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The rationale behind this new tool is the necessity to describe interactions at the molecular level to be able to grasp emergent and meaningful biological behaviour. We are particularly interested in characterising and quantifying the various effects that facilitate biocatalysis. Enzymes may display high specificity for their substrates and this information is crucial to the engineering and optimisation of bioprocesses. Simulation results demonstrate that molecule distributions, reaction rate parameters, and structural parameters can be adjusted separately in the simulation allowing a comprehensive study of individual effects in the context of realistic cell environments. While higher percentage of collisions with occurrence of reaction increases the affinity of the enzyme to the substrate, a faster reaction (i.e., turnover number) leads to a smaller number of time steps. Slower diffusion rates and molecular crowding (physical hurdles) decrease the collision rate of reactants, hence reducing the reaction rate, as expected. Also, the random distribution of molecules affects the results significantly.<\/jats:p>","DOI":"10.1155\/2015\/769471","type":"journal-article","created":{"date-parts":[[2015,3,22]],"date-time":"2015-03-22T17:07:56Z","timestamp":1427044076000},"page":"1-12","source":"Crossref","is-referenced-by-count":6,"title":["Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework"],"prefix":"10.1155","volume":"2015","author":[{"given":"Gael","family":"P\u00e9rez-Rodr\u00edguez","sequence":"first","affiliation":[{"name":"Escuela Superior de Ingenier\u00eda Inform\u00e1tica (ESEI), Edificio Polit\u00e9cnico, Universidad de Vigo, Campus Universitario As Lagoas s\/n, 32004 Ourense, Spain"}]},{"given":"Mart\u00edn","family":"P\u00e9rez-P\u00e9rez","sequence":"additional","affiliation":[{"name":"Escuela Superior de Ingenier\u00eda Inform\u00e1tica (ESEI), Edificio Polit\u00e9cnico, Universidad de Vigo, Campus Universitario As Lagoas s\/n, 32004 Ourense, 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