Related papers: A non extensive approach for DNA breaking by ioniz…
Probability distributions defined on the half space are known to be quite different from those in the full space. Here, a nonextensive entropic treatment is presented for the half space in an analytic and self-consistent way. In this…
The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer…
An ion-beam compressed by an external electric force is characterized by a unique non-equilibrium distribution function. This is a special case of Tsallis distribution with entropy index q=2, which allows the system to possess appreciably…
Polarization mechanism by Strutinsky-Denisov gives rise to the electric dipole radiation from fragments. Its probability calculated within the LDM turns out to be ~3.5x10-2 per fission. The radiation occurs during thermolization of the…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
The q-exponential distributions, which are generalizations of the Zipf-Mandelbrot power-law distribution, are frequently encountered in complex systems at their stationary states. From the viewpoint of the principle of maximum entropy, they…
Intracellular positive ions neutralise negative charges on the phosphates of a DNA strand conferring greater strength on the hydrogen bonds that connect complementary strands into a double helix and so confer enhanced stability. Beyond a…
A tandem cell is proposed for DNA sequencing in which an exonuclease enzyme cleaves bases (mononucleotides) from a strand of DNA for identification inside a nanopore. It has two nanopores and three compartments with the structure [cis1,…
We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip…
It is possible to derive the maximum entropy principle from thermodynamic stability requirements. Using as a starting point the equilibrium probability distribution, currently used in non-extensive thermostatistics, it turns out that the…
Distributions of inelastically scattered neutrons can be quantum dynamically described by a scattering kernel. We present an accurate and computationally efficient rejection method for sampling a given scattering kernel of any isotropic…
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…
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…
The distance-resolved effective interaction potential between two parallel DNA molecules is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. Adding counterions first yields an attractive minimum…
When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very…
Based on the Tsallis entropy, the nonextensive thermodynamic properties are studied as a q-deformation of classical statistical results using only probabilistic methods and straightforward calculations. It is shown that the constant in the…
In this paper, we investigate new procedures for statistical testing based on Tsallis entropy, a parametric generalization of Shannon entropy. Focusing on multivariate generalized Gaussian and $q$-Gaussian distributions, we develop…
Quasi-power law ensembles are discussed from the perspective of nonextensive Tsallis distributions characterized by a nonextensive parameter $q$. A number of possible sources of such distributions are presented in more detail. It is further…
We report a study of DNA (150 bp fragments) conformations in very low added salt $<0.05$mM, across wide DNA concentration range $0.0015\leq c \leq 8$~mM (bp). We found an intermediate DNA conformation in the region $0.05 < c < 1$~mM, by…
A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis…