Related papers: Tautomeric Transitions in DNA
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast.…
The two-dimensional generalization of the Polyelectolite model of DNA is proposed. It is reduced to the boundary problem for nonlinear completely integrable equation $\sh$-Gordon. In the linearisible version the exact solution is…
We suggest that Davidov's solitons, propagating through the backbone of a protein, can mediate conformational transition and folding of a protein to its native state. A simple toy model is presented in which a Non Linear Schrodinger (NLS)…
Due to its polyionic character the DNA double helix is stable and biologically active only in salty aqueous media where its charge is compensated by solvent counterions. Monovalent metal ions are ubiquitous in DNA environment and they are…
We investigate the electron (hole) transport through short double-stranded DNA wires in which the electrons are strongly coupled to the specific vibrational modes (vibrons) of the DNA. We analyze the problem starting from a tight-binding…
A single semiflexible polymer chain folds into a toroidal object under poor solvent conditions. In this study, we examined the morphological change in such a toroidal state as a function of the width and stiffness of the chain together with…
The rapid progress in the field of molecular electronics has led to an increasing interest on DNA oligomers as possible components of electronic circuits at the nanoscale. For this, however, an understanding of charge transfer and transport…
Nonlinear classical Hamiltonian lattices exhibit generic solutions in the form of discrete breathers. These solutions are time-periodic and (typically exponentially) localized in space. The lattices exhibit discrete translational symmetry.…
We study generic aspects of bubble dynamics in DNA under time dependent perturbations, for example temperature change, by mapping the associated Fokker-Planck equation to a quantum time-dependent Schroedinger equation with imaginary time.…
We study interaction of a soliton in a parity-time (PT) symmetric coupler which has local perturbation of the coupling constant. Such a defect does not change the PT-symmetry of the system, but locally can achieve the exceptional point. We…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…
Topological transitions are fundamental phenomena in electronics, photonics, and quantum technologies. However, the scalability and tunability of Topological transitions in these systems have still been constrained by their material…
The tunability of the interlayer coupling by twisting one layer with respect to another layer of two-dimensional materials provides a unique way to manipulate the phonons and related properties. We refer to this engineering of phononic…
Nuclei exhibit quantum phase transitions (earlier called ground state phase transitions) between different shapes as the number of nucleons is modified, resulting in changes in the ground and low lying nuclear states. Special solutions of…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
The temperature-induced structural and electronic transformation in VO$_2$ between the monoclinic M1 and tetragonal rutile phases was studied by means of \textit{ab initio} molecular dynamics, based on density functional theory with Hubbard…
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…