Isomerization dynamics of a buckled nanobeam

We analyze the dynamics of a model of a nanobeam under compression. The model is a two mode truncation of the Euler-Bernoulli beam equation subject to compressive stress. We consider parameter regimes where the first mode is unstable and the second mode can be either stable or unstable, and the remaining modes (neglected) are always stable. Material parameters used correspond to silicon. The two mode model Hamiltonian is the sum of a (diagonal) kinetic energy term and a potential energy term. The form of the potential energy function suggests an analogy with isomerisation reactions in chemistry. We therefore study the dynamics of the buckled beam using the conceptual framework established for the theory of isomerisation reactions. When the second mode is stable the potential energy surface has an index one saddle and when the second mode is unstable the potential energy surface has an index two saddle and two index one saddles. Symmetry of the system allows us to construct a phase space dividing surface between the two "isomers" (buckled states). The energy range is sufficiently wide that we can treat the effects of the index one and index two saddles in a unified fashion. We have computed reactive fluxes, mean gap times and reactant phase space volumes for three stress values at several different energies. In all cases the phase space volume swept out by isomerizing trajectories is considerably less than the reactant density of states, proving that the dynamics is highly nonergodic. The associated gap time distributions consist of one or more `pulses' of trajectories. Computation of the reactive flux correlation function shows no sign of a plateau region; rather, the flux exhibits oscillatory decay, indicating that, for the 2-mode model in the physical regime considered, a rate constant for isomerization does not exist.Comment: 42 pages, 6 figure

Current-induced dynamics of composite free layer with antiferromagnetic interlayer exchange coupling

Current-induced dynamics in spin valves including composite free layer with antiferromagnetic interlayer exchange coupling is studied theoretically within the diffusive transport regime. We show that current-induced dynamics of a synthetic antiferromagnet is significantly different from dynamics of a synthetic ferrimagnet. From macrospin simulations we obtain conditions for switching the composite free layer, as well as for appearance of various self-sustained dynamical modes. Numerical simulations are compared with simple analytical models of critical current based on linearized Landau-Lifshitz-Gilbert equation.Comment: 11 pages, 7 figure

Noise and Correlations in a Spatial Population Model with Cyclic Competition

Noise and spatial degrees of freedom characterize most ecosystems. Some aspects of their influence on the coevolution of populations with cyclic interspecies competition have been demonstrated in recent experiments [e.g. B. Kerr et al., Nature {\bf 418}, 171 (2002)]. To reach a better theoretical understanding of these phenomena, we consider a paradigmatic spatial model where three species exhibit cyclic dominance. Using an individual-based description, as well as stochastic partial differential and deterministic reaction-diffusion equations, we account for stochastic fluctuations and spatial diffusion at different levels, and show how fascinating patterns of entangled spirals emerge. We rationalize our analysis by computing the spatio-temporal correlation functions and provide analytical expressions for the front velocity and the wavelength of the propagating spiral waves.Comment: 4 pages of main text, 3 color figures + 2 pages of supplementary material (EPAPS Document). Final version for Physical Review Letter

Spinal Cord Injury Causes Reduction of Galanin and Gastrin Releasing Peptide mRNA Expression in the Spinal Ejaculation Generator of Male Rats

Spinal cord injury (SCI) in men is commonly associated with sexual dysfunction, including anejaculation, and chronic mid-thoracic contusion injury in male rats also impairs ejaculatory reflexes. Ejaculation is controlled by a spinal ejaculation generator consisting of a population of lumbar spinothalamic (LSt) neurons that control ejaculation through release of four neuropeptides including galanin and gastrin releasing peptide (GRP) onto lumbar and sacral autonomic and motor nuclei. It was recently demonstrated that spinal contusion injury in male rats caused reduction of GRP-immunoreactivity, but not galanin-immunoreactivity in LSt cells, indicative of reduced GRP peptide levels, but inconclusive results for galanin. The current study further tests the hypothesis that contusion injury causes a disruption of GRP and galanin mRNA in LSt cells. Male rats received mid-thoracic contusion injury and galanin and GRP mRNA were visualized 8 weeks later in the lumbar spinal cord using fluorescent in situ hybridization. Spinal cord injury significantly reduced GRP and galanin mRNA in LSt cells. Galanin expression was higher in LSt cells compared to GRP. However, expression of the two transcripts were positively correlated in LSt cells in both sham and SCI animals, suggesting that expression for the two neuropeptides may be co-regulated. Immunofluorescent visualization of galanin and GRP peptides demonstrated a significant reduction in GRP-immunoreactivity, but not galanin in LSt cells, confirming the previous observations. In conclusion, SCI reduced GRP and galanin expression in LSt cells with an apparent greater impact on GRP peptide levels. GRP and galanin are both essential for triggering ejaculation and thus such reduction may contribute to ejaculatory dysfunction following SCI in rats

