Related papers: A non extensive approach for DNA breaking by ioniz…
In recent years, significant progress in understanding the properties of supercoiled DNA has been obtained due to nanotechniques that made stretching and twisting of single molecules possible. Quantitative interpretation of such experiments…
We show that the simple analytical model proposed by Zhang and Marko (Phys. Rev. E 77, 031916 (2008)) to illustrate Maxwell relations for single-DNA experiments can be improved by including the zero-force entropy of a Gaussian chain. The…
DNA-based storage is an emerging technology that enables digital information to be archived in DNA molecules. This method enjoys major advantages over magnetic and optical storage solutions such as exceptional information density, enhanced…
It is shown that there is a mapping of the replica approach to disordered systems with finite replica index $n$ on the Tsallis non-extensive statistics, if the average thermodynamic entropy differs from the information entropy for the…
Cancer treatment with radiotherapy aims to kill tumor cells and spare healthy tissue.Thus,the experimentally observed sparing of healthy tissue by the FLASH effect during irradiations with ultra-high dose rates (UHDR) enables clinicians to…
Damaged or mismatched bases in DNA can be repaired by Base Excision Repair (BER) enzymes that replace the defective base. Although the detailed molecular structures of many BER enzymes are known, how they colocalize to lesions remains…
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,…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
A family of nonlinear ordinary differential equations with arbitrary order is obtained by using nonextensive concepts related to the Tsallis entropy. Applications of these equations are given here. In particular, a connection between…
We consider Shannon entropy, Fisher information, R\'enyi entropy, and Tsallis entropy to study the quantum droplet phase in Bose-Einstein condensates. In the beyond mean-field description, the Gross-Pitaevskii equation with Lee-Huang-Yang…
Gel electrophoresis, a widely used technique to separate DNA according to their size and weight, generates images that can be analyzed automatically. Manual or semiautomatic image processing presents a bottleneck for further development and…
Finding a theoretical formula for the persistence length of polyelectrolytes for the whole experimental range of salt concentration is a long standing challenge. Using the Tethered Particle Motion technique, the double-stranded DNA…
The purpose of this work is to extend the Geant4-DNA Monte Carlo toolkit to include electron interactions with the four DNA bases using a set of cross sections recently implemented in Geant-DNA CPA100 models and available for liquid water.…
Tsallis' non-extensive entropy is extended to incorporate the dependence on affinities between the microstates of a system. At the core of our construction of the extended entropy ($\mathcal{H}$) is the concept of the effective number of…
This work presents a theoretical analysis of the probability of successfully retrieving data encoded with MDS codes (e.g., Reed-Solomon codes) in DNA storage systems. We study this probability under independent and identically distributed…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
We study by using Monte Carlo simulations the hysteresis in unzipping and rezipping of a double stranded DNA (dsDNA) by pulling its strands in opposite directions in the fixed force ensemble. The force is increased, at a constant rate from…
Recent experiments at free-electron laser x-ray sources have been able to resolve the intensity distributions about Bragg peaks in nanocrystals of large biomolecules. Information derived from small shifts in the peak positions augment the…
DNA storage is now being considered as a new archival storage method for its durability and high information density, but still facing some challenges like high costs and low throughput. By reducing sequencing sample size for decoding…