Related papers: Nonlinear DNA dynamics: nonlinearity versus disper…
We consider the modulational instability of nonlinearly interacting two-dimensional waves in deep water, which are described by a pair of two-dimensional coupled nonlinear Schroedinger equations. We derive a nonlinear dispersion relation.…
We develop a general criterion about coarsening for a class of nonlinear evolution equations describing one dimensional pattern-forming systems. This criterion allows one to discriminate between the situation where a coarsening process…
Many scientific problems involve data exhibiting both temporal and cross-sectional dependencies. While linear dependencies have been extensively studied, the theoretical analysis of regression estimators under nonlinear dependencies remains…
A recent experiment [Sadoon AA, Wang Y. 2018 Phys. Rev. E 98, 042411] has revealed that nucleoid associated proteins (i.e., DNA-binding proteins) exhibit highly heterogeneous diffusion processes in bacteria where not only the diffusion…
We present a new dynamical model of DNA. This model has two degrees of freedom per base-pair: one radial variable related to the opening of the hydrogen bonds and an angular one related to the twisting of each base-pair responsible for the…
Diffusion of colloidal particles in a complex environment such as polymer networks or biological cells is a topic of high complexity with significant biological and medical relevance. In such situations, the interaction between the…
A stochastic differential equation for the plasma density dynamics is derived, consistent with the experimentally measured distribution and the theoretical quadratic nonlinearity. The plasma density is driven by a multiplicative Wiener…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a…
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet,…
Nonlinear molecular excitations in DNA have traditionally been modelled using the nonlinear Schr\"odinger equation (NLSE). An alternative approach is based on the plane-base rotator model and the SU(2)/U(1) generalized spin coherent states,…
A recent first-principles approach to the non-linear rheology of dense colloidal suspensions is evaluated and compared to simulation results of sheared systems close to their glass transitions. The predicted scenario of a universal…
Using the isospin dependent quantum molecular dynamics model, we study the effect of charge asymmetry and isospin dependent cross-section on $\frac{dN}{d(<Cos2\phi>)}$ and $\frac{dN}{p_tdp_t}$. Simulations have been carried out for the…
The beam-plasma instability can be addressed as a reduced model in several contexts of plasma physics, from space to fusion plasma. In this paper, we review and refine some non-linear features of this model. Specifically, by analyzing the…
We consider a nonlinear coupled discrete-time model of population dynamics. This model describes the movement of populations within a heterogeneous landscape, where the growth of subpopulations are modelled by (possibly different) bounded…
The viscosity of dilute and semidilute unentangled DNA solutions, in steady simple shear flow, has been measured across a range of temperatures and concentrations. For polystyrene solutions, measurements of viscosity have been carried out…
We study the basepairing dynamics of DNA with repetitive sequences where local strand slippage can create, annihilate, and move bulge loops. Using an explicit theoretical model, we find a rich dynamical behavior as a function of an applied…
We introduce a new nonlinear model for classification, in which we model the joint distribution of response variable, y, and covariates, x, non-parametrically using Dirichlet process mixtures. We keep the relationship between y and x linear…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…