Related papers: Generalized Poland-Scheraga model for DNA hybridiz…
In this paper, we discuss the embedding problem for centrosymmetric matrices, which are higher order generalizations of the matrices occurring in Strand Symmetric Models. These models capture the substitution symmetries arising from the…
Despite the significance of the high flexibility exhibited by short DNAs, there remains an incomplete understanding of their anomalous persistence length. In this study, we propose a novel approach wherein each fundamental characteristic of…
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…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling $G$ between twisting and bending, known to arise from…
It has been suggested by several authors that nonlinear excitations, in particular solitary waves, could play a fundamental functional role in the process of DNA transcription, effecting the opening of the double chain needed for RNA…
A strategy to couple continuous Galerkin (CG) and hybridizable discontinuous Galerkin (HDG) discretizations based only on the HDG hybrid variable is presented for linear thermal and elastic problems. The hybrid CG-HDG coupling exploits the…
By means of the Brownian dynamics (BD) method of simulations we have developed, we study dynamics of individual DNA undergoing constant field gel electrophoresis (CFGE), focusing on the relevance of the `defect' concept due to de Gennes in…
We introduce and numerically study a model designed to mimic the bulk behavior of a system composed of single-stranded DNA dendrimers. Complementarity of the base sequences of different strands results in the formation of strong cooperative…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both…
The photoelectron properties of DNA and RNA bases are studied using many-body perturbation theory within the GW approximation, together with a recently developed Lanczos-chain approach. Calculated vertical ionization potentials, electron…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
Dielectric spectroscopy is used to investigate fundamental length scales of 146 bp short-fragment (nucleosomal) dilute Na-DNA solutions. Two relaxation modes are detected: the high- and the low-frequency mode. Dependence of the…
Modern machine learning models are often over-parameterized and as a result they can interpolate the training data. Under such a scenario, we study the convergence properties of a sampling-without-replacement variant of stochastic gradient…
We present a statistical mechanical model of aggregation in colloidal systems with DNA mediated interactions. We obtain a general result for the two-particle binding energy in terms of the hybridization free energy $\Delta G$ of DNA and two…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…