Some Notes on the Interplay Between P Systems and Chemotaxis in Bacteria

We describe some chemotactic behaviors of bacteria, that is, their movement response to changes in the environment, and the underlying molecular mechanisms. We outline how such processes could be linked to membrane computing, by taking inspiration from them for new type of rules or new features to be introduced in P systems, as well as by considering how the application of recent P system-based models can produce relevant results for the description and the analysis of chemotaxis processes

On Modelling Ion Fluxes Across Biological Membranes with P Systems

In this report we address the challenge of using P systems to integrate at the whole cell level both active and passive transport of different ions, done by different types of membrane transport proteins which work simultaneously and concurrently

New Proposals for the Formalization of Membrane Proteins

This paper presents three new proposals to take advantage, in the framework of P systems, from proteins acting in bacteria. One attempt aims to focus on the transport protein that act as a logic AND gate at the cell membrane. The multiplicity of type of transporters involved in maintaining osmotic pressure within physiological values, both at short and long term level are also presented, as an example of parallelism occurring in living cell. Finally, the change of enzyme activity by reversible aggregation could be important for P systems as a new rule to follow, and process to model

GPU-powered Simulation Methodologies for Biological Systems

The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological systems in a quantitative manner. Computer algorithms allow to faithfully reproduce the dynamics of the corresponding biological system, and, at the price of a large number of simulations, it is possible to extensively investigate the system functioning across a wide spectrum of natural conditions. To enable multiple analysis in parallel, using cheap, diffused and highly efficient multi-core devices we developed GPU-powered simulation algorithms for stochastic, deterministic and hybrid modeling approaches, so that also users with no knowledge of GPUs hardware and programming can easily access the computing power of graphics engines.Comment: In Proceedings Wivace 2013, arXiv:1309.712

Dynamical Probabilistic P Systems: Definitions and Applications

We introduce dynamical probabilistic P systems, a variant where probabilities associated to the rules change during the evolution of the system, as a new approach to the analysis and simulation of the behavior of complex systems. We define the notions for the analysis of the dynamics and we show some applications for the investigation of the properties of the Brusselator (a simple scheme for the Belousov-Zabothinskii reaction), the Lotka-Volterra system and the decay process

Size and Power of Extended Gemmating P Pystems

In P systems with gemmation of mobile membranes were ex- amined. It was shown that (extended) systems with eight membranes are as powerful as the Turing machines. Moreover, it was also proved that extended gemmating P systems with only pre-dynamical rules are still computationally complete: in this case nine membranes are needed to obtain this computational power. In this paper we improve the above results concerning the size bound of extended gemmating P systems, namely we prove that these systems with at most ¯ve membranes (with meta-priority relations and without (in=out) communication rules) form a class of universal computing devices, while in the case of extended systems with only pre-dynamical rules six membranes are enough to determine any recursively enumerable language

Two Universality Results for (Mem)Brane Systems

We prove that P systems with mate and drip operations and using at most five membranes during any step of a computation are universal. This improves a recent similar result from, where eleven membranes are used. The proof of this result has the "drawback" that the output of a computation is obtained on an inner membrane of the system. A universality proof is then given for the case when the result of a computation is found on the skin membrane (on its external side, hence "visible" from the environment), but in this case we use one more membrane, as well as another basic brane operation exo; moreover, the operations are now of the projective type, as introduced in

Stochastic Approaches in P Systems for Simulating Biological Systems

Different stochastic strategies for modeling biological systems with P systems are reviewed in this paper, such as the multi-compartmental approach and dynamical probabilistic P systems. The respective results obtained from the simulations of a test case study (the quorum sensing phenomena in Vibrio Fischeri colonies) are shown, compared and discussed

Advantages of GPU-accelerated approach for solving the Parker equation in the heliosphere

The increasing of experimental observations' accuracy and model complexity requires the development of a new class of numerical solvers. In this work, we present a GPU-accelerated approach for solving the Parker equation in the heliosphere using a stochastic differential equation (SDE) approach. The presented method was applied to a generic system of SDE using the CUDA programming language. Our approach achieves significant speedup compared to a CPU implementation, allowing us to efficiently solve for the modulated spectra of charged particles in the heliosphere. We demonstrate the accuracy and efficiency of our method through numerical experiments on a realistic model of the heliosphere

Reaction Cycles in Membrane Systems and Molecular Dynamics

We are considering molecular dynamics and (sequential) membrane systems from the viewpoint of Markov chain theory. The first step is to understand the structure of the configuration space, with respect to communicating classes. Instead of a reachability analysis by traditional methods, we use the explicit monoidal structure of this space with respect to rule applications. This leads to the notion of precycle, which is an element of the integer kernel of the stoichiometric matrix. The generators of the set of precycles can be effectively computed by an incremental algorithm due to Contejean and Devie. To arrive at a characterization of cycles, we introduce the notion of defect, which is a set of geometric constraints on a configuration to allow a precycle to be enabled, that is, be a cycle. An important open problem is the effcient calculation of the defects. We also discuss aspects of asymptotic behavior and connectivity, as well as give a biological example, showing the usefulness of the method for model checking