Related papers: Nonlinear DNA dynamics: nonlinearity versus disper…
External flows, such as shear flow, add directional biases to particle motion, introducing anisotropic behavior into the system. Here, we explore the non-equilibrium dynamics that emerge from the interplay between linear shear flow and…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…
Evolution is simultaneously driven by a number of processes such as mutation, competition and random sampling. Understanding which of these processes is dominating the collective evolutionary dynamics in dependence on system properties is a…
Motivated by recent experiments in optics and atomic physics, we derive an averaged nonlinear partial differential equation describing the dynamics of the complex field in a nonlinear Schroedinger model in the presence of a periodic…
We study the spreading of initially localized states in a nonlinear disordered lattice described by the nonlinear Schr\"odinger equation with random on-site potentials - a nonlinear generalization of the Anderson model of localization. We…
Using high-resolution confocal rheometry, we study the shear profiles of well-entangled DNA solutions under large amplitude oscillatory shear (LAOS) in a rectilinear planar shear cell. With increasing Weissenberg number (Wi), we observe…
The observation that phenotypic variability is ubiquitous in isogenic populations has led to a multitude of experimental and theoretical studies seeking to probe the causes and consequences of this variability. Whether it be in the context…
Shear cracks propagation is a basic dynamical process that mediates interfacial failure. We develop a general weakly nonlinear elastic theory of shear cracks and show that these experience tensile-mode crack tip deformation, including…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
Heterogeneity in physical and functional characteristics of cells (e.g. size, cycle time, growth rate, protein concentration) proliferates within an isogenic population due to stochasticity in intracellular biochemical processes and in the…
Fully describing light propagation in a rotating, anisotropic medium with thermal nonlinearity requires modeling the interplay between nonlinear refraction, birefringence, and the nonlinear group index. Incorporating these factors into a…
We present a nonparametric framework to model a short sequence of probability distributions that vary both due to underlying effects of sequential progression and confounding noise. To distinguish between these two types of variation and…
The internal motions of DNA immersed in bio-fluid are investigated. The interactions between the fragments of DNA and the surrounding bio-fluid are modeled using the gauge fluid lagrangian. In the model, the bio-fluid is coupled to the…
The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without…
In this chapter, we discuss experiments that realize the discrete nonlinear Schr\"odinger (DNLS) equations. The relevance of such descriptions arises from the competition of three common features: nonlinearity, dispersion, and a medium to…
The distribution of bubble lengths in double-stranded DNA is presented for segments of varying guanine-cytosine (GC) content, obtained with Monte Carlo simulations using the Peyrard-Bishop-Dauxois model at 310 K. An analytical description…
The nonlinear excitations induced in DNA by external force are considered on the basis of Peyrard-Bishop-Dauxois model. It is shown that such impact can lead to creation of bubbles which can propogate through the molecule. The interaction…
Step meandering due to a deterministic morphological instability on vicinal surfaces during growth is studied. We investigate nonlinear dynamics of a step model with asymmetric step kinetics, terrace and line diffusion, by means of a…
The study of wave propagation in chains of anharmonic periodic systems is of fundamental importance to understand the response of dynamical absorbers of vibrations and acoustic metamaterials working in nonlinear regime. Here, we derive an…