CIOBANU , Gabriel

The reactivity of the living cells provides the real complexity of biological systems. This paper presents a reactive P system where the rules are triggered by certain conditions, and pumps are the parallel processors of a membrane. The computation of a reactive P system is given by parallel composition of conditional rules regarding the pumps,...

We first present the formal semantics of a parallel rule-based formalism inspired by biological cells, and then provide a faithful parallel implementation of this computational model by using GridGain and taking care of various synchronization issues. Synchronization is achieved by using barriers and preconditions; both refer to the fact that a...

We introduce a new class of membrane systems called simple P systems, and study its computational complexity using the classical theory. We start by presenting the knapsack problem and analyzing its space and time complexities. Then we study the computational complexity of simple P systems by considering the static allocation of resources...

In this paper we provide algorithms for solving the SAT problem using P systems with active membranes with neither polarization nor division rules. The semi- uniform solutions are given under the assumption that initial con gurations (either al- phabet or structure) of exponential size are pre-computed by well-de ned P systems (P systems with...

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...

In this paper we introduce mutual mobile membranes with surface objects, systems which have biological motivation. In P systems with mobile membranes with surface objects, a membrane may enter or exit another membrane. The second membrane just undergoes the action, meaning that it has no control on when the movement takes place. This kind of...

In this paper we de ne and study Scenario Based P Systems, a model of computation inspired by the metabolic pathways and networks. Starting from the classical de nition of P systems with symbol objects and multiset rewriting rules, we de ne regular expressions able to capture the causal dependencies among di erent executions of the rules. The...

We introduce and study a multiset-based type system with ratio thresholds motivated by an important regulatory mechanism inside a cell which try to maintain a \life-death" ratio between some given lower and upper thresholds. We use such a type system to control ratio thresholds in a bio-inspired and multisets-based formalism. For this type...

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Starting from Shannon theory of information, we present the case of producing information in the form of multisets, and encoding information using multisets. We compute the entropy of a multiset information source by constructing an equientropic string source (with interdependent symbols), and we compare this with a string information source...

We investigate the relationship of time Petri nets and di erent variants of membrane systems. First we show that the added feature of \time" in time Petri nets makes it possible to simulate the maximal parallel rule application of membrane systems without introducing maximal parallelism to the Petri net semantics, then we de ne local time P...

In this paper we present an open-source web-enabled simulator for P sys- tems. We use CLIPS embedded in C, and make the simulator available as a web application, complemented by a query language to specify the results.

Following, we present in this paper various number encodings and operations over multisets. We obtain the most compact encoding and several other interesting encodings and study their properties using elements of combinatorics over multisets. We also construct P systems that implement their associated operations. We quantify the effect of...

We present a transformation of membrane systems, possibly with pro- moter/inhibitor rules, priority relations, and membrane dissolution, into formulas of the chemical calculus such that terminating computations of membranes correspond to terminating reduction sequences of formulas and vice versa. In the end, the same result can be extracted...

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A current research topic in membrane computing is to find more realistic P systems from a biological point of view, and one target in this respect is to relax the condition of using the rules in a maximally parallel way. We contribute in this paper to this issue by considering the minimal parallelism of using the rules: if at least a rule from...

In this paper various molecular chemical interactions are modelled under different computational paradigms. P systems and -calculus are used to describe intra-cellular reactions like protein-protein interactions and gene regulation control.

Reversible computation allows computation to proceed not only in the standard, forward direction, but also backward, recovering past states. While reversible computation has attracted interest for its multiple applications, covering areas as different as low-power computing , simulation, robotics and debugging, such applications need to be...