Simulation of P systems with active membranes on CUDA

P systems or Membrane Systems provide a high-level computational modelling framework that combines the structure and dynamic aspects of biological systems in a relevant and understandable way. They are inherently parallel and non-deterministic computing devices. In this article, we discuss the motivation, design principles and key of the implementation of a simulator for the class of recognizer P systems with active membranes running on a (GPU). We compare our parallel simulator for GPUs to the simulator developed for a single central processing unit (CPU), showing that GPUs are better suited than CPUs to simulate P systems due to their highly parallel nature.Ministerio de Educación y Ciencia TIN2006-13425Junta de Andalucía P08–TIC-0420

On the Power of Dissolution in P Systems with Active Membranes

In this paper we study membrane dissolution rules in the framework of P systems with active membranes but without using electrical charges. More precisely, we prove that the polynomial computational complexity class associated with the class of recognizer P systems with active membranes, without polarizations and without dissolution coincides with the standard complexity class P. Furthermore, we demonstrate that if we consider dissolution rules, then the resulting complexity class contains the class NP.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

Computational efficiency of dissolution rules in membrane systems

Trading (in polynomial time) space for time in the framework of membrane systems is not sufficient to efficiently solve computationally hard problems. On the one hand, an exponential number of objects generated in polynomial time is not sufficient to solve NP-complete problems in polynomial time. On the other hand, when an exponential number of membranes is created and used as workspace, the situation is very different. Two operations in P systems (membrane division and membrane creation) capable of constructing an exponential number of membranes in linear time are studied in this paper. NP-complete problems can be solved in polynomial time using P systems with active membranes and with polarizations, but when electrical charges are not used, then dissolution rules turn out to be very important. We show that in the framework of P systems with active membranes but without polarizations and in the framework of P systems with membrane creation, dissolution rules play a crucial role from the computational efficiency point of view.Ministerio de Educación y Ciencia TIN2005-09345-C04-0

Further Remarks on P Systems with Active Membranes, Separation, Merging, and Release Rules

The P systems are a class of distributed parallel computing devices of a biochemical type. In this note, we show that by using membrane separation to obtain exponential workspace, SAT problem can be solved in linear time in a uniform and con°uent way by active P systems without polarizations. This improves some results already obtained by A. Alhazov, Ts. Ishdorj. A universality result related to membrane separation is also obtained

A Prolog Simulator for Deterministic P Systems with Active Membranes

In this paper we propose a new way to represent P systems with active membranes based on Logic Programming techniques. This representation allows us to express the set of rules and the configuration of the P system in each step of the evolution as literals of an appropriate language of first order logic. We provide a Prolog program to simulate the evolution of these P systems and present some auxiliary tools to simulate the evolution of a P system with active membranes using 2-division which solves the SAT problem following the techniques presented inMinisterio de Ciencia y Tecnología TIC2002-04220-C03-0

Remarks on the Computational Power of Some Restricted Variants of P Systems with Active Membranes

In this paper we consider three restricted variants of P systems with active membranes: (1) P systems using out communication rules only, (2) P systems using elementary membrane division and dissolution rules only, and (3) polarizationless P systems using dissolution and restricted evolution rules only. We show that every problem in P can be solved with uniform families of any of these variants. This, using known results on the upper bound of the computational power of variants (1) and (3) yields new characterizations of the class P. In the case of variant (2) we provide a further characterization of P by giving a semantic restriction on the computations of P systems of this varian

From distribution to replication in cooperative systems with active membranes: A frontier of the efficiency

P systems with active membranes use evolution, communication, dissolution and division(or separation) rules. They do not use cooperation neither priorities, but they haveelectrical charges associated with membranes, which can be modified by rule applications.The inspiration comes from the behaviourof living cells, who “compute” with theirproteins in order to obtain energy, create components, send information to other cells,kill themselves (in a process called apoptosis), and so on. In these models, mitosisissimulated by divisionrules (for elementary and non-elementary membranes) and meiosis,that is, membrane fission inspiration, is captured in separationrules. The parent’s objectsare replicated into both child membranes when a division occurs, while in the caseof separation, objects are distributed (according to a prefixed partition). In both cases,active membranes have been proved to be too powerful for solving computationally hardproblems in an efficient way. Due to this, polarizationless P systems withactive membraneshave been widely studied from a complexity point of view. Evolution rules simulate the transformation of components in membranes, but it iswell known that in Biology elements interact with each other in order to obtain newcomponents. In this paper, (restricted) cooperation in object evolution rules is considered,and the efficiency of the corresponding models is studied

Solving Multidimensional 0-1 Knapsack Problem by P Systems with Input and Active Membranes

P systems are parallel molecular computing models based on pro- cessing multisets of objects in cell-like membrane structures. In this paper we give a membrane algorithm to multidimensional 0-1 knapsack problem in lin- ear time by recognizer P systems with input and with active membranes using 2-division. This algorithm can also be modi¯ed to solve general 0-1 integer programming problem

On the complexity of active P systems

We are going to present a polynomially uniform solution to the Quanti ed 3SAT decision problem with restricted instances where the quanti ers alternate, based on recognizer P systems with active membranes and no input membrane, having three polarizations using only dissolution and division rules