Coarse-graining the Dynamics of a Driven Interface in the Presence of Mobile Impurities: Effective Description via Diffusion Maps

Developing effective descriptions of the microscopic dynamics of many physical phenomena can both dramatically enhance their computational exploration and lead to a more fundamental understanding of the underlying physics. Previously, an effective description of a driven interface in the presence of mobile impurities, based on an Ising variant model and a single empirical coarse variable, was partially successful; yet it underlined the necessity of selecting additional coarse variables in certain parameter regimes. In this paper we use a data mining approach to help identify the coarse variables required. We discuss the implementation of this diffusion map approach, the selection of a similarity measure between system snapshots required in the approach, and the correspondence between empirically selected and automatically detected coarse variables. We conclude by illustrating the use of the diffusion map variables in assisting the atomistic simulations, and we discuss the translation of information between fine and coarse descriptions using lifting and restriction operators.Comment: 28 pages, 10 figure

UNIETD – Assessment of Third Party Data as Information Source for Drivers and Road Operators

The paper deals with the assessment of third party data such as crowd sourced/social media and floating vehicle data as information source for road operators in addition to traditional infrastructure-based techniques. For purposes of quality assessment of different types of data and available ground truths existing test/evaluation methodologies have been assessed. A new methodology has been designed for assessment of speeds and travel times using normalized (between 0 and 1) quality indicators that can distinguish between “detection rate” and “false alarm rate” concepts. In terms of harvesting social media the relevance of social media content has been assessed against a range of traffic management requirements. Furthermore the level of content that will be available has been estimated as well as commercial sources and business models for road authorities. Analyses cover unstructured data from Twitter and Facebook both historical data and three months of contemporary data. In addition surveys are conducted in England and Austria to retrieve information from the public in terms of which social media platforms are commonly used to share information about traffic related incidents

Social familiarity improves fast-start escape performance in schooling fish

Using social groups (i.e. schools) of the tropical damselfish Chromis viridis, we test how familiarity through repeated social interactions influences fast-start responses, the primary defensive behaviour in a range of taxa, including fish, sharks, and larval amphibians. We focus on reactivity through response latency and kinematic performance (i.e. agility and propulsion) following a simulated predator attack, while distinguishing between first and subsequent responders (direct response to stimulation versus response triggered by integrated direct and social stimulation, respectively). In familiar schools, first and subsequent responders exhibit shorter latency than unfamiliar individuals, demonstrating that familiarity increases reactivity to direct and, potentially, social stimulation. Further, familiarity modulates kinematic performance in subsequent responders, demonstrated by increased agility and propulsion. These findings demonstrate that the benefits of social recognition and memory may enhance individual fitness through greater survival of predator attacks

Backbone and Sidechain Ordering in a small Protein

We investigate the relation between backbone and side-chain ordering in a small protein. For this purpos e we have performed multicanonical simulations of the villin headpiece subdomain HP-36, an often used to y model in protein studies. Concepts of circular statistics are introduced to analyze side-chain fluctuations. In contrast to earlier studies on homopolypeptides (Wei et al., J. Phys. Chem. B, 111 (2007) 4244) we do not find collective effects leading to a separate transition. Rather, side-chain ordering is spread over a wide temperature range. Our results indicate a thermal hierarchy of ordering events, with side-chain ordering appearing at temperatures below the helix-coil transition but above the folding transition. We conjecture that this thermal hierarchy reflects an underlying temporal order, and that side-chain ordering facilitates the search for the correct backbone topology.Comment: accepted in J. Chem. Phy

Role of Water Flow Regime in the Swimming Behaviour and Escape Performance of a Schooling Fish

Animals are exposed to variable and rapidly changing environmental flow conditions, such as wind in terrestrial habitats and currents in aquatic systems. For fishes, previous work suggests that individuals exhibit flow-induced changes in aerobic swimming performance. Yet, no one has examined whether similar plasticity is found in fast-start escape responses, which are modulated by anaerobic swimming performance, sensory stimuli and neural control. In this study, we used fish from wild schools of the tropical damselfish Chromis viridis from shallow reefs surrounding Lizard Island in the Great Barrier Reef, Australia. The flow regime at each site was measured to ascertain differences in mean water flow speed and its temporal variability. Swimming and escape behaviour in fish schools were video-recorded in a laminar-flow swim tunnel. Though each school\u27s swimming behaviour (i.e. alignment and cohesion) was not associated with local flow conditions, traits linked with fast-start performance (particularly turning rate and the distance travelled with the response) were significantly greater in individuals from high-flow habitats. This stronger performance may occur due to a number of mechanisms, such as an in situ training effect or greater selection pressure for faster performance phenotypes in areas with high flow speed

