BigraphER: rewriting and analysis engine for bigraphs

BigraphER is a suite of open-source tools providing an effi- cient implementation of rewriting, simulation, and visualisation for bigraphs, a universal formalism for modelling interacting systems that evolve in time and space and first introduced by Milner. BigraphER consists of an OCaml library that provides programming interfaces for the manipulation of bigraphs, their constituents and reaction rules, and a command-line tool capable of simulating Bigraphical Reactive Systems (BRSs) and computing their transition systems. Other features are native support for both bigraphs and bigraphs with sharing, stochastic reaction rules, rule priorities, instantiation maps, parameterised controls, predicate checking, graphical output and integration with the probabilistic model checker PRISM

Model Atmospheres for X-ray Bursting Neutron Stars

The hydrogen and helium accreted by X-ray bursting neutron stars is periodically consumed in runaway thermonuclear reactions that cause the entire surface to glow brightly in X-rays for a few seconds. With models of the emission, the mass and radius of the neutron star can be inferred from the observations. By simultaneously probing neutron star masses and radii, X-ray bursts are one of the strongest diagnostics of the nature of matter at extremely high densities. Accurate determinations of these parameters are difficult, however, due to the highly non-ideal nature of the atmospheres where X-ray bursts occur. Observations from X-ray telescopes such as RXTE and NuStar can potentially place strong constraints on nuclear matter once uncertainties in atmosphere models have been reduced. Here we discuss current progress on modeling atmospheres of X-ray bursting neutron stars and some of the challenges still to be overcome.Comment: 25 pages, 14 figure

Toward a physiological explanation of juvenile growth curves

Juvenile growth curves are generally sigmoid in shape: Growth is initially nearly exponential, but it slows to near zero as the animal approaches maturity. The drop‐off in growth rate is puzzling because, everything else being equal, selection favors growing as fast as possible. Existing theory posits sublinear scaling of resource acquisition with juvenile body mass and linear scaling of the requirement for maintenance, so the difference, fuel for growth, decreases as the juvenile increases in size. Experimental evidence, however, suggests that maintenance metabolism increases sublinearly not linearly with size. Here, we develop a new theory consistent with the experimental evidence. Our theory is based on the plausible assumption that there is a trade‐off in the capacity of capillaries to supply growing and developed cells. As the proportion of non‐growing cells increases, they take up more macromolecules from the capillaries, leaving fewer to support growing cells. The predicted growth curves are realistic and similar to those of previous models (Bertalanffy, Gompertz, and Logistic) but have the advantage of being derived from a plausible physiological model. We hope that our focus on resource delivery in capillaries will encourage new experimental work to identify the detailed physiological basis of the trade‐off underlying juvenile growth curves

Process algebra modelling styles for biomolecular processes

We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed

Context in 3D planar navigation

One of the most frustrating barriers to the widespread use of 3D visualisation is the additional complexity in navigating 3D data. This paper details a new approach to improving navigation in 3D environments where the navigation is mainly planar. Data at a distance from the viewpoint is distorted as if projected onto a partial cylinder to approximate a plan view, thereby exposing information that may have been obscured. Previous approaches are compared with this new technique and screenshots presented. Implementation details of the technique are discussed as well as possible performance and useability issues

Seasonal Occurrence of Epifauna on Test Panels In Hampton Roads, Virginia

A two-year study was made on settling patterns of some marine epifaunal frmcrtebrales in the port of Hampton Roads, Virginia. Asbestos fiber test panels, submerged to a depth of 5 m from a pier at the Norfolk Navy Base, wf:re used as substrates. The fouling assemblage consisted of species characteristic of the temperate North American Atlantic coast. Over half of the 41 species identified were either coelenterates or arthropods, although sponges, tttrbellarians, ectoprocts, J\u3eolychaetes, mollusks, and ascidians were present as well. Four species, Aselomaris michaeli, Clytia edwardsi, Obelia bicuspidata and 0. commissuralis, all hydroids, represent new distributional records for Virginia. The large annual range of water temperature results in distinct seasonal patterns of settlement. Attachment was heaviest froni May to November and lightest fi·om January to March. Barnacles (Balanus improvisus) were prevalent during spring and autumn, while ascidians (Molgula manhattensis, Botryllus schlosseri) and serpulids (Hydroides hexagona) were predominant in summer. Only Balanus improvisus occurred on the panels throughout the year

Trend-based analysis of a population model of the AKAP scaffold protein

We formalise a continuous-time Markov chain with multi-dimensional discrete state space model of the AKAP scaffold protein as a crosstalk mediator between two biochemical signalling pathways. The analysis by temporal properties of the AKAP model requires reasoning about whether the counts of individuals of the same type (species) are increasing or decreasing. For this purpose we propose the concept of stochastic trends based on formulating the probabilities of transitions that increase (resp. decrease) the counts of individuals of the same type, and express these probabilities as formulae such that the state space of the model is not altered. We define a number of stochastic trend formulae (e.g. weakly increasing, strictly increasing, weakly decreasing, etc.) and use them to extend the set of state formulae of Continuous Stochastic Logic. We show how stochastic trends can be implemented in a guarded-command style specification language for transition systems. We illustrate the application of stochastic trends with numerous small examples and then we analyse the AKAP model in order to characterise and show causality and pulsating behaviours in this biochemical system