Please use this identifier to cite or link to this item: https://hdl.handle.net/10216/104894
Author(s): Gael Pérez Rodríguez
Martín Pérez Pérez
Daniel Glez Peña
Florentino Fdez Riverola
Nuno F. Azevedo
Anália Lourenco
Title: Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework
Issue Date: 2015
Abstract: 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.
Subject: Outras ciências médicas
Other medical sciences
Scientific areas: Ciências médicas e da saúde::Outras ciências médicas
Medical and Health sciences::Other medical sciences
URI: https://hdl.handle.net/10216/104894
Related Information: info:eu-repo/grantAgreement/FCT - Fundação para a Ciência e Tecnologia/Projetos Estratégicos/UID/EQU/00511/2013 - POCI-01-0145-FEDER-006939/Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia/LEPABE
Document Type: Artigo em Revista Científica Internacional
Rights: openAccess
Appears in Collections:FEUP - Artigo em Revista Científica Internacional

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