6,571 research outputs found
Playing with Derivation Modes and Halting Conditions
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
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
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
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
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
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
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
<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
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