Utilize este identificador para referenciar este registo:
https://hdl.handle.net/10216/104894
Autor(es): | Gael Pérez Rodríguez Martín Pérez Pérez Daniel Glez Peña Florentino Fdez Riverola Nuno F. Azevedo Anália Lourenco |
Título: | Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework |
Data de publicação: | 2015 |
Resumo: | 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. |
Assunto: | Outras ciências médicas Other medical sciences |
Áreas do conhecimento: | Ciências médicas e da saúde::Outras ciências médicas Medical and Health sciences::Other medical sciences |
URI: | https://hdl.handle.net/10216/104894 |
Informação Relacionada: | info:eu-repo/grantAgreement/FCT - Fundação para a Ciência e a Tecnologia/Projetos Estratégicos/UID/EQU/00511/2013 - POCI-01-0145-FEDER-006939/Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia/LEPABE |
Tipo de Documento: | Artigo em Revista Científica Internacional |
Condições de Acesso: | openAccess |
Aparece nas coleções: | FEUP - Artigo em Revista Científica Internacional |
Ficheiros deste registo:
Ficheiro | Descrição | Tamanho | Formato | |
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104731.pdf | Artigo original publicado | 2.22 MB | Adobe PDF | Ver/Abrir |
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