Correct and Efficient Antichain Algorithms for Refinement Checking

The notion of refinement plays an important role in software engineering. It is the basis of a stepwise development methodology in which the correctness of a system can be established by proving, or computing, that a system refines its specification. Wang et al. describe algorithms based on antichains for efficiently deciding trace refinement, stable failures refinement and failures-divergences refinement. We identify several issues pertaining to the soundness and performance in these algorithms and propose new, correct, antichain-based algorithms. Using a number of experiments we show that our algorithms outperform the original ones in terms of running time and memory usage. Furthermore, we show that additional run time improvements can be obtained by applying divergence-preserving branching bisimulation minimisation

The crystal structure of superoxide dismutase from Plasmodium falciparum

Background: Superoxide dismutases (SODs) are important enzymes in defence against oxidative stress. In Plasmodium falciparum, they may be expected to have special significance since part of the parasite life cycle is spent in red blood cells where the formation of reactive oxygen species is likely to be promoted by the products of haemoglobin breakdown. Thus, inhibitors of P. falciparum SODs have potential as anti-malarial compounds. As a step towards their development we have determined the crystal structure of the parasite's cytosolic iron superoxide dismutase. Results: The cytosolic iron superoxide dismutase from P. falciparum (PfFeSOD) has been overexpressed in E. coli in a catalytically active form. Its crystal structure has been solved by molecular replacement and refined against data extending to 2.5 angstrom resolution. The structure reveals a two-domain organisation and an iron centre in which the metal is coordinated by three histidines, an aspartate and a solvent molecule. Consistent with ultracentrifugation analysis the enzyme is a dimer in which a hydrogen bonding lattice links the two active centres. Conclusion: The tertiary structure of PfFeSOD is very similar to those of a number of other iron-and manganese-dependent superoxide dismutases, moreover the active site residues are conserved suggesting a common mechanism of action. Comparison of the dimer interfaces of PfFeSOD with the human manganese-dependent superoxide dismutase reveals a number of differences, which may underpin the design of parasite-selective superoxide dismutase inhibitors

Towards Assume-Guarantee Profiles for Autonomous Vehicles

Rules or specifications for autonomous vehicles are currently formulated on a case-by-case basis, and put together in a rather ad-hoc fashion. As a step towards eliminating this practice, we propose a systematic procedure for generating a set of supervisory specifications for self-driving cars that are 1) associated with a distributed assume-guarantee structure and 2) characterizable by the notion of consistency and completeness. Besides helping autonomous vehicles make better decisions on the road, the assume-guarantee contract structure also helps address the notion of blame when undesirable events occur. We give several game-theoretic examples to demonstrate applicability of our framework

Reasoned modelling critics: turning failed proofs into modelling guidance

The activities of formal modelling and reasoning are closely related. But while the rigour of building formal models brings significant benefits, formal reasoning remains a major barrier to the wider acceptance of formalism within design. Here we propose reasoned modelling critics — an approach which aims to abstract away from the complexities of low-level proof obligations, and provide high-level modelling guidance to designers when proofs fail. Inspired by proof planning critics, the technique combines proof-failure analysis with modelling heuristics. Here, we present the details of our proposal, implement them in a prototype and outline future plans