On the Construction of Sorted Reactive Systems

We develop a theory of sorted bigraphical reactive systems. Every application of bigraphs in the literature has required an extension, a sorting, of pure bigraphs. In turn, every such application has required a redevelopment of the theory of pure bigraphical reactive systems for the sorting at hand. Here we present a general construction of sortings. The constructed sortings always sustain the behavioural theory of pure bigraphs (in a precise sense), thus obviating the need to redevelop that theory for each new application. As an example, we recover Milner’s local bigraphs as a sorting on pure bigraphs. Technically, we give our construction for ordinary reactive systems, then lift it to bigraphical reactive systems. As such, we give also a construction of sortings for ordinary reactive systems. This construction is an improvement over previous attempts in that it produces smaller and much more natural sortings, as witnessed by our recovery of local bigraphs as a sorting

Bigraphical models for protein and membrane interactions

We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules representing biologically admissible interactions. At the protein level, these bigraphic reactive systems correspond exactly to systems of kappa-calculus. Membrane-level interactions are represented by just two general rules, whose application can be triggered by protein-level interactions in a well-de\"ined and precise way. This framework can be used to compare and merge models at different abstraction levels; in particular, higher-level (e.g. mobility) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. As examples, we formalize in our framework the vesiculation and the phagocytosis processes

Abstract State Machines 1988-1998: Commented ASM Bibliography

An annotated bibliography of papers which deal with or use Abstract State Machines (ASMs), as of January 1998.Comment: Also maintained as a BibTeX file at http://www.eecs.umich.edu/gasm

The Project Scheduling Problem with Non-Deterministic Activities Duration: A Literature Review

Purpose: The goal of this article is to provide an extensive literature review of the models and solution procedures proposed by many researchers interested on the Project Scheduling Problem with nondeterministic activities duration. Design/methodology/approach: This paper presents an exhaustive literature review, identifying the existing models where the activities duration were taken as uncertain or random parameters. In order to get published articles since 1996, was employed the Scopus database. The articles were selected on the basis of reviews of abstracts, methodologies, and conclusions. The results were classified according to following characteristics: year of publication, mathematical representation of the activities duration, solution techniques applied, and type of problem solved. Findings: Genetic Algorithms (GA) was pointed out as the main solution technique employed by researchers, and the Resource-Constrained Project Scheduling Problem (RCPSP) as the most studied type of problem. On the other hand, the application of new solution techniques, and the possibility of incorporating traditional methods into new PSP variants was presented as research trends. Originality/value: This literature review contents not only a descriptive analysis of the published articles but also a statistical information section in order to examine the state of the research activity carried out in relation to the Project Scheduling Problem with non-deterministic activities duration.Peer Reviewe

A framework for protein and membrane interactions

We introduce the BioBeta Framework, a meta-model for both protein-level and membrane-level interactions of living cells. This formalism aims to provide a formal setting where to encode, compare and merge models at different abstraction levels; in particular, higher-level (e.g. membrane) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. A BioBeta specification provides a protein signature together a set of protein reactions, in the spirit of the kappa-calculus. Moreover, the specification describes when a protein configuration triggers one of the only two membrane interaction allowed, that is "pinch" and "fuse". In this paper we define the syntax and semantics of BioBeta, analyse its properties, give it an interpretation as biobigraphical reactive systems, and discuss its expressivity by comparing with kappa-calculus and modelling significant examples. Notably, BioBeta has been designed after a bigraphical metamodel for the same purposes. Hence, each instance of the calculus corresponds to a bigraphical reactive system, and vice versa (almost). Therefore, we can inherith the rich theory of bigraphs, such as the automatic construction of labelled transition systems and behavioural congruences

Computation of nucleation of a non-equilibrium first-order phase transition using a rare-event algorithm

We introduce a new Forward-Flux Sampling in Time (FFST) algorithm to efficiently measure transition times in rare-event processes in non-equilibrium systems, and apply it to study the first-order (discontinuous) kinetic transition in the Ziff-Gulari-Barshad model of catalytic surface reaction. The average time for the transition to take place, as well as both the spinodal and transition points, are clearly found by this method.Comment: 12 pages, 10 figure

Programming in logic without logic programming

In previous work, we proposed a logic-based framework in which computation is the execution of actions in an attempt to make reactive rules of the form if antecedent then consequent true in a canonical model of a logic program determined by an initial state, sequence of events, and the resulting sequence of subsequent states. In this model-theoretic semantics, reactive rules are the driving force, and logic programs play only a supporting role. In the canonical model, states, actions and other events are represented with timestamps. But in the operational semantics, for the sake of efficiency, timestamps are omitted and only the current state is maintained. State transitions are performed reactively by executing actions to make the consequents of rules true whenever the antecedents become true. This operational semantics is sound, but incomplete. It cannot make reactive rules true by preventing their antecedents from becoming true, or by proactively making their consequents true before their antecedents become true. In this paper, we characterize the notion of reactive model, and prove that the operational semantics can generate all and only such models. In order to focus on the main issues, we omit the logic programming component of the framework.Comment: Under consideration in Theory and Practice of Logic Programming (TPLP

Feedback Controlled Software Systems

Software systems generally suffer from a certain fragility in the face of disturbances such as bugs, unforeseen user input, unmodeled interactions with other software components, and so on. A single such disturbance can make the machine on which the software is executing hang or crash. We postulate that what is required to address this fragility is a general means of using feedback to stabilize these systems. In this paper we develop a preliminary dynamical systems model of an arbitrary iterative software process along with the conceptual framework for stabilizing it in the presence of disturbances. To keep the computational requirements of the controllers low, randomization and approximation are used. We describe our initial attempts to apply the model to a faulty list sorter, using feedback to improve its performance. Methods by which software robustness can be enhanced by distributing a task between nodes each of which are capable of selecting the best input to process are also examined, and the particular case of a sorting system consisting of a network of partial sorters, some of which may be buggy or even malicious, is examined

Monoreactive high affinity and polyreactive low affinity rheumatoid factors are produced by CD5+ B cells from patients with rheumatoid arthritis.

In patients with rheumatoid arthritis (RA), circulating CD5+ B lymphocytes, but not CD5- B lymphocytes, are increased in number and size, exist in an activated state, spontaneously proliferate, and secrete Ig that binds to the Fc fragment of IgG. By constructing continuous mAb-secreting cell lines from CD5+ B lymphocytes, the properties and dissociation constants (Kd) of these antibodies were determined. Two types of rheumatoid factors (RFs) with discrete reactivities were produced. The first type is polyreactive and binds with relatively low affinity (Kd, 10(-5) mol/liter) to the Fc fragment of IgG. These antibodies are similar to those produced by CD5+ B cells from healthy subjects. The second type of RF is monoreactive and binds with higher affinity (Kd, 10(-7) mol/liter) to the Fc fragment of IgG. These latter autoantibodies are produced by CD5+ B cells of RA patients, but not healthy subjects. Long-term longitudinal studies are needed to determine the role of these two types of RFs in the pathogenesis of RA