Bio-molecular engine: A simulation environment for bio-inspired architectural models of molecular-scale devices based machines

Asynchronous processing elements (PE) arrays have gained attention as suitable architectures for computational machines based on molecular scale devices. This kind of systems make design simpler, their regular structure potentially allows manufacturing techniques based on molecular self-organization and lack of a clock allows avoiding signal propagation troubles. PE array architectures have a great impact on computation that has to be spread on the space. Mapping applications onto discrete grid implies a correct assessment of distribution degree, interconnections topology and PE interactions. Moreover a deep analysis of computational paradigms is required to evaluate what PE instruction-sets are suitable and their properties. In this paper we propose a practical approach to the analysis of such kind of systems by means of a software tool named Bio-Molecular Engine (BME).