Stationary and moving breathers in a simplified model of curved alpha--helix proteins

The existence, stability and movability of breathers in a model for alpha-helix proteins is studied. This model basically consists a chain of dipole moments parallel to it. The existence of localized linear modes brings about that the system has a characteristic frequency, which depends on the curvature of the chain. Hard breathers are stable, while soft ones experiment subharmonic instabilities that preserve, however the localization. Moving breathers can travel across the bending point for small curvature and are reflected when it is increased. No trapping of breathers takes place.Comment: 19 pages, 11 figure

Thermal Resonance in Signal Transmission

We use temperature tuning to control signal propagation in simple one-dimensional arrays of masses connected by hard anharmonic springs and with no local potentials. In our numerical model a sustained signal is applied at one site of a chain immersed in a thermal environment and the signal-to-noise ratio is measured at each oscillator. We show that raising the temperature can lead to enhanced signal propagation along the chain, resulting in thermal resonance effects akin to the resonance observed in arrays of bistable systems.Comment: To appear in Phys. Rev.

Nonlinearity-induced conformational instability and dynamics of biopolymers

We propose a simple phenomenological model for describing the conformational dynamics of biopolymers via the nonlinearity-induced buckling and collapse (i.e. coiling up) instabilities. Taking into account the coupling between the internal and mechanical degrees of freedom of a semiflexible biopolymer chain, we show that self-trapped internal excitations (such as amide-I vibrations in proteins, base-pair vibrations in DNA, or polarons in proteins) may produce the buckling and collapse instabilities of an initially straight chain. These instabilities remain latent in a straight infinitely long chain, because the bending of such a chain would require an infinite energy. However, they manifest themselves as soon as we consider more realistic cases and take into account a finite length of the chain. In this case the nonlinear localized modes may act as drivers giving impetus to the conformational dynamics of biopolymers. The buckling instability is responsible, in particular, for the large-amplitude localized bending waves which accompany the nonlinear modes propagating along the chain. In the case of the collapse instability, the chain folds into a compact three-dimensional coil. The viscous damping of the aqueous environment only slows down the folding of the chain, but does not stop it even for a large damping. We find that these effects are only weakly affected by the peculiarities of the interaction potentials, and thus they should be generic for different models of semiflexible chains carrying nonlinear localized excitations.Comment: 4 pages (RevTeX) with 5 figures (EPS

Enhanced Pulse Propagation in Non-Linear Arrays of Oscillators

The propagation of a pulse in a nonlinear array of oscillators is influenced by the nature of the array and by its coupling to a thermal environment. For example, in some arrays a pulse can be speeded up while in others a pulse can be slowed down by raising the temperature. We begin by showing that an energy pulse (1D) or energy front (2D) travels more rapidly and remains more localized over greater distances in an isolated array (microcanonical) of hard springs than in a harmonic array or in a soft-springed array. Increasing the pulse amplitude causes it to speed up in a hard chain, leaves the pulse speed unchanged in a harmonic system, and slows down the pulse in a soft chain. Connection of each site to a thermal environment (canonical) affects these results very differently in each type of array. In a hard chain the dissipative forces slow down the pulse while raising the temperature speeds it up. In a soft chain the opposite occurs: the dissipative forces actually speed up the pulse while raising the temperature slows it down. In a harmonic chain neither dissipation nor temperature changes affect the pulse speed. These and other results are explained on the basis of the frequency vs energy relations in the various arrays

Fractal entropy of a chain of nonlinear oscillators

We study the time evolution of a chain of nonlinear oscillators. We focus on the fractal features of the spectral entropy and analyze its characteristic intermediate timescales as a function of the nonlinear coupling. A Brownian motion is recognized, with an analytic power-law dependence of its diffusion coefficient on the coupling.Comment: 6 pages, 3 figures, revised version to appear in Phys. Rev.

Understanding illnesses through a film festival: an observational study

Audio-visual materials play a fundamental role in the context of education, care and clinical treatment, as they seem to have a high impact on public awareness. This study aims to describe what messages are perceived by the society at an International Festival of Short Films and Art on Diseases that may help to understand difficult topics, such as illness, dying and suffering. Through an observational, descriptive, cross-sectional study, using full participant observation and an open, self-administered questionnaire, 32 short films were analysed during a healthcare art festival. Categories were developed using inductive content analysis. The message perceived by the participants, after the viewing of the shorts and reflection of the debates among the attendees, were considered in four categories: i) creative and positive education is possible; ii) awareness of preconception and practical duties; iii) meaning of life changes the experience of illness; iv) family and caregivers also experienced suffering. The short films are considered as an excellent tool to generate social dialogue and debate. Public events can be understood as an opportunity to ac- quire, in an emotional and critical manner, other competencies for public awareness. Together, they are capable of communicating difficult messages through a fast, positive, and creative way