Coarse-grained dynamics of an activity bump in a neural field model

We study a stochastic nonlocal PDE, arising in the context of modelling spatially distributed neural activity, which is capable of sustaining stationary and moving spatially-localized ``activity bumps''. This system is known to undergo a pitchfork bifurcation in bump speed as a parameter (the strength of adaptation) is changed; yet increasing the noise intensity effectively slowed the motion of the bump. Here we revisit the system from the point of view of describing the high-dimensional stochastic dynamics in terms of the effective dynamics of a single scalar "coarse" variable. We show that such a reduced description in the form of an effective Langevin equation characterized by a double-well potential is quantitatively successful. The effective potential can be extracted using short, appropriately-initialized bursts of direct simulation. We demonstrate this approach in terms of (a) an experience-based "intelligent" choice of the coarse observable and (b) an observable obtained through data-mining direct simulation results, using a diffusion map approach.Comment: Corrected aknowledgement

Top Predators Negate the Effect of Mesopredators on Prey Physiology

Predation theory and empirical evidence suggest that top predators benefit the survival of resource prey through the suppression of mesopredators. However, whether such behavioural suppression can also affect the physiology of resource prey has yet to be examined. Using a three‐tier reef fish food web and intermittent‐flow respirometry, our study examined changes in the metabolic rate of resource prey exposed to combinations of mesopredator and top predator cues. Under experimental conditions, the mesopredator (dottyback, Pseudochromis fuscus ) continuously foraged and attacked resource prey (juveniles of the damselfish Pomacentrus amboinensis ) triggering an increase in prey O2 uptake by 38 ± 12·9% (mean ± SE). The visual stimulus of a top predator (coral trout, Plectropomus leopardus ) restricted the foraging activity of the mesopredator, indirectly allowing resource prey to minimize stress and maintain routine O2 uptake. Although not as strong as the effect of the top predator, the sight of a large non‐predator species (thicklip wrasse, Hemigymnus melapterus ) also reduced the impact of the mesopredator on prey metabolic rate. We conclude that lower trophic‐level species can benefit physiologically from the presence of top predators through the behavioural suppression that top predators impose on mesopredators. By minimizing the energy spent on mesopredator avoidance and the associated stress response to mesopredator attacks, prey may be able to invest more energy in foraging and growth, highlighting the importance of the indirect, non‐consumptive effects of top predators in marine food webs

Difficulties in Management of Functional Movement Disorders: Three Illustrative Cases

Background Some patients with FND and FEVD cannot re-establish walking ability with standard treatment alone. Cases Novel invasive treatment of FEVD trialed in three females, aged 19, 30 and 33 years with >18 month history of FND. None could walk and all were wheelchair-dependent needing home carers. Standard treatment plus novel step-wise escalation of invasive “intervention+” was individually tailored to correct FEVD; functional electrical stimulation, botulinum toxin injections, tibial nerve block, serial casting, and for Case 3, manipulation under anesthetic and surgical tendon lengthening. All regained walking ability and discontinued carers. Case 1 resumed dancing and Case 3 returned to employment. Improvements were largely maintained at 3 and 6 month follow-up. Conclusions As a last resort, invasive adjuncts may be considered in a very small proportion of FND patients who fail to regain walking ability with standard treatment alone and reach a “dead end” where no further progress is feasible

Seizure-induced basal dendrites on granule cells

Seizure-induced hilar basal dendrites on dentate granule cells are observed in several rodent models of temporal lobe epilepsy. Ultrastructural evidence showed that basal dendrites receive predominantly excitatory synapses, including many from mossy fibers. Such highly interconnected granule cells with basal dendrites are suggested to enhance hyperexcitability within the dentate network. For an expanded treatment of this topic see Jasper's Basic Mechanisms of the Epilepsies, Fourth Edition (Noebels JL, Avoli M, Rogawski MA, Olsen RW, Delgado-Escueta AV, eds) published by Oxford University Press (available on the National Library of Medicine Bookshelf [NCBI] at). © 2010 International League Against Epilepsy