Related papers: Kink solitons in DNA
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…
DNA supercoils are generated in genome regulation processes such as transcription and replication, and provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
We analyze the dynamics of structural transitions between normal right-handed B form and unusual left-handed Z form for a linear DNA molecule. The dynamics under the external torque in physiological buffer is modeled by a Langevin equation,…
We demonstrate that periodic modulation of the nonlinearity coefficient in the discrete nonlinear Schr\"{o}dinger (DNLS) equation can strongly facilitate creation of traveling solitons in the lattice. We predict this possibility in an…
Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending…
Positions of protons in DNA hydrogen bonds are fundamental for the fidelity of the replication process. Because the hydrogen bond is partially covalent the electronic structure of DNA plays an important role in the replication process.…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
This thesis presents an extensive analysis of the behavior of topological solitons when one or more of their internal modes are activated. The first part of this manuscript is devoted to the study of the simplest topological solitons in…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
We study properties of the localized solitons to the sine-Gordon equation excited on the attractive impurity by a moving kink. The cases of one- and two-dimensional spatially extended impurities are considered. For the case of…
We use quantum sine-Gordon model to describe the low energy dynamics of a pair of coupled one-dimensional condensates of interacting atoms. We show that the nontrivial excitation spectrum of the quantum sine-Gordon model, which includes…
The transition from integrable to non-integrable highly-dispersive nonlinear models is investigated. The sine-Gordon and $\phi^4$-equations with the additional fourth-order spatial and spatio-temporal derivatives, describing the higher…
The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understanding the self-assembly and replication of this structure are…
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…
The nonstationary dynamics of topological solitons (dislocations, domain walls, fluxons) and their bound states in one-dimensional systems with high dispersion are investigated. Dynamical features of a moving kink emitting radiation and…
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…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…