Related papers: Kink solitons in DNA
We investigate the nonlinear dynamics of a damped Peyrard-Bishop DNA model taking into account long-range interactions with distance dependence |l|^-s on the elastic coupling constant between different DNA base pairs. Considering both…
Biological filaments such as DNA or bacterial flagella are typically curved in their natural states. To elucidate the interplay of viscous drag, twisting, and bending in the overdamped dynamics of such filaments, we compute the steady-state…
We study the evolution of fronts in the Klein-Gordon equation when the nonlinear term is non-homogeneous. Extending previous works on homogeneous nonlinear terms, we describe the derivation of an equation governing the front motion, which…
Conventional analysis of in vitro assays of motor proteins rests on the assumption that all proteins with the same chemical composition function identically; however molecule-to-molecule variation is often seen even in well-controlled…
While slowly turning the ends of a single molecule of DNA at constant applied force, a discontinuity was recently observed at the supercoiling transition, when a small plectoneme is suddenly formed. This can be understood as an abrupt…
Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…
We investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) to study how the translocation dynamics depend on the details of the DNA sequences.…
We theoretically analyse the equation of topological solitons in a chain of particles interacting via a repulsive power-law potential and confined by a periodic lattice. Starting from the discrete model, we perform a gradient expansion and…
In this report, the various 1D single soliton and multi-soliton solutions of the Sine-Gordon equation are explored. First the topological kink solitons and their properties for the Sine-Gordon, as well as the $\phi^{4}$ model are…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
In this work, we show that by varying the experimental conditions, the driving amplitude, a dynamic force microscope allows DNA properties to be selectively imaged. The substrate on which the DNA is fixed is a silica surface grafted with…
The sine-Gordon equation on a metric graph with a structure represented by a $\mathcal{Y}$-junction, is considered. The model is endowed with boundary conditions at the graph-vertex of $\delta'$-interaction type, expressing continuity of…
We modify the recently proposed model of Speight and Ward to make it possess time dependent solutions. We find that for each lattice spacing and for each velocity of the sine Gordon kink we can find a modification of the model for which…
The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counter-ions. It is well known that the structural collapse of DNA is favored in the presence of…
We establish the full asymptotic stability of the sine-Gordon kink outside symmetry under small perturbations in weighted Sobolev norms. Our proof consists of a space-time resonances approach based on the distorted Fourier transform to…
We study theoretically a binary system in which an attraction of unlike particles is combined with a type-independent soft core repulsion. The possible experimental implementation of the system is a mixture of DNA-covered colloids, in which…
We propose an Ashkin-Teller like model for elastic response of DNA molecule to external force and torque. The base-stacking interaction is described in a simple and uniform way. We obtain the phase diagram of dsDNA, and in particular, the…