Search

The model of membrane computing, also known under the name of P systems, is a bio-inspired large-scale parallel computing paradigm having a good potential for the design of massively parallel algorithms. For its implementation it is very natural to choose hardware platforms that have important inherent parallelism, such as field-programmable gate arrays (FPGAs) or compute unified device architecture (CUDA)-enabled graphic processing units (GPUs). This article performs an overview of all existing approaches of hardware implementation in the area of P systems. The quantitative and qualitative attributes of FPGA-based implementations and CUDA-enabled GPU-based simulations are compared to evaluate the two methodologies. Ministerio de Economía, Industria y Competitividad TIN2017-89842-P (MABICAP)

A reaction system is a modeling framework for investigating the functioning of the living cell, focused on capturing cause&ndash, effect relationships in biochemical environments. Biochemical processes in this framework are seen to interact with each other by producing the ingredients enabling and/or inhibiting other reactions. They can also be influenced by the environment seen as a systematic driver of the processes through the ingredients brought into the cellular environment. In this paper, the first attempt is made to implement reaction systems in the hardware. We first show a tight relation between reaction systems and synchronous digital circuits, generally used for digital electronics design. We describe the algorithms allowing us to translate one model to the other one, while keeping the same behavior and similar size. We also develop a compiler translating a reaction systems description into hardware circuit description using field-programming gate arrays (FPGA) technology, leading to high performance, hardware-based simulations of reaction systems. This work also opens a novel interesting perspective of analyzing the behavior of biological systems using established industrial tools from electronic circuits design.