Related papers: Nonlinear DNA dynamics: nonlinearity versus disper…
Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such…
Neural activity patterns related to behavior occur at many scales in time and space from the atomic and molecular to the whole brain. Here we explore the feasibility of interpreting neurophysiological data in the context of many-body…
DNA is structurally and mechanically altered by the binding of intercalator molecules. Intercalation strongly affects the force-extension behavior of DNA, in particular the overstretching transition. We present a statistical model that…
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine…
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…
We present a phenomenological dynamical model able to describe the stretching features of the curve of DNA length vs applied force. As concerns the chain, the model is based on the discrete wormlike chain model with elastic modifications,…
It is shown that information transmission inside a cell can occur by means of mechanical waves transmitted through DNA. The propagation of the waves is strongly dependent on the shape of the DNA thus proteins that change the shape of DNA…
In this paper we investigate the dynamical properties of a spatially periodic reaction-diffusion system {whose reaction terms are of hybrid nature in the sense that they are partly competitive and partly cooperative depending on the value…
We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous…
Within the framework of the thermal wave model, an investigation is made of the longitudinal dynamics of high energy charged particle beams. The model includes the self-consistent interaction between the beam and its surroundings in terms…
The idea of the inheritance of biological processes, such as the developmental process or the life cycle of an organism, has been discussed in the biology literature, but formal mathematical descriptions and plausible data analysis…
We study the evolution of a wave packet in a nonlinear Schr\"odinger lattice equation subject to a dc bias. In the absence of nonlinearity all normal modes are spatially localized giving rise to a Stark ladder with an equidistant eigenvalue…
The Kronig-Penney model is used to Study the effect of nonlinear interaction on the transmissive properties of both ordered and disordered chains. In the ordered case, the nonlinearity can either localize or delocalize the electronic states…
We present a very simple model for the study of charge transport in a molecule patterned on B-DNA. In this model we use a discrete non-linear Schr\"{o}dinger equation to describe electrons propagating along the sugar-phosphate backbone of…
All solids, whether crystalline or disordered, support elastic wave propagation with a linear dispersion relation in the long-wavelength limit. These waves, corresponding to low-frequency phonons, feature a vibrational density of states…
When it is viewed at the scale of a base pair, DNA appears as a nonlinear lattice. Modelling its properties is a fascinating goal. The detailed experiments that can be performed on this system impose constraints on the models and can be…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
A general theory of nonlinear signal-noise interactions for wavelength division multiplexed fiber-optic coherent transmission systems is presented. This theory is based on the regular perturbation treatment of the nonlinear Schrodinger…
We uncover a strong coupling between nonlinearity and diffraction in a photonic crystal at the supercollimation point. We show this is modeled by a nonlinear diffraction term in a nonlinear schroedinger type equation, in which the…