokker-Planck approach, the characteristic time…
The Separability Problem is approached from the perspective of Ellipsoidal Classification. A Density Operator of dimension N can be represented as a vector in a real vector space of dimension $N^{2}- 1$, whose components are the projections…