Switching to nonhyperbolic cycles from codimension two bifurcations of equilibria of delay differential equations

In this paper we perform the parameter-dependent center manifold reduction near the generalized Hopf (Bautin), fold-Hopf, Hopf-Hopf and transcritical-Hopf bifurcations in delay differential equations (DDEs). This allows us to initialize the continuation of codimension one equilibria and cycle bifurcations emanating from these codimension two bifurcation points. The normal form coefficients are derived in the functional analytic perturbation framework for dual semigroups (sun-star calculus) using a normalization technique based on the Fredholm alternative. The obtained expressions give explicit formulas which have been implemented in the freely available numerical software package DDE-BifTool. While our theoretical results are proven to apply more generally, the software implementation and examples focus on DDEs with finitely many discrete delays. Together with the continuation capabilities of DDE-BifTool, this provides a powerful tool to study the dynamics near equilibria of such DDEs. The effectiveness is demonstrated on various models

Conformations of dendrimers in dilute solution

Conformations of isolated homo- dendrimers of G=1-7 generations with D=1-6 spacers have been studied in the good and poor solvents, as well as across the coil-to-globule transition, by means of a version of the Gaussian self-consistent (GSC) method and Monte Carlo (MC) simulation in continuous space based on the same coarse-grained model. The latter includes harmonic springs between connected monomers and the pair-wise Lennard-Jones potential with a hard core repulsion. The scaling law for the dendrimer size, the degrees of bond stretching and steric congestion, as well as the radial density, static structure factor, and asphericity have been analysed. It is also confirmed that while smaller dendrimers have a dense core, larger ones develop a hollow domain at some separation from the centre.Comment: RevTeX, 14 pages, 19 PS figures, Accepted for publication in J. Chem. Phy

On Local Bifurcations in Neural Field Models with Transmission Delays

Neural field models with transmission delay may be cast as abstract delay differential equations (DDE). The theory of dual semigroups (also called sun-star calculus) provides a natural framework for the analysis of a broad class of delay equations, among which DDE. In particular, it may be used advantageously for the investigation of stability and bifurcation of steady states. After introducing the neural field model in its basic functional analytic setting and discussing its spectral properties, we elaborate extensively an example and derive a characteristic equation. Under certain conditions the associated equilibrium may destabilise in a Hopf bifurcation. Furthermore, two Hopf curves may intersect in a double Hopf point in a two-dimensional parameter space. We provide general formulas for the corresponding critical normal form coefficients, evaluate these numerically and interpret the results

Intra-chain correlation functions and shapes of homopolymers with different architectures in dilute solution

We present results of Monte Carlo study of the monomer-monomer correlation functions, static structure factor and asphericity characteristics of a single homopolymer in the coil and globular states for three distinct architectures of the chain: ring, open and star. To rationalise the results we introduce the dimensionless correlation functions rescaled via the corresponding mean-squared distances between monomers. For flexible chains with some architectures these functions exhibit a large degree of universality by falling onto a single or several distinct master curves. In the repulsive regime, where a stretched exponential times a power law form (de Cloizeaux scaling) can be applied, the corresponding exponents $\delta$ and $\theta$ have been obtained. The exponent $\delta=1/\nu$ is found to be universal for flexible strongly repulsive coils and in agreement with the theoretical prediction from improved higher-order Borel-resummed renormalisation group calculations. The short-distance exponents $\theta_{\upsilon}$ of an open flexible chain are in a good agreement with the theoretical predictions in the strongly repulsive regime also. However, increasing the Kuhn length in relation to the monomer size leads to their fast cross-over towards the Gaussian behaviour. Likewise, a strong sensitivity of various exponents $\theta_{ij}$ on the stiffness of the chain, or on the number of arms in star polymers, is observed. The correlation functions in the globular state are found to have a more complicated oscillating behaviour and their degree of universality has been reviewed. Average shapes of the polymers in terms of the asphericity characteristics, as well as the universal behaviour in the static structure factors, have been also investigated.Comment: RevTeX 12 pages, 10 PS figures. Accepted by J. Chem. Phy

Monte Carlo simulations of infinitely dilute solutions of amphiphilic diblock star copolymers

Single-chain Monte Carlo simulations of amphiphilic diblock star copolymers were carried out in continuous space using implicit solvents. Two distinct architectures were studied: stars with the hydrophobic blocks attached to the core, and stars with the polar blocks attached to the core, with all arms being of equal length. The ratio of the lengths of the hydrophobic block to the length of the polar block was varied from 0 to 1. Stars with 3, 6, 9 or 12 arms, each of length 10, 15, 25, 50, 75 and 100 Kuhn segments were analysed. Four distinct types of conformations were observed for these systems. These, apart from studying the snapshots from the simulations, have been quantitatively characterised in terms of the mean-squared radii of gyration, mean-squared distances of monomers from the centre-of-mass, asphericity indices, static scattering form factors in the Kratky representation as well as the intra-chain monomer-monomer radial distribution functions.Comment: 12 pages, 11 ps figures. Accepted for publication in J. Chem. Phy

Prion proteins: evolution and preservation of secondary structure

AbstractPrions cause a variety of neurodegenerative disorders that seem to result from a conformational change in the prion protein (PrP). Thirty-two PrP sequences have been subjected to phylogenetic analysis followed by reconstruction of the most probable evolutionary spectrum of amino acid replacements. The replacement rates suggest that the protein does not seem to be very conservative, but in the course of evolution amino acids have only been substituted within the elements of the secondary structure by those with very similar physico-chemical properties. Analysis of the full spectrum of single-step amino acid substitutions in human PrP using secondary structure prediction algorithms shows an over-representation of substitutions that tend to destabilize α-helices

On the non-equivalence of Lorenz System and Chen System

In this paper, we prove that the Chen system with a set of chaotic parameters is not smoothly equivalent to the Lorenz system with any parameters

Biophysical and atomic force microscopy characterization of the RNA from satellite tobacco mosaic virus

Agarose gel electrophoresis, circular dichroism and differential scanning calorimetry showed that single-stranded RNA from satellite tobacco mosaic virus transforms from a conformationally ‘closed state’ at 4°C to a more conformationally ‘open state’ at 65°C. The transition is reversible and shows no hysteresis. Atomic force microscopy (AFM) allowed visualization of the two states and indicated that the conformationally ‘closed state’ probably corresponds to the native encapsidated conformation, and that the ‘open state’ represents a conformation, characterized as short, thick chains of domains, as a consequence of the loss of tertiary interactions. Heating from 75°C to 85°C in the presence of EDTA was necessary to further unravel the ‘open’ conformation RNA into extended chains of lengths >280 nm. Virus exposed to low concentrations of phenol at 65°C, extruded RNA as distinctive ‘pigtails’ in a synchronous fashion, and these ‘pigtails’ then elongated, as the RNA was further discharged by the particles. Moderate concentrations of phenol at 65°C produced complete disruption of virions and only remains of decomposed particles and disordered RNA were evident. AFM images of RNA emerging from disrupted virions appear most consistent with linear arrangements of structural domains