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

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

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

Cyclooxygenase-2 and prostaglandin E(2)(PGE(2)) receptor messenger RNAs are affected by bovine oocyte maturation time and cumulus-oocyte complex quality, and PGE(2) induces moderate expansion of the bovine cumulus in vitro.

Expression of cyclooxygenase-2 (COX-2) and prostaglandin E(2) (PGE(2)) receptor 2 (EP2) are necessary for rodent cumulus expansion in vivo. Prostaglandin E(2) receptor 3 (EP3) has been detected in bovine preovulatory follicles and corpora lutea. The current experiments examined the effect of PGE(2) on bovine cumulus expansion in vitro and expression of COX-2, EP1, EP2, EP3, and EP4 mRNAs in bovine cumulus-oocyte complexes (COCs) at 0, 6, 12, 18, and 24 h time points during maturation in vitro. Concentrations of PGE(2) above 50 ng/ml resulted in moderate cumulus expansion of bovine COCs, but expansion did not occur in the absence of serum. COX-2 mRNA expression increased in bovine COCs at 6 h and 12 h of maturation, then decreased. EP2 mRNA was detectable by reverse transcription-polymerase chain reaction at all time points. EP3 mRNA expression increased in COCs from 0 to 6 h and remained at this higher level through the culture period. Very low levels of EP4 mRNA expression were detectable, but EP1 was not detected in bovine COCs. Because EP receptor mRNAs and COX-2 mRNA are expressed in bovine COCs, there exists the potential for a prostaglandin autocrine/paracrine regulatory pathway during oocyte maturation. Differential expression of the EP3 mRNA among varying COC classes indicates that this gene product may be a useful marker of oocyte competence. Although the PGE(2) pathway is involved in cumulus expansion, serum factors are required to mediate PGE(2)-induced expansion

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

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

Life-threatening mesenchymal hamartoma of the chest wall in a neonate

Mesenchymal hamartomas of the chest wall are unusual tumours diagnosed in neonates. They mostly resolve spontaneously hence conservative management has been advocated. Some compress vital structures in the thoracic cavity or bleed warranting surgical intervention. We present a neonate with mesenchymal hamartoma of the chest wall presenting as unilateral multifocal lesions with life threatening complications. He responded well to surgical intervention and was successfully discharged