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

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

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

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

Magnetic structure determination of Ca3_3LiOsO6_6 using neutron and x-ray scattering

We present a neutron and x-ray scattering investigation of Ca$_3$LiOsO$_6$, a material predicted to host magnetic ordering solely through an extended superexchange pathway involving two anions, an interaction mechanism that has undergone relatively little investigation. This contrasts with the ubiquitous superexchange interaction mechanism involving a single anion that has well defined and long standing rules. Despite the apparent 1D nature and triangular units of magnetic osmium ions the onset of magnetic correlations has been observed at a high temperature of 117 K in bulk measurements. We experimentally determine the magnetically ordered structure and show it to be long range and three dimensional. Our results support the model of extended superexchange interaction

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