Related papers: Compound Poisson Statistics and Models of Clusteri…
In our last paper, we have reported the direct interact between energetic ions and DNA, and its components, pointing out that damage to DNA is actually of highest biological consequence, as the integrity of DNA sequence is essential for…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
Clustering of proteins is of interest in cancer cell biology. This article proposes a hierarchical Bayesian model for protein (variable) clustering hinging on correlation structure. Starting from a multivariate normal likelihood, we enforce…
Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of…
The elucidation of fundamental mechanisms underlying ion-induced radiation damage of biological systems is crucial for the advancement of radiotherapy with ion beams and for radiation protection in space. The study of ion-induced biodamage…
We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed…
We calculate the entropic part of partition function of a bubble embedded in a double stranded DNA (dsDNA) by considering the total weights of possible configurations of a system of two single stranded DNA (ssDNA) of given length which…
We study the effect of the composition of the genetic sequence on the melting temperature of double stranded DNA, using some simple analytically solvable models proposed in the framework of the wetting problem. We review previous work on…
The experiment that the high spin selectivity and the length-dependent spin polarization are observed in double-stranded DNA [Science ${\bf 331}$, 894 (2011)], is elucidated by considering the combination of the spin-orbit coupling, the…
Gibbs-type priors are widely used as key components in several Bayesian nonparametric models. By virtue of their flexibility and mathematical tractability, they turn out to be predominant priors in species sampling problems, clustering and…
The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the…
Single-strand breaks (SSBs) are the major DNA damage in the genome arising spontaneously as the outcome of genotoxins and intermediates of DNA transactions. SSBs play a crucial role in various biological processes and show a non-random…
In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…
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 propose a multi-scale approach to understanding physics related to the ion/proton-beam cancer therapy and calculation of the probability of the DNA damage as a result of irradiation of patients with energetic (up to 430 MeV/u) ions. This…
A clustering aspect is explained for the $^9$Be nucleus in charged-lepton deep inelastic scattering. Nuclear modifications of the structure function $F_2$ are studied by the ratio $R_{\rm EMC} = F_2^A /F_2^D$, where $A$ and $D$ are a…
Ionizing radiation is known to delay the cell cycle progression. In particular after particle exposure significant delays have been observed and it has been shown that the extent of delay affects the expression of damage such as chromosome…
We present an extension of the continuous damage fiber bundle model to describe the gradual degradation of highly heterogeneous materials under an increasing external load. Breaking of a fiber in the model is preceded by a sequence of…
The formation of alpha-clusters in nuclei close to the decay thresholds is discussed. These states can be considered to be boson-condensates, which are formed in a second order phase transition in a mixture of nucleons and alpha-particles.…