Related papers: A Model for Double-Stranded Excitations of DNA
Oscillatory gene circuits are ubiquitous to biology and are involved in fundamental processes of cell cycle, circadian rhythms and developmental systems. The synthesis of small, non-natural oscillatory genetic circuits have been…
We examine the BPS and low energy non-BPS excitations of the D-string, in terms of open strings that travel on the D-string. We use this to study the energy thresholds for exciting a long D-string, for arbitrary winding number. We also…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
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…
We call \textit{monomer} a B-DNA base pair and study, analytically and numerically, electron or hole oscillations in \textit{monomers}, \textit{dimers} and \textit{trimers}. We employ two Tight Binding (TB) approaches: (I) at the base-pair…
This paper presents a numerical study of the dynamics of DNA double helix breakage under the influence of external forces using the Peyrard-Bishop-Dauxois (PBD) model. The PBD model represents DNA as a chain of nonlinearly coupled…
We deduced the torque applied on a single stretched and twisted DNA by integrating with respect to force the change in the molecule's extension as it is coiled. While consistent with previous direct measurements of the torque at high forces…
Excitable waves arise in many spatially-extended systems of either biological, chemical, or physical nature due to the interplay between local reaction and diffusion processes. Here we demonstrate that similar phenomena are encoded in the…
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 spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
In order to study the molecular damage induced in the form of single-strand and double-strand breaks by the ionizing radiation at the DNA level, Geant4-DNA Monte Carlo simulation code for complete transportation of primary protons and other…
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is…
Local periodic perturbations induce frequency-dependent propagation waves in an excitable spatio-temporally chaotic system. We show how segments of noise-contaminated and chaotic perturbations induce characteristic sequences of excitations…
The elastic scattering of spinless vortex electrons on realistic target atoms has been investigated. In particular, expressions are derived in different approximations for the elastic angular-differential cross sections. We develop a…
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in…
The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…
In this work we report the study of conformation dependent electronic transport properties of DNA double-helix within tight-binding framework including its helical symmetry. We have studied the changes in localization properties of DNA as…
We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to…
Recent experiments [J. van Mameren et al. PNAS 106, 18231 (2009)] provide a detailed spatial picture of overstretched DNA, showing that under certain conditions the two strands of the double helix separate at about 65 pN. It was proposed…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…