Related papers: Double chains with base pairing: delocalization ir…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
We propose that supercoiling energizes double-stranded DNA (dsDNA) so as to facilitate thermal fluctuations to an unzipped state. We support this with a model of two elastic rods coupled via forces that represent base pair interactions.…
Some recent results for a three--dimensional, semi--classical, tight--binding model for DNA show that there are two types of polarons, named radial and twist polarons, that can transport charge along the DNA molecule. However, the existence…
When it is viewed at the scale of a base pair, DNA appears as a nonlinear lattice. Modelling its properties is a fascinating goal. The detailed experiments that can be performed on this system impose constraints on the models and can be…
1D diagonally disordered chain with Frenkel exciton and long range exponential intersite interaction is considered. It is shown that some states of this disordered system are delocalised (extended) contrary to the popular statement that all…
We study the Anderson localization in systems, in which transport channels with rather different properties are coupled together. This problem arises naturally in systems of hybrid particles, such as exciton-polaritons, where it is not…
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…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent…
Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…
The Poland-Scheraga model for DNA denaturation, besides playing a central role in applications, has been widely studied in the physical and mathematical literature over the past decades. More recently a natural generalization has been…
The interplay between interaction, disorder, and dissipation has shown a rich phenomenology. Here we investigate a disordered XXZ spin chain in contact with a bath which, alone, would drive the system towards a highly delocalized and…
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
A generalization of the $t-J$ model in a system of two coupled chains or planes is studied by numerical diagonalization of small clusters. In particular, the effect of density fluctuations between these one- or two-dimensional coupled…
We show that, in a system with defects, two-particle states may experience destructive quantum interference, or antiresonance. It prevents an excitation localized on a defect from decaying even where the decay is allowed by energy…
We present a theoretical analysis of the environment effects on charge transport in double-stranded synthetic poly(G)-poly(C) DNA molecules attached to two ideal leads. Coupling of the DNA to the environment results in two effects: (i)…
We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
When multivalent salts are added to dilute DNA solution, the DNA chains condense into bundles of a well-defined size. We explore two physical problems motivated by this phenomenon: the origin of the attractive interactions between the…