Surface Hardening and Self-Organized Fractality Through Etching of Random Solids

When a finite volume of etching solution is in contact with a disordered solid, complex dynamics of the solid-solution interface develop. If the etchant is consumed in the chemical reaction, the dynamics stop spontaneously on a self-similar fractal surface. As only the weakest sites are corroded, the solid surface gets progressively harder and harder. At the same time it becomes rougher and rougher uncovering the critical spatial correlations typical of percolation. From this, the chemical process reveals the latent percolation criticality hidden in any random system. Recently, a simple minimal model has been introduced by Sapoval et al. to describe this phenomenon. Through analytic and numerical study, we obtain a detailed description of the process. The time evolution of the solution corroding power and of the distribution of resistance of surface sites is studied in detail. This study explains the progressive hardening of the solid surface. Finally, this dynamical model appears to belong to the universality class of Gra dient Percolation.Comment: 14 pages, 15 figures (1457 Kb

Plankton lattices and the role of chaos in plankton patchiness

Spatiotemporal and interspecies irregularities in planktonic populations have been widely observed. Much research into the drivers of such plankton patches has been initiated over the past few decades but only recently have the dynamics of the interacting patches themselves been considered. We take a coupled lattice approach to model continuous-in-time plankton patch dynamics, as opposed to the more common continuum type reaction-diffusion-advection model, because it potentially offers a broader scope of application and numerical study with relative ease. We show that nonsynchronous plankton patch dynamics (the discrete analog of spatiotemporal irregularity) arise quite naturally for patches whose underlying dynamics are chaotic. However, we also observe that for parameters in a neighborhood of the chaotic regime, smooth generalized synchronization of nonidentical patches is more readily supported which reduces the incidence of distinct patchiness. We demonstrate that simply associating the coupling strength with measurements of (effective) turbulent diffusivity results in a realistic critical length of the order of 100 km, above which one would expect to observe unsynchronized behavior. It is likely that this estimate of critical length may be reduced by a more exact interpretation of coupling in turbulent flows

Energy funneling in a bent chain of Morse oscillators with long-range coupling

A bent chain of coupled Morse oscillators with long-range dispersive interaction is considered. Moving localized excitations may be trapped in the bending region. Thus chain geometry acts like an impurity. An energy funneling effect is observed in the case of random initial conditions.Comment: 6 pages, 12 figures. Submitted to Physical Review E, Oct. 13, 200

Differential cargo mobilisation within Weibel-Palade bodies after transient fusion with the plasma membrane.

Inflammatory chemokines can be selectively released from Weibel-Palade bodies (WPBs) during kiss-and-run exocytosis. Such selectivity may arise from molecular size filtering by the fusion pore, however differential intra-WPB cargo re-mobilisation following fusion-induced structural changes within the WPB may also contribute to this process. To determine whether WPB cargo molecules are differentially re-mobilised, we applied FRAP to residual post-fusion WPB structures formed after transient exocytosis in which some or all of the fluorescent cargo was retained. Transient fusion resulted in WPB collapse from a rod to a spheroid shape accompanied by substantial swelling (>2 times by surface area) and membrane mixing between the WPB and plasma membranes. Post-fusion WPBs supported cumulative WPB exocytosis. To quantify diffusion inside rounded organelles we developed a method of FRAP analysis based on image moments. FRAP analysis showed that von Willebrand factor-EGFP (VWF-EGFP) and the VWF-propolypeptide-EGFP (Pro-EGFP) were immobile in post-fusion WPBs. Because Eotaxin-3-EGFP and ssEGFP (small soluble cargo proteins) were largely depleted from post-fusion WPBs, we studied these molecules in cells preincubated in the weak base NH4Cl which caused WPB alkalinisation and rounding similar to that produced by plasma membrane fusion. In these cells we found a dramatic increase in mobilities of Eotaxin-3-EGFP and ssEGFP that exceeded the resolution of our method (∼ 2.4 µm2/s mean). In contrast, the membrane mobilities of EGFP-CD63 and EGFP-Rab27A in post-fusion WPBs were unchanged, while P-selectin-EGFP acquired mobility. Our data suggest that selective re-mobilisation of chemokines during transient fusion contributes to selective chemokine secretion during transient WPB exocytosis. Selective secretion provides a mechanism to regulate intravascular inflammatory processes with reduced risk of thrombosis