Please use this identifier to cite or link to this item: http://hdl.handle.net/1822/34933

TitleAgent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework
Author(s)Pérez-Rodríguez, Gael
Pérez-Pérez, Martín
Glez-Peña, Daniel
Fdez-Riverola, Florentino
Azevedo, N. F.
Lourenço, Anália
Issue date2015
PublisherHindawi Publishing Corporation
JournalBiomed Research International
Abstract(s)Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods framework. 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.
Typearticle
URIhttp://hdl.handle.net/1822/34933
DOI10.1155/2015/769471
ISSN2314-6133
e-ISSN2314-6141
Publisher versionhttp://www.hindawi.com/journals/bmri/
Peer-Reviewedyes
AccessopenAccess
Appears in Collections:CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

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