MCMAS-SLK: A Model Checker for the Verification of Strategy Logic Specifications

We introduce MCMAS-SLK, a BDD-based model checker for the verification of systems against specifications expressed in a novel, epistemic variant of strategy logic. We give syntax and semantics of the specification language and introduce a labelling algorithm for epistemic and strategy logic modalities. We provide details of the checker which can also be used for synthesising agents' strategies so that a specification is satisfied by the system. We evaluate the efficiency of the implementation by discussing the results obtained for the dining cryptographers protocol and a variant of the cake-cutting problem

Strategies for synthesis of yardsticks and abaci for nanometre distance measurements by pulsed EPR

Silvia Valera is grateful for support by EPSRC and Bela E. Bode acknowledges support by EastCHEM.Pulsed electron paramagnetic resonance (EPR) techniques have been found to be an efficient tool for elucidation of structure in complex biological systems as they give access to distances in the nanometre range. These measurements can provide additional structural information such as relative orientations, structural flexibility or aggregation states. A wide variety of model systems for calibration and optimisation of pulsed experiments has been synthesised. Their design is based on mimicking biological systems or materials in specific properties such as the distances themselves and the distance distributions. Here, we review selected approaches to the synthesis of chemical systems bearing two or more spin centres, such as nitroxide or trityl radicals, metal ions or combinations thereof and sketch their application in pulsed EPR distance measurements.Publisher PDFPeer reviewe

Probing the (H3-H4)(2) histone tetramer structure using pulsed EPR spectroscopy combined with site-directed spin labelling

The (H3-H4)2 histone tetramer forms the central core of nucleosomes and, as such, plays a prominent role in assembly, disassembly and positioning of nucleosomes. Despite its fundamental role in chromatin, the tetramer has received little structural investigation. Here, through the use of pulsed electron-electron double resonance spectroscopy coupled with site-directed spin labelling, we survey the structure of the tetramer in solution. We find that tetramer is structurally more heterogeneous on its own than when sequestered in the octamer or nucleosome. In particular, while the central region including the H3-H3′ interface retains a structure similar to that observed in nucleosomes, other regions such as the H3 αN helix display increased structural heterogeneity. Flexibility of the H3 αN helix in the free tetramer also illustrates the potential for post-translational modifications to alter the structure of this region and mediate interactions with histone chaperones. The approach described here promises to prove a powerful system for investigating the structure of additional assemblies of histones with other important factors in chromatin assembly/fluidity

A Modal Logic for Termgraph Rewriting

We propose a modal logic tailored to describe graph transformations and discuss some of its properties. We focus on a particular class of graphs called termgraphs. They are first-order terms augmented with sharing and cycles. Termgraphs allow one to describe classical data-structures (possibly with pointers) such as doubly-linked lists, circular lists etc. We show how the proposed logic can faithfully describe (i) termgraphs as well as (ii) the application of a termgraph rewrite rule (i.e. matching and replacement) and (iii) the computation of normal forms with respect to a given rewrite system. We also show how the proposed logic, which is more expressive than propositional dynamic logic, can be used to specify shapes of classical data-structures (e.g. binary trees, circular lists etc.)

GM food technology abroad and its implications for Australia and New Zealand

The potential economic benefits from agricultural biotechnology adoption by ANZ need to be weighed against any likely loss of market access abroad for crops that may contain genetically modified (GM) organisms. This paper uses the global GTAP model to estimate effects of other countries' GM policies without and with ANZ farmers adopting GM varieties of various grains and oilseeds. The benefits to ANZ from adopting GM crops under a variety of scenarios are positive even in the presence of the ban on imports from GM-adopting countries by the EU (but not if East Asia also applied such a ban).Biotechnology, GMOs, regulation, trade policy, computable general equilibrium, Crop Production/Industries, Food Consumption/Nutrition/Food Safety, C68, D58, F13, O3, Q17, Q18,

Dynamic Package Interfaces - Extended Version

A hallmark of object-oriented programming is the ability to perform computation through a set of interacting objects. A common manifestation of this style is the notion of a package, which groups a set of commonly used classes together. A challenge in using a package is to ensure that a client follows the implicit protocol of the package when calling its methods. Violations of the protocol can cause a runtime error or latent invariant violations. These protocols can extend across different, potentially unboundedly many, objects, and are specified informally in the documentation. As a result, ensuring that a client does not violate the protocol is hard. We introduce dynamic package interfaces (DPI), a formalism to explicitly capture the protocol of a package. The DPI of a package is a finite set of rules that together specify how any set of interacting objects of the package can evolve through method calls and under what conditions an error can happen. We have developed a dynamic tool that automatically computes an approximation of the DPI of a package, given a set of abstraction predicates. A key property of DPI is that the unbounded number of configurations of objects of a package are summarized finitely in an abstract domain. This uses the observation that many packages behave monotonically: the semantics of a method call over a configuration does not essentially change if more objects are added to the configuration. We have exploited monotonicity and have devised heuristics to obtain succinct yet general DPIs. We have used our tool to compute DPIs for several commonly used Java packages with complex protocols, such as JDBC, HashSet, and ArrayList.Comment: The only changes compared to v1 are improvements to the Abstract and Introductio

Modelling Discourse-related terminology in OntoLingAnnot’s ontologies

Recently, computational linguists have shown great interest in discourse annotation in an attempt to capture the internal relations in texts. With this aim, we have formalized the linguistic knowledge associated to discourse into different linguistic ontologies. In this paper, we present the most prominent discourse-related terms and concepts included in the ontologies of the OntoLingAnnot annotation model. They show the different units, values, attributes, relations, layers and strata included in the discourse annotation level of the OntoLingAnnot model, within which these ontologies are included, used and evaluated

A Markov Chain Model Checker

Markov chains are widely used in the context of performance and reliability evaluation of systems of various nature. Model checking of such chains with respect to a given (branching) temporal logic formula has been proposed for both the discrete [17,6] and the continuous time setting [4,8]. In this paper, we describe a prototype model checker for discrete and continuous-time Markov chains, the Erlangen Twente Markov Chain Checker $(E \vdash MC^2$), where properties are expressed in appropriate extensions of CTL. We illustrate the general bene ts of this approach and discuss the structure of the tool. Furthermore we report on first successful applications of the tool to non-trivial examples, highlighting lessons learned during development and application of $(E \vdash MC^2$)

Solitonic sectors, alpha-induction and symmetry breaking boundaries

We develop a systematic approach to boundary conditions that break bulk symmetries in a general way such that left and right movers are not necessarily connected by an automorphism. In the context of string compactifications, such boundary conditions typically include non-BPS branes. Our formalism is based on two dual fusion rings, one for the bulk and one for the boundary fields. Only in the Cardy case these two structures coincide. In general they are related by a version of alpha-induction. Symmetry breaking boundary conditions correspond to solitonic sectors. In examples, we compute the annulus amplitudes and boundary states.Comment: 13 pages, LaTeX2e; v2: typos correcte