Number of adaptive steps to a local fitness peak

We consider a population of genotype sequences evolving on a rugged fitness landscape with many local fitness peaks. The population walks uphill until it encounters a local fitness maximum. We find that the statistical properties of the walk length depend on whether the underlying fitness distribution has a finite mean. If the mean is finite, all the walk length cumulants grow with the sequence length but approach a constant otherwise. Experimental implications of our analytical results are also discussed

StochKit-FF: Efficient Systems Biology on Multicore Architectures

The stochastic modelling of biological systems is an informative, and in some cases, very adequate technique, which may however result in being more expensive than other modelling approaches, such as differential equations. We present StochKit-FF, a parallel version of StochKit, a reference toolkit for stochastic simulations. StochKit-FF is based on the FastFlow programming toolkit for multicores and exploits the novel concept of selective memory. We experiment StochKit-FF on a model of HIV infection dynamics, with the aim of extracting information from efficiently run experiments, here in terms of average and variance and, on a longer term, of more structured data.Comment: 14 pages + cover pag

Stronger computational modelling of signalling pathways using both continuous and discrete-state methods

Starting from a biochemical signalling pathway model expresses in a process algebra enriched with quantitative information, we automatically derive both continuous-space and discrete-space representations suitable for numerical evaluation. We compare results obtained using approximate stochastic simulation thereby exposing a flaw in the use of the differentiation procedure producing misleading results

The role of N∗(1535)N^*(1535) in pp→ppϕpp \to pp \phi and π−p→nϕ\pi^- p \to n \phi reactions

The near threshold $\phi$ meson production in proton-proton and $\pi^- p$ collisions is studied with the assumption that the production mechanism is due to the sub-$N\phi$-threshold $N^*(1535)$ resonance. The $\pi^0$, $\eta$ and $\rho^0$-meson exchanges for proton-proton collisions are considered. It is shown that the contribution to the $pp \to pp \phi$ reaction from the t-channel $\pi^0$ meson exchange is dominant. With a significant $N^*(1535)N\phi$ coupling ($g^2_{N^*(1535)N \phi}/4 \pi$ = 0.13), both $pp \to pp \phi$ and $\pi^- p \to n \phi$ data are very well reproduced. The significant coupling of the $N^*(1535)$ resonance to $N \phi$ is compatible with previous indications of a large $s \bar{s}$ component in the quark wave function of the $N^*(1535)$ resonance and may be the real origin of the significant enhancement of the $\phi$ production over the naive OZI-rule predictions.Comment: 15 pages, 6 figure

Stochastic modeling of cargo transport by teams of molecular motors

Many different types of cellular cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather persistent directionality. Different theoretical approaches have been suggested in order to explore the origin of this kind of motion. An effective theoretical approach, introduced by M\"uller et al., describes the cargo dynamics as a tug-of-war between different kinds of motors. An alternative approach has been suggested recently by Kunwar et al., who considered the coupling between motor and cargo in more detail. Based on this framework we introduce a model considering single motor positions which we propagate in continuous time. Furthermore, we analyze the possible influence of the discrete time update schemes used in previous publications on the system's dynamic.Comment: Cenference proceedings - Traffic and Granular Flow 1

Numerical simulation of unconstrained cyclotron resonant maser emission

When a mainly rectilinear electron beam is subject to significant magnetic compression, conservation of magnetic moment results in the formation of a horseshoe shaped velocity distribution. It has been shown that such a distribution is unstable to cyclotron emission and may be responsible for the generation of Auroral Kilometric Radiation (AKR) an intense rf emission sourced at high altitudes in the terrestrial auroral magnetosphere. PiC code simulations have been undertaken to investigate the dynamics of the cyclotron emission process in the absence of cavity boundaries with particular consideration of the spatial growth rate, spectral output and rf conversion efficiency. Computations reveal that a well-defined cyclotron emission process occurs albeit with a low spatial growth rate compared to waveguide bounded simulations. The rf output is near perpendicular to the electron beam with a slight backward-wave character reflected in the spectral output with a well defined peak at 2.68GHz, just below the relativistic electron cyclotron frequency. The corresponding rf conversion efficiency of 1.1% is comparable to waveguide bounded simulations and consistent with the predictions of kinetic theory that suggest efficient, spectrally well defined radiation emission can be obtained from an electron horseshoe distribution in the absence of radiation boundaries.Publisher PD

Vasilii Belov and the Russian idea

Vasilii Ivanovich Belov (1932-2012) was one of the most wellknown and outspoken of the ‘village writers’ who came to prominence in the Soviet Union in the 1960s, and in the age of ‘glasnost’ and post-Soviet times attracted much attention and even vilification for his nationalist and apparently xenophobic views. In his documentary account of village life and customs published in the journal Nash sovremennik between 1979 and 1982, and subsequently in illustrated book form, Belov provides in great detail and with much personal warmth the history of the northern Russian village, its people, customs and way of life as it has developed over the centuries, showing a place seemingly outside of time and untouched by historical developments. Lad: ocherki o narodnoi estetike may yet prove to be his most enduring contribution to post-Soviet reflections on ‘the Russian idea’, and Russia’s relationship with Europe

Investigation of potential diseases associated with Northern Territory mammal declines

There is compelling evidence of broad-scale declines in populations of small terrestrial native mammals in northern Australia, including the Top End of the Northern Territory (NT) over the past 20 years. Causes under consideration include changed fire regimes, introduced fauna (including predators) and disease. To date information on health and disease in northern Australian mammals has been limited. Disease is increasingly recognised as a primary driver of some wildlife population declines and extinctions e.g., Tasmanian devil facial tumour disease, white nose syndrome in bats and chytrid fungus in amphibians. Disease has been identified as a risk factor for extinction in declining and fragmented wildlife populations globally, particularly in situations of increased environmental stressors, changing ecosystems, arrival of new vertebrate threats or climate change. Unless wild populations are studied in detail over long periods of time, the effects of disease are easily overlooked and may be difficult to determine. This study is the largest and most comprehensive study of health and disease in small mammals in northern Australia and is one of a small number of studies worldwide to have approached investigation of wildlife populations in this comprehensive manner

Extreme value distributions for weakly correlated fitnesses in block model

We study the limit distribution of the largest fitness for two models of weakly correlated and identically distributed random fitnesses. The correlated fitness is given by a linear combination of a fixed number of independent random variables drawn from a common parent distribution. We find that for certain class of parent distributions, the extreme value distribution for correlated random variables can be related either to one of the known limit laws for independent variables or the parent distribution itself. For other cases, new limiting distributions appear. The conditions under which these results hold are identified.Comment: Expanded, added reference