Compact phases of polymers with hydrogen bonding

We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen bond formation respectively. By means of Monte Carlo simulations, we are able to trace out the complete phase diagram for different values of the relative strength of the two competing interactions. For strong enough hydrogen bonding, the ground state is a helical conformation, whereas with decreasing hydrogen bonding strength, helices get eventually destabilized at low temperature in favor of more compact conformations resembling $\beta$-sheets appearing in native structures of proteins. For weaker hydrogen bonding helices are not thermodynamically relevant anymore.Comment: 5 pages, 3 figures; revised version published in PR

On scattering of solitons for the Klein-Gordon equation coupled to a particle

We establish the long time soliton asymptotics for the translation invariant nonlinear system consisting of the Klein-Gordon equation coupled to a charged relativistic particle. The coupled system has a six dimensional invariant manifold of the soliton solutions. We show that in the large time approximation any finite energy solution, with the initial state close to the solitary manifold, is a sum of a soliton and a dispersive wave which is a solution of the free Klein-Gordon equation. It is assumed that the charge density satisfies the Wiener condition which is a version of the ``Fermi Golden Rule''. The proof is based on an extension of the general strategy introduced by Soffer and Weinstein, Buslaev and Perelman, and others: symplectic projection in Hilbert space onto the solitary manifold, modulation equations for the parameters of the projection, and decay of the transversal component.Comment: 47 pages, 2 figure

Topological Defects, Orientational Order, and Depinning of the Electron Solid in a Random Potential

We report on the results of molecular dynamics simulation (MD) studies of the classical two-dimensional electron crystal in the presence disorder. Our study is motivated by recent experiments on this system in modulation doped semiconductor systems in very strong magnetic fields, where the magnetic length is much smaller than the average interelectron spacing $a_0$, as well as by recent studies of electrons on the surface of helium. We investigate the low temperature state of this system using a simulated annealing method. We find that the low temperature state of the system always has isolated dislocations, even at the weakest disorder levels investigated. We also find evidence for a transition from a hexatic glass to an isotropic glass as the disorder is increased. The former is characterized by quasi-long range orientational order, and the absence of disclination defects in the low temperature state, and the latter by short range orientational order and the presence of these defects. The threshold electric field is also studied as a function of the disorder strength, and is shown to have a characteristic signature of the transition. Finally, the qualitative behavior of the electron flow in the depinned state is shown to change continuously from an elastic flow to a channel-like, plastic flow as the disorder strength is increased.Comment: 31 pages, RevTex 3.0, 15 figures upon request, accepted for publication in Phys. Rev. B., HAF94MD

The Frequency Dependence of Critical-velocity Behavior in Oscillatory Flow of Superfluid Helium-4 Through a 2-micrometer by 2-micrometer Aperture in a Thin Foil

The critical-velocity behavior of oscillatory superfluid Helium-4 flow through a 2-micrometer by 2-micrometer aperture in a 0.1-micrometer-thick foil has been studied from 0.36 K to 2.10 K at frequencies from less than 50 Hz up to above 1880 Hz. The pressure remained less than 0.5 bar. In early runs during which the frequency remained below 400 Hz, the critical velocity was a nearly-linearly decreasing function of increasing temperature throughout the region of temperature studied. In runs at the lowest frequencies, isolated 2 Pi phase slips could be observed at the onset of dissipation. In runs with frequencies higher than 400 Hz, downward curvature was observed in the decrease of critical velocity with increasing temperature. In addition, above 500 Hz an alteration in supercritical behavior was seen at the lower temperatures, involving the appearance of large energy-loss events. These irregular events typically lasted a few tens of half-cycles of oscillation and could involve hundreds of times more energy loss than would have occurred in a single complete 2 Pi phase slip at maximum flow. The temperatures at which this altered behavior was observed rose with frequency, from ~ 0.6 K and below, at 500 Hz, to ~ 1.0 K and below, at 1880 Hz.Comment: 35 pages, 13 figures, prequel to cond-mat/050203

Scaling in a Nonconservative Earthquake Model of Self-Organised Criticality

We numerically investigate the Olami-Feder-Christensen model for earthquakes in order to characterise its scaling behaviour. We show that ordinary finite size scaling in the model is violated due to global, system wide events. Nevertheless we find that subsystems of linear dimension small compared to the overall system size obey finite (subsystem) size scaling, with universal critical coefficients, for the earthquake events localised within the subsystem. We provide evidence, moreover, that large earthquakes responsible for breaking finite size scaling are initiated predominantly near the boundary.Comment: 6 pages, 6 figures, to be published in Phys. Rev. E; references sorted correctl

Asymptotic stability of breathers in some Hamiltonian networks of weakly coupled oscillators

We consider a Hamiltonian chain of weakly coupled anharmonic oscillators. It is well known that if the coupling is weak enough then the system admits families of periodic solutions exponentially localized in space (breathers). In this paper we prove asymptotic stability in energy space of such solutions. The proof is based on two steps: first we use canonical perturbation theory to put the system in a suitable normal form in a neighborhood of the breather, second we use dispersion in order to prove asymptotic stability. The main limitation of the result rests in the fact that the nonlinear part of the on site potential is required to have a zero of order 8 at the origin. From a technical point of view the theory differs from that developed for Hamiltonian PDEs due to the fact that the breather is not a relative equilibrium of the system

