A partial evaluation methodology for optimizing rewrite theories incrementally

Partial evaluation (PE) is a branch of computer science that achieves code optimization via specialization. This article describes a PE methodology for optimizing rewrite theories that encode concurrent as well as nondeterministic systems by means of the Maude language. The main advantages of the proposed methodology can be summarized as follows: • An automatic program optimization technique for rewrite theories featuring several PE criteria that support the specialization of a broad class of rewrite theories. • An incremental partial evaluation modality that allows the key specialization components to be encapsulated at the desired granularity level to facilitate progressive refinements of the specialization. • All executability theory requirements are preserved by the PE transformation. Also the transformation ensures the semantic equivalence between the original rewrite theory and the specialized theory under rather mild conditions

3-Col problem modelling using simple kernel P systems

This paper presents the newly introduced class of (simple) kernel P systems ((s)kP systems) and investigates through a 3-colouring problem case study the expressive power and efficiency of kernel P systems. It describes two skP systems that model the problem and analyses them in terms of efficiency and complexity. The skP models prove to be more succinct (in terms of number of rules, objects, number of cells and execution steps) than the corresponding tissue P system, available in the literature, that solves the same problem, at the expense of a greater length of the rules.Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08-TIC-0420

Formal Modelling and Simulation of Biological Systems with Spatiality

In Systems Biology, spatial modelling allows an accurate description of phenomena whose behaviour is influenced by the spatial arrangement of the elements. In this thesis, we present various modelling formalisms with spatial features, each using a different abstraction level of the real space. From the formalisms with the most abstract notion of space, to the most concrete, we formally define the MIM Calculus with compartments, the Spatial P systems, and the Spatial CLS. Each formalism is suitable for the description of different kinds of systems, which call for the use of different space modelling abstractions. We present models of various real-world systems which benefit from the ability to precisely describe space-dependent behaviours. We define the MIM Calculus, inspired by Molecular Interaction Maps, a graphical notation for bioregulatory networks. The MIM Calculus provides high-level operators with a direct biological meaning, which are used to describe the interaction capabilities of the elements of such systems. Its spatial extension includes the most abstract notion of space, namely it only allows the modelling of compartments. Such a feature allows distinguishing only the abstract position where an element is, identified by the name of the compartment. Subsequently, we propose a spatial extension to the membrane computing formalism P systems. In this case, we follow a more precise approach to spatial modelling, by embedding membranes and objects in a two-dimensional discrete space. Some objects of a Spatial P system can be declared as mutually exclusive objects, with the constraint that each position can accommodate at most one of them. The distinction between ordinary and mutually exclusive objects can be thought of as an abstraction on the size of the objects. We study the computational complexity of the formalism and the problem of efficient simulation of some kinds of models. Finally, we present the Spatial Calculus of Looping Sequences (Spatial CLS), which is an extension of the Calculus of Looping Sequences (CLS), a formalism geared towards the modelling of cellular systems. In this case, models are based on two/three dimensional continuous space, and allow an accurate description of the motion of the elements, and of their size. In particular, Spatial CLS allows the description of the space occupied by elements and membranes, which can change their sizes dynamically as the system evolves. Space conflicts which may occur can be resolved by performing a rearrangement of elements and membranes. As example applications of the calculus we present a model of cell proliferation, and a model of the quorum sensing process in Pseudomonas aeruginosa

Twenty years of rewriting logic

AbstractRewriting logic is a simple computational logic that can naturally express both concurrent computation and logical deduction with great generality. This paper provides a gentle, intuitive introduction to its main ideas, as well as a survey of the work that many researchers have carried out over the last twenty years in advancing: (i) its foundations; (ii) its semantic framework and logical framework uses; (iii) its language implementations and its formal tools; and (iv) its many applications to automated deduction, software and hardware specification and verification, security, real-time and cyber-physical systems, probabilistic systems, bioinformatics and chemical systems