Analysis of signalling pathways using the prism model checker

We describe a new modelling and analysis approach for signal transduction networks in the presence of incomplete data. We illustrate the approach with an example, the RKIP inhibited ERK pathway [1]. Our models are based on high level descriptions of continuous time Markov chains: reactions are modelled as synchronous processes and concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis of queries such as if a concentration reaches a certain level, will it remain at that level thereafter? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable

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

The Open Navigation Surface Project

Many hydrographic and oceanographic agencies have moved or are moving towards gridded bathymetric products. However, there is no accepted format to allow these grids to be exchanged while maintaining data and metadata integrity. This paper describes the Open Navigation Surface (ONS) Project, which aims to fill this gap. The ONS Project is an open-source software project designed to provide a freely available, portable source-code library to encapsulate gridded bathymetric surfaces with associated uncertainty values. The data file format is called a Bathymetric Attributed Grid (BAG). The BAG is developed and maintained by the ONS Working Group (ONSWG), and the source code is available via the ONS websit

Spin and orbital dynamics through the metal-to-insulator transition in Cd2_2Os2_2O7_7 probed with high-resolution RIXS

High-resolution resonant inelastic x-ray scattering (RIXS) measurements ($\Delta$E = 46 meV) have been performed on Cd$_2$Os$_2$O$_7$ through the metal-to-insulator transition (MIT). A magnetic excitation at 125 meV evolves continuously through the MIT, in agreement with recent Raman scattering results, and provides further confirmation for an all-in, all-out magnetic ground state. Asymmetry of this feature is likely a result of coupling between the electronic and magnetic degrees of freedom. We also observe a broad continuum of interband excitations centered at 0.3 eV energy loss. This is indicative of significant hybridization between Os 5$d$ and O 2$p$ states, and concurrent itinerant nature of the system. In turn, this suggests a possible break down of the free-ion model for Cd$_2$Os$_2$O$_7$.Comment: Accepted in Physical Review B (10 pages

Flame Evolution During Type Ia Supernovae and the Deflagration Phase in the Gravitationally Confined Detonation Scenario

We develop an improved method for tracking the nuclear flame during the deflagration phase of a Type Ia supernova, and apply it to study the variation in outcomes expected from the gravitationally confined detonation (GCD) paradigm. A simplified 3-stage burning model and a non-static ash state are integrated with an artificially thickened advection-diffusion-reaction (ADR) flame front in order to provide an accurate but highly efficient representation of the energy release and electron capture in and after the unresolvable flame. We demonstrate that both our ADR and energy release methods do not generate significant acoustic noise, as has been a problem with previous ADR-based schemes. We proceed to model aspects of the deflagration, particularly the role of buoyancy of the hot ash, and find that our methods are reasonably well-behaved with respect to numerical resolution. We show that if a detonation occurs in material swept up by the material ejected by the first rising bubble but gravitationally confined to the white dwarf (WD) surface (the GCD paradigm), the density structure of the WD at detonation is systematically correlated with the distance of the deflagration ignition point from the center of the star. Coupled to a suitably stochastic ignition process, this correlation may provide a plausible explanation for the variety of nickel masses seen in Type Ia Supernovae.Comment: 14 pages, 10 figures, accepted to the Astrophysical Journa