Related papers: Nonlinear excitations in DNA: Aperiodic models vs …
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
We study electronic transport in long DNA chains using the tight-binding approach for a ladder-like model of DNA. We find insulating behavior with localizaton lengths xi ~ 25 in units of average base-pair seperation. Furthermore, we observe…
We consider the propagation of sine-Gordon kinks in a planar curved strip as a model of nonlinear wave propagation in curved wave guides. The homogeneous Neumann transverse boundary conditions, in the curvilinear coordinates, allow to…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…
Normal and anomalous diffusion are ubiquitous in many complex systems [1] . Here, we define a time and space generalized diffusion equation (GDE), which uses fractional-time derivatives and transformed d-path Laplacian operators on…
We study the nonlinear dynamics of a deformed Deoxyribonucleic acid (DNA) molecular chain which is governed by a perturbed sine-Gordon equation coupled with a linear wave equation representing the lattice deformation. The DNA chain…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
We develop a dynamical model of the propagating nonlinear localized excitations, supersonic kinks, in the cation layer in a silicate mica crystal. We start from purely electrostatic Coulomb interaction and add the Ziegler-Biersack-Littmark…
We study collisions of kinks in the one-space and one-time dimensional noncanonical nonintegrable scalar $\phi^{6}$ model. We examine the energy density of the kink, and we find that, as a function of the parameters that control the…
We study the effect of transcription on the kinetics of DNA supercoiling in 3D by means of Brownian dynamics simulations of a single nucleotide resolution coarse-grained model for double stranded DNA. By accounting for the action of a…
We had combined the Neukirch-Marko model that describes the extension, torque and supercoiling in single, stretched and twisted DNA of infinite contour length, with a form of the free energy suggested by Sinha and Samuels to describe short…
A high-symmetry crystal surface may undergo a kinetic instability during the growth, such that its late stage evolution resembles a phase separation process. This parallel is rigorous in one dimension, if the conserved surface current is…
We demonstrate that the modulation instability of the zone boundary mode in a finite (periodic) Fermi-Pasta-Ulam chain is the necessary but not sufficient condition for the efficient energy transfer by localized excitations. This transfer…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…
We use the helicoidal Peyrard-Bishop model of DNA in the current work. We solve a dynamical equation of motion using a continuum approximation, resulting in kink-solitary waves that travel along the chain. We demonstrate that, whereas…
We present an experimentally realizable, simple mechanical system with linear interactions whose geometric nature leads to nontrivial, nonlinear dynamical equations. The equations of motion are derived and their ground state structures are…
We highlight a few recent results on the effect of the diffusion process in deterministic area preserving maps with noncompact phase space, namely the standard map. In more detail, we focus on the anomalous diffusion arising due to the…
The origin of nonlinear responses in cells has been suggested to be crucial for various cell functions including the propagation of the nervous impulse. In physics nonlinear behavior often originates from phase transitions. Evidence for…