6,571 research outputs found

    Playing with Derivation Modes and Halting Conditions

    Get PDF
    In the area of P systems, besides the standard maximally parallel derivation mode, many other derivation modes have been investigated, too. In this paper, many variants of hierarchical P systems and tissue P systems using different derivation modes are considered and the effects of using di erent derivation modes, especially the maximally parallel derivation modes and the maximally parallel set derivation modes, on the generative and accepting power are illustrated. Moreover, an overview on some control mechanisms used for (tissue) P systems is given. Furthermore, besides the standard total halting mode, we also consider different halting conditions such as unconditional halting and partial halting and explain how the use of different halting modes may considerably change the computing power of P systems and tissue P systems

    Networks of Cells and Petri Nets

    Get PDF
    We introduce a new class of P systems, called networks of cells, with rules allowing several cells to simultaneously interact with each other in order to produce some new objects inside some other output cells. We define different types of behavior for networks of cells by considering alternative strategies for the application of the rules: sequential application, free parallelism, maximal parallelism, locally-maximal parallelism and minimal parallelism. We devise a way for translating network of cells into place- transition nets with localities (PTL-nets, for short) - a specific class of Petri nets. Then, for such a construction, we show a behavioral equivalence between network of cells and corresponding PTL-nets only in the case maximal parallelism, sequential execution, and free parallelism, whereas we observe that, in the case of locally-maximal parallelism and minimal parallelism, the corresponding PTL-nets are not always able to mimic the behavior of network of cells. Also, we address the reverse problem of finding a corresponding network of cells for a given PTL-net by obtaining similar results concerning the relation- ships between their semantics. Finally, we present network-of-cells-based models of two classical synchronization problems: producer/consumer and dining philosophers

    New Choice for Small Universal Devices: Symport/Antiport P Systems

    Full text link
    Symport/antiport P systems provide a very simple machinery inspired by corresponding operations in the living cell. It turns out that systems of small descriptional complexity are needed to achieve the universality by these systems. This makes them a good candidate for small universal devices replacing register machines for different simulations, especially when a simulating parallel machinery is involved. This article contains survey of these systems and presents different trade-offs between parameters

    Verifying P Systems with Costs by Using Priced-Timed Maude

    Get PDF
    We consider P systems that assigns storage costs per step to membranes, and execution costs to rules. We present an abstract syntax of the new class of membrane systems, and then deal with costs by extending the operational semantics of P systems with promoters, inhibitors and registers.We use Priced-Timed Maude to implement the P systems with costs. By using such a rewriting engine which corresponds to the semantics of membrane systems with costs, we are able to prove the operational correctness of this implementation. Based on such an operational correspondence, we can analyze properly the evolutions of the P systems with costs, and verify several reachability properties, including the cost of computations that reach a given membrane con guration. This approach opens the way to various optimization problems related to membrane systems, problems making sense in a bio-inspired model which now can be veri ed by using a complex software platform

    P Systems with Antiport Rules for Evolution Rules

    Get PDF
    We investigate a variant of evolution-communication P systems where the computation is performed in two substeps. First, all possible an- tiport rules are applied in a non-deterministic, maximally parallel way, moving evolution rules across membranes. In the second substep, evolution rules are applied to suitable objects in a maximally parallel way, too. Thus, objects can be the subject of change, but are never moved themselves. As result of a halt- ing computation, we consider the multiset of objects present in a designated output membrane. When using catalytic evolution rules, we already obtain universal computational power with only one catalyst and one membrane. For systems without catalysts we obtain a characterization of the Parikh images of ET0L languages

    An Implementation of Membrane Computing Using Reconfigurable Hardware

    Get PDF
    Because of their inherent large-scale parallelism, membrane computing models can be fully exploited only through the use of a parallel computing platform. We have fully implemented such a computing platform based on reconfigurable hardware that is intended to support the efficient execution of membrane computing models. This computing platform is the first of its type to implement parallelism at both the system and region levels. In this paper, we describe how our computing platform implements the core features of membrane computing models in hardware, and present a theoretical performance analysis of the algorithm it executes in hardware. The performance analysis suggests that the computing platform can significantly outperform sequential implementations of membrane computing as well as Petreska and Teuscher's hardware implementation, the only other complete hardware implementation of membrane computing in existence

    First Steps Towards a Geometry of Computation

    Get PDF
    We introduce a geometrical setting which seems promising for the study of computation in multiset rewriting systems, but could also be applied to register machines and other models of computation. This approach will be applied here to membrane systems (also known as P systems) without dynamical membrane creation. We discuss the role of maximum parallelism and further simplify our model by considering only one membrane and sequential application of rules, thereby arriving at asynchronous multiset rewriting systems (AMR systems). Considering only one membrane is no restriction, as each static membrane system has an equivalent AMR system. It is further shown that AMR systems without a priority relation on the rules are equivalent to Petri Nets. For these systems we introduce the notion of asymptotically exact computation, which allows for stochastic appearance checking in a priori bounded (for some complexity measure) computations. The geometrical analogy in the lattice Nd0 ; d 2 N, is developed, in which a computation corresponds to a trajectory of a random walk on the directed graph induced by the possible rule applications. Eventually this leads to symbolic dynamics on the partition generated by shifted positive cones C+ p , p 2 Nd0 , which are associated with the rewriting rules, and their intersections. Complexity measures are introduced and we consider non-halting, loop-free computations and the conditions imposed on the rewriting rules. Eventually, two models of information processing, control by demand and control by availability are discussed and we end with a discussion of possible future developments

    Rule-based multi-level modeling of cell biological systems

    Get PDF
    <p>Abstract</p> <p>Background</p> <p>Proteins, individual cells, and cell populations denote different levels of an organizational hierarchy, each of which with its own dynamics. Multi-level modeling is concerned with describing a system at these different levels and relating their dynamics. Rule-based modeling has increasingly attracted attention due to enabling a concise and compact description of biochemical systems. In addition, it allows different methods for model analysis, since more than one semantics can be defined for the same syntax.</p> <p>Results</p> <p>Multi-level modeling implies the hierarchical nesting of model entities and explicit support for downward and upward causation between different levels. Concepts to support multi-level modeling in a rule-based language are identified. To those belong rule schemata, hierarchical nesting of species, assigning attributes and solutions to species at each level and preserving content of nested species while applying rules. Further necessities are the ability to apply rules and flexibly define reaction rate kinetics and constraints on nested species as well as species that are nested within others. An example model is presented that analyses the interplay of an intracellular control circuit with states at cell level, its relation to cell division, and connections to intercellular communication within a population of cells. The example is described in ML-Rules - a rule-based multi-level approach that has been realized within the plug-in-based modeling and simulation framework JAMES II.</p> <p>Conclusions</p> <p>Rule-based languages are a suitable starting point for developing a concise and compact language for multi-level modeling of cell biological systems. The combination of nesting species, assigning attributes, and constraining reactions according to these attributes is crucial in achieving the desired expressiveness. Rule schemata allow a concise and compact description of complex models. As a result, the presented approach facilitates developing and maintaining multi-level models that, for instance, interrelate intracellular and intercellular dynamics.</p
    corecore