In Situ Characterisation of Permanent Magnetic Quadrupoles for focussing proton beams

High intensity laser driven proton beams are at present receiving much attention. The reasons for this are many but high on the list is the potential to produce compact accelerators. However two of the limitations of this technology is that unlike conventional nuclear RF accelerators lasers produce diverging beams with an exponential energy distribution. A number of different approaches have been attempted to monochromise these beams but it has become obvious that magnetic spectrometer technology developed over many years by nuclear physicists to transport and focus proton beams could play an important role for this purpose. This paper deals with the design and characterisation of a magnetic quadrupole system which will attempt to focus and transport laser-accelerated proton beams.Comment: 20 pages, 42 figure

Phase-space structure of two-dimensional excitable localized structures

In this work we characterize in detail the bifurcation leading to an excitable regime mediated by localized structures in a dissipative nonlinear Kerr cavity with a homogeneous pump. Here we show how the route can be understood through a planar dynamical system in which a limit cycle becomes the homoclinic orbit of a saddle point (saddle-loop bifurcation). The whole picture is unveiled, and the mechanism by which this reduction occurs from the full infinite-dimensional dynamical system is studied. Finally, it is shown that the bifurcation leads to an excitability regime, under the application of suitable perturbations. Excitability is an emergent property for this system, as it emerges from the spatial dependence since the system does not exhibit any excitable behavior locally.Comment: 10 pages, 9 figure

Must naive realists be relationalists?

Relationalism maintains that perceptual experience involves, as part of its nature, a distinctive kind of conscious perceptual relation between a subject of experience and an object of experience. Together with the claim that perceptual experience is presentational, relationalism is widely believed to be a core aspect of the naive realist outlook on perception. This is a mistake. I argue that naive realism about perception can be upheld without a commitment to relationalism

Bubbles and Filaments: Stirring a Cahn-Hilliard Fluid

The advective Cahn-Hilliard equation describes the competing processes of stirring and separation in a two-phase fluid. Intuition suggests that bubbles will form on a certain scale, and previous studies of Cahn-Hilliard dynamics seem to suggest the presence of one dominant length scale. However, the Cahn-Hilliard phase-separation mechanism contains a hyperdiffusion term and we show that, by stirring the mixture at a sufficiently large amplitude, we excite the diffusion and overwhelm the segregation to create a homogeneous liquid. At intermediate amplitudes we see regions of bubbles coexisting with regions of hyperdiffusive filaments. Thus, the problem possesses two dominant length scales, associated with the bubbles and filaments. For simplicity, we use use a chaotic flow that mimics turbulent stirring at large Prandtl number. We compare our results with the case of variable mobility, in which growth of bubble size is dominated by interfacial rather than bulk effects, and find qualitatively similar results.Comment: 20 pages, 27 figures. RevTeX

Relaxation Dynamics of Semiflexible Polymers

We study the relaxation dynamics of a semiflexible chain by introducing a time-dependent tension. The chain has one of its ends attached to a large bead, and the other end is fixed. We focus on the initial relaxation of the chain that is initially strongly stretched. Using a tension that is self-consistently determined, we obtain the evolution of the end-to-end distance with no free parameters. Our results are in good agreement with single molecule experiments on double stranded DNA

The role of body rotation in bacterial flagellar bundling

In bacterial chemotaxis, E. coli cells drift up chemical gradients by a series of runs and tumbles. Runs are periods of directed swimming, and tumbles are abrupt changes in swimming direction. Near the beginning of each run, the rotating helical flagellar filaments which propel the cell form a bundle. Using resistive-force theory, we show that the counter-rotation of the cell body necessary for torque balance is sufficient to wrap the filaments into a bundle, even in the absence of the swirling flows produced by each individual filament