Matrix Languages, Register Machines, Vector Addition Systems

We give a direct and simple proof of the equality of Parikh images of lan- guages generated by matrix grammars with appearance checking with the sets of vectors generated by register machines. As a particular case, we get the equality of the Parikh images of languages generated by matrix grammars without appearance checking with the sets of vectors generated by partially blind register machines. Then, we consider pure matrix grammars (i.e., grammars which do not distinguish terminal and nonterminal symbols), and prove the inclusion of the family of Parikh images of languages generated by such grammars (without appearance checking) in the family of sets of vectors generated by blind register machines, as well as the inclusion of reachability sets of vector addition systems in the family of Parikh images of pure matrix languages. For pure matrix grammars with a certain restriction on the form of matrices, also the converse of the latter inclusion is obtained. Thus, in view of the result from, we obtain the semilin- earity of languages generated by pure matrix grammars (without appearance checking) with alphabets with at most five letters, with the considered restrictions on the form of matrices. A pure matrix grammar with five symbols, but without restrictions on the form of matrices, is produced which generates a non-semilinear language

On spiking neural P systems

This work deals with several aspects concerning the formal verification of SN P systems and the computing power of some variants. A methodology based on the information given by the transition diagram associated with an SN P system is presented. The analysis of the diagram cycles codifies invariants formulae which enable us to establish the soundness and completeness of the system with respect to the problem it tries to resolve. We also study the universality of asynchronous and sequential SN P systems and the capability these models have to generate certain classes of languages. Further, by making a slight modification to the standard SN P systems, we introduce a new variant of SN P systems with a special I/O mode, called SN P modules, and study their computing power. It is demonstrated that, as string language acceptors and transducers, SN P modules can simulate several types of computing devices such as finite automata, a-finite transducers, and systolic trellis automata.Ministerio de Educación y Ciencia TIN2006-13425Junta de Andalucía TIC-58

Normal Forms for Spiking Neural P Systems

The spiking neural P systems are a class of computing devices recently introduced as a bridge between spiking neural nets and membrane computing. In this paper we prove a series of normal forms for spiking neural P systems, concerning the regular expressions used in the firing rules, the delay between firing and spiking, the forgetting rules used, and the outdegree of the graph of synapses. In all cases, surprising simplifications are found, without losing the computational universality – sometimes at the price of (slightly) increasing other parameters which describe the complexity of these systems

Simulating FAS-induced apoptosis by using P systems

In contrast to differential equations, P systems are an unconven- tional model of computation which takes into consideration the discrete character of the quantity of components and the inherent randomness that exists in biological phenomena. The key feature of P systems is their compartmentalised structure which represents the heterogeneity of the structural organisation of the cells, and where one can take into account the role played by membranes in the functioning of the system, for example signalling at the cell surface [13], selective uptake of sub- stances from the media [14], diffusion across different compartments [15], etc. We show here that P systems can be a reliable tool for Systems Biology and could even outperform in some cases the current simu- lation techniques based on differential equations. We will also use a strategy based on the well known Gillespie algorithm [4] but running on more than one compartment called Multi-compartmental Gillespie Algorithm [13]

Simulating Apoptosis Using Discrete Methods: a Membrane System and a Stochastic Approach

Membrane Systems provide an intriguing method for modeling biological systems at a molecular level. The hierarchical structure of Membrane Systems lends itself readily to mimic the nature and behavior of cells.We have refined a technique for modeling the type I and type II FAS-induced apoptosis signalling cascade. Improve- ments over our previous modeling work on apoptosis include increased efficiency for storing and sorting waiting times of reactions, a nondeterministic approach for han- dling reactions competing over limited reactants and improvements, and refinements of the model reactions. The modular nature of our systems provides flexibility with respect to future discover- ies on the signal cascade. We provide a breakdown of our algorithms and explanations on improvements we have implemented. We also give an exhaustive comparison to an established ordinary differential equations technique. Based on the results of our sim- ulations, we conclude that Membrane Systems are a useful simulation tool in Systems Biology that could provide new insight into the subcellular processes, and provide also the argument that Membrane Systems may outperform ordinary differential equation simulations when simulating cascades of reactions (as they are observed in cells

Diseño Conceptual de un Gasificador de Biomasa de Lecho Fijo en Equicorriente a Escala Piloto

This study presents the conceptual design of a pilot-scale downdraft fixed-bed gasifier of lignocellulosic biomass. The dimensions of the reactor were determined based on the requirement of electric power output (150 kWt) and on the simulation of the gasification process with a one-dimension kinetic model. The simulations were aimed to obtaining high thermodynamic efficiencies (60% and 75%) for different biomass moisture contents. Depending on the reactor size and biomass moisture content, the simulations identified two best configurations for the gasifier that allowed generation of 117 kWt and 200 kWt withthermodynamic efficiencies of 43% and 70% respectively. The designed gasifier is 1,8 m long and produces between 25 kWe and 50 kWe as it makes use of the adiabatic characteristics of the endothermic zone and the gas sensitive enthalpy for biomass drying and devolatilization