Spatial Logics for Bigraphs

Bigraphs are emerging as an interesting model for concurrent calculi, like CCS, pi-calculus, and Petri nets. Bigraphs are built orthogonally on two structures: a hierarchical place graph for locations and a link (hyper-)graph for connections. With the aim of describing bigraphical structures, we introduce a general framework for logics whose terms represent arrows in monoidal categories. We then instantiate the framework to bigraphical structures and obtain a logic that is a natural composition of a place graph logic and a link graph logic. We explore the concepts of separation and sharing in these logics and we prove that they generalise some known spatial logics for trees, graphs and tree contexts

Composing Software from Multiple Concerns: A Model and Composition Anomalies

Constructing software from components is considered to be a key requirement for managing the complexity of software. Separation of concerns makes only sense if the realizations of these concerns can be composed together effectively into a working program. Various publications have shown that composability of software is far from trivial and fails when components express complex behavior such as constraints, synchronization and history-sensitiveness. We believe that to address the composability problems, we need to understand and define the situations where composition fails. To this aim, in this paper we (a) introduce a general model of multi-dimensional concern composition, and (b) define so-called composition anomalies

A formal support to business and architectural design for service-oriented systems

Architectural Design Rewriting (ADR) is an approach for the design of software architectures developed within Sensoria by reconciling graph transformation and process calculi techniques. The key feature that makes ADR a suitable and expressive framework is the algebraic handling of structured graphs, which improves the support for specification, analysis and verification of service-oriented architectures and applications. We show how ADR is used as a formal ground for high-level modelling languages and approaches developed within Sensoria

An Abstract Approach to Stratification in Linear Logic

We study the notion of stratification, as used in subsystems of linear logic with low complexity bounds on the cut-elimination procedure (the so-called light logics), from an abstract point of view, introducing a logical system in which stratification is handled by a separate modality. This modality, which is a generalization of the paragraph modality of Girard's light linear logic, arises from a general categorical construction applicable to all models of linear logic. We thus learn that stratification may be formulated independently of exponential modalities; when it is forced to be connected to exponential modalities, it yields interesting complexity properties. In particular, from our analysis stem three alternative reformulations of Baillot and Mazza's linear logic by levels: one geometric, one interactive, and one semantic

Information processing in biological molecular machines

Biological molecular machines are bi-functional enzymes that simultaneously catalyze two processes: one providing free energy and second accepting it. Recent studies show that most protein enzymes have a rich dynamics of stochastic transitions between the multitude of conformational substates that make up their native state. It often manifests in fluctuating rates of the catalyzed processes and the presence of short-term memory resulting from the preference of selected conformations. For any stochastic protein machine dynamics we proved a generalized fluctuation theorem that leads to the extension of the second law of thermodynamics. Using them to interpret the results of random walk on a complex model network, we showed the possibility of reducing free energy dissipation at the expense of creating some information stored in memory. The subject of our analysis is the time course of the catalyzed processes expressed by sequences of jumps at random moments of time. Since similar signals can be registered in the observation of real systems, all theses of the paper are open to experimental verification. From a broader physical point of view, the division of free energy into the operation and organization energies is worth emphasizing. Information can be assigned a physical meaning of a change in the value of both these functions of state.Comment: The manuscript contains 14 pages, 7 figure