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

Magnetic order in the two-dimensional metal-organic framework manganese pyrazinecarboxylate with Mn-Mn dimers

The magnetic properties of [Mn(pyrazinecarboxylate)2]n (Mn-pyrazine), empirical formula C10H6MnN4O4, are investigated through susceptibility, heat capacity and neutron scattering measurements. The structure of Mn-pyrazine consists of Mn-Mn dimers linked on a distorted 2D hexagonal structure. The weak out of plane interactions create a quasi-2D magnetic material within the larger three dimensional metal organic framework (MOF) structure. We show that this material undergoes a two stage magnetic transition, related to the low dimensionality of the Mn lattice. First at 5 K, which is assigned to the initial development of short range order in the 2D layers. This is followed by long range order at 3.3 K. Applied field measurements reveal the potential to induce magnetic transitions in moderately small fields of 2 T. Neutron powder diffraction enabled the determination of a unique magnetic space group P21'/c (#14.77) at 1.5 K. This magnetic structure consists of antiferromagnetically coupled Mn-Mn dimers with spins principally along the out of plane a-axis

Accessing five- and seven-membered phosphorus-based heterocycles via cycloaddition reactions of azophosphines

Heterocycles containing both phosphorus and nitrogen have seen increasing use in recent years in luminescent materials, coordination chemistry and as building blocks for inorganic polymers, yet their chemistry is currently dominated by five- and six-membered derivatives. Seven-membered P/N heterocycles are comparatively scarce and lack general, high yielding syntheses. Here, we explore the synthesis and characterisation of 1,2,5-diazaphosphepines from azophosphines. The mechanism has been probed in detail with both computational and experimental studies supporting a stepwise mechanism to form a five-membered ring, and subsequent ring expansion to the diazaphosphepine. Regioselective synthesis of five- and seven-membered rings is possible using asymmetric alkynes. The Lewis acidic borane B(C6F5)3 could either catalyse the formation of the seven-membered ring (iPr derivative) or trap out a key intermediate via a frustrated Lewis pair (FLP) mechanism (tBu derivative)

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