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Register a new userHeterogeneity and chaos in the Peyrard-Bishop-Dauxois DNA model
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We discuss the effect of heterogeneity on the chaotic properties of the Peyrard-Bishop-Dauxois nonlinear model of DNA. Results are presented for the maximum Lyapunov exponent and the deviation vector distribution. Different compositions of adenine-thymine (AT) and guanine-cytosine (GC) base pairs are examined for various energies up to the melting point of the corresponding sequence. We also consider the effect of the alternation index, which measures the heterogeneity of the DNA chain through the number of alternations between different types (AT or GC) of base pairs, on the chaotic behavior of the system. Biological gene promoter sequences have been also investigated, showing no distinct behavior of the maximum Lyapunov exponent.
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As a first step in the search of an analytical study of mechanical denaturation of DNA in terms of the sequence, we study stable, stationary solutions in the discrete, finite and homogeneous Peyrard-Bishop DNA model. We find and classify all the stationary solutions of the model, as well as analytic approximations of them, both in the continuum and in the discrete limits. Our results explain the structure of the solutions reported by Theodorakopoulos {em et al.} [Phys. Rev. Lett. {bf 93}, 258101 (2004)] and provide a way to proceed to the analysis of the generalized version of the model incorporating the genetic information.
Red blood cells (RBCs) are the major component of blood and the flow of blood is dictated by that of RBCs. We employ vesicles, which consist of closed bilayer membranes enclosing a fluid, as a model system to study the behavior of RBCs under a confined Poiseuille flow. We extensively explore two main parameters: i) the degree of confinement of vesicles within the channel, and ii) the flow strength. Rich and complex dynamics for vesicles are revealed ranging from steady-state shapes (in the form of parachute and slipper) to chaotic dynamics of shape. Chaos occurs through a cascade of multiple periodic oscillations of the vesicle shape. We summarize our results in a phase diagram in the parameter plane (degree of confinement, flow strength). This finding highlights the level of complexity of a flowing vesicle in the small Reynolds number where the flow is laminar in the absence of vesicles and can be rendered turbulent due to elasticity of vesicles.
The local density of states (LDOS) is a distribution that characterizes the effect of perturbations on quantum systems. Recently, it was proposed a semiclassical theory for the LDOS of chaotic billiards and maps. This theory predicts that the LDOS is a Breit-Wigner distribution independent of the perturbation strength and also gives a semiclassical expression for the LDOS witdth. Here, we test the validity of such an approximation in quantum maps varying the degree of chaoticity, the region in phase space where the perturbation is applying and the intensity of the perturbation. We show that for highly chaotic maps or strong perturbations the semiclassical theory of the LDOS is accurate to describe the quantum distribution. Moreover, the width of the LDOS is also well represented for its semiclassical expression in the case of mixed classical dynamics.
We probe the limits of nonlinear wave spreading in disordered chains which are known to localize linear waves. We particularly extend recent studies on the regimes of strong and weak chaos during subdiffusive spreading of wave packets [EPL {bf 91}, 30001 (2010)] and consider strong disorder, which favors Anderson localization. We probe the limit of infinite disorder strength and study Frohlich-Spencer-Wayne models. We find that the assumption of chaotic wave packet dynamics and its impact on spreading is in accord with all studied cases. Spreading appears to be asymptotic, without any observable slowing down. We also consider chains with spatially inhomogeneous nonlinearity which give further support to our findings and conclusions.
Experiments with superconducting microwave cavities have been performed in our laboratory for more than two decades. The purpose of the present article is to recapitulate some of the highlights achieved. We briefly review (i) results obtained with flat, cylindrical microwave resonators, so-called microwave billiards, concerning the universal fluctuation properties of the eigenvalues of classically chaotic systems with no, a threefold and a broken symmetry; (ii) summarize our findings concerning the wave-dynamical chaos in three-dimensional microwave cavities; (iii) present a new approach for the understanding of the phenomenon of dynamical tunneling which was developed on the basis of experiments that were performed recently with unprecedented precision, and finally, (iv) give an insight into an ongoing project, where we investigate universal properties of (artificial) graphene with superconducting microwave photonic crystals that are enclosed in a microwave resonator, i.e., so-called Dirac billiards.
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