Modal logics for reasoning about object-based component composition

Component-oriented development of software supports the adaptability and maintainability of large systems, in particular if requirements change over time and parts of a system have to be modified or replaced. The software architecture in such systems can be described by components and their composition. In order to describe larger architectures, the composition concept becomes crucial. We will present a formal framework for component composition for object-based software development. The deployment of modal logics for defining components and component composition will allow us to reason about and prove properties of components and compositions

Observation and abstract behaviour in specification and implementation of state-based systems

Classical algebraic specification is an accepted framework for specification. A criticism which applies is the fact that it is functional, not based on a notion of state as most software development and implementation languages are. We formalise the idea of a state-based object or abstract machine using algebraic means. In contrast to similar approaches we consider dynamic logic instead of equational logic as the framework for specification and implementation. The advantage is a more expressive language allowing us to specify safety and liveness conditions. It also allows a clearer distinction of functional and state-based parts which require different treatment in order to achieve behavioural abstraction when necessary. We shall in particular focus on abstract behaviour and observation. A behavioural notion of satisfaction for state-elements is needed in order to abstract from irrelevant details of the state realisation

Heuristic Refinement Method for the Derivation of Protein Solution Structures: Validation on Cytochrome B562

A method is described for determining the family of protein structures compatible with solution data obtained primarily from nuclear magnetic resonance (NMR) spectroscopy. Starting with all possible conformations, the method systematically excludes conformations until the remaining structures are only those compatible with the data. The apparent computational intractability of this approach is reduced by assembling the protein in pieces, by considering the protein at several levels of abstraction, by utilizing constraint satisfaction methods to consider only a few atoms at a time, and by utilizing artificial intelligence methods of heuristic control to decide which actions will exclude the most conformations. Example results are presented for simulated NMR data from the known crystal structure of cytochrome b562 (103 residues). For 10 sample backbones an average root-mean-square deviation from the crystal of 4.1 A was found for all alpha-carbon atoms and 2.8 A for helix alpha-carbons alone. The 10 backbones define the family of all structures compatible with the data and provide nearly correct starting structures for adjustment by any of the current structure determination methods