4.7 Article

Simulation of P systems with active membranes on CUDA

Journal

BRIEFINGS IN BIOINFORMATICS
Volume 11, Issue 3, Pages 313-322

Publisher

OXFORD UNIV PRESS
DOI: 10.1093/bib/bbp064

Keywords

natural computing; membrane computing; P Systems; parallel computing; GPU; CUDA

Funding

  1. Fundacion Seneca (Agencia Regional de Ciencia y Tecnologia, Region de Murcia) [00001/CS/2007]
  2. Spanish MEC
  3. European Commission FEDER [CSD2006-00046]
  4. Ministerio de Educacion y Ciencia of Spain [TIN2006-13425]
  5. FEDER
  6. Junta de Andalucia [P08-TIC04200]

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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.

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