Population dynamics in compressible flows

Organisms often grow, migrate and compete in liquid environments, as well as on solid surfaces. However, relatively little is known about what happens when competing species are mixed and compressed by fluid turbulence. In these lectures we review our recent work on population dynamics and population genetics in compressible velocity fields of one and two dimensions. We discuss why compressible turbulence is relevant for population dynamics in the ocean and we consider cases both where the velocity field is turbulent and when it is static. Furthermore, we investigate populations in terms of a continuos density field and when the populations are treated via discrete particles. In the last case we focus on the competition and fixation of one species compared to anotherComment: 16 pages, talk delivered at the Geilo Winter School 201

Developmental alterations in noxious-evoked EEG activity recorded from rat primary somatosensory cortex

Primary somatosensory cortex (S1) contains a nociceptive map that localizes potential tissue damage on the body and encodes stimulus intensity. An objective and specific biomarker of pain however is currently lacking and is urgently required for use in non-verbal clinical populations as well as in the validation of pre-clinical pain models. Here we describe studies to see if the responses of the S1 in juvenile rats are different to those in the adult. We recorded electroencephalogram (EEG) responses from S1 of lightly-anesthetized Sprague–Dawley rats at either postnatal day 21 or postnatal day 40 during the presentation of noxious (55 °C) or innocuous (30 °C) thermal stimuli applied to the plantar surface of the left hindpaw. The total EEG power across the recording period was the same in both ages after stimulation but the frequency distribution was significantly affected by age. Noxious heat evoked a significant increase in theta band (4–8 Hz) activity in adults only (P < 0.0001 compared to baseline; P < 0.0001 compared to juveniles). There were no significant differences in EEG responses to innocuous thermal stimuli. These data show that there are significant alterations in the processing of nociceptive inputs within the maturing cortex and that cortical theta activity is involved only in the adult cortical response to noxious stimulation

GABA-mediated changes in inter-hemispheric beta frequency activity in early-stage Parkinson's disease

In Parkinson's disease (PD), elevated beta (15-35Hz) power in subcortical motor networks is widely believed to promote aspects of PD symptomatology, moreover, a reduction in beta power and coherence accompanies symptomatic improvement following effective treatment with l-DOPA. Previous studies have reported symptomatic improvements that correlate with changes in cortical network activity following GABAA receptor modulation. In this study we have used whole-head magnetoencephalography to characterize neuronal network activity, at rest and during visually cued finger abductions, in unilaterally symptomatic PD and age-matched control participants. Recordings were then repeated following administration of sub-sedative doses of the hypnotic drug zolpidem (0.05mg/kg), which binds to the benzodiazepine site of the GABAA receptor. A beamforming based 'virtual electrode' approach was used to reconstruct oscillatory power in the primary motor cortex (M1), contralateral and ipsilateral to symptom presentation in PD patients or dominant hand in control participants. In PD patients, contralateral M1 showed significantly greater beta power than ipsilateral M1. Following zolpidem administration contralateral beta power was significantly reduced while ipsilateral beta power was significantly increased resulting in a hemispheric power ratio that approached parity. Furthermore, there was highly significant correlation between hemispheric beta power ratio and Unified Parkinson's Disease Rating Scale (UPDRS). The changes in contralateral and ipsilateral beta power were reflected in pre-movement beta desynchronization and the late post-movement beta rebound. However, the absolute level of movement-related beta desynchronization was not altered. These results show that low-dose zolpidem not only reduces contralateral beta but also increases ipsilateral beta, while rebalancing the dynamic range of M1 network oscillations between the two hemispheres. These changes appear to underlie the symptomatic improvements afforded by low-dose zolpidem

A review of Monte Carlo simulations of polymers with PERM

In this review, we describe applications of the pruned-enriched Rosenbluth method (PERM), a sequential Monte Carlo algorithm with resampling, to various problems in polymer physics. PERM produces samples according to any given prescribed weight distribution, by growing configurations step by step with controlled bias, and correcting "bad" configurations by "population control". The latter is implemented, in contrast to other population based algorithms like e.g. genetic algorithms, by depth-first recursion which avoids storing all members of the population at the same time in computer memory. The problems we discuss all concern single polymers (with one exception), but under various conditions: Homopolymers in good solvents and at the $\Theta$ point, semi-stiff polymers, polymers in confining geometries, stretched polymers undergoing a forced globule-linear transition, star polymers, bottle brushes, lattice animals as a model for randomly branched polymers, DNA melting, and finally -- as the only system at low temperatures, lattice heteropolymers as simple models for protein folding. PERM is for some of these problems the method of choice, but it can also fail. We discuss how to recognize when a result is reliable, and we discuss also some types of bias that can be crucial in guiding the growth into the right directions.Comment: 29 pages, 26 figures, to be published in J. Stat. Phys. (2011