Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework
Autor(a) principal: | |
---|---|
Data de Publicação: | 2015 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | https://hdl.handle.net/10216/104894 |
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. |
id |
RCAP_1640191fe5bec3cc496e8af55996d3b4 |
---|---|
oai_identifier_str |
oai:repositorio-aberto.up.pt:10216/104894 |
network_acronym_str |
RCAP |
network_name_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository_id_str |
7160 |
spelling |
Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON FrameworkOutras ciências médicasOther medical sciencesAgent-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.20152015-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/10216/104894eng2314-613310.1155/2015/769471Gael Pérez RodríguezMartín Pérez PérezDaniel Glez PeñaFlorentino Fdez RiverolaNuno F. AzevedoAnália Lourencoinfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-29T12:31:09Zoai:repositorio-aberto.up.pt:10216/104894Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T23:21:51.167611Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework |
title |
Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework |
spellingShingle |
Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework Gael Pérez Rodríguez Outras ciências médicas Other medical sciences |
title_short |
Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework |
title_full |
Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework |
title_fullStr |
Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework |
title_full_unstemmed |
Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework |
title_sort |
Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework |
author |
Gael Pérez Rodríguez |
author_facet |
Gael Pérez Rodríguez Martín Pérez Pérez Daniel Glez Peña Florentino Fdez Riverola Nuno F. Azevedo Anália Lourenco |
author_role |
author |
author2 |
Martín Pérez Pérez Daniel Glez Peña Florentino Fdez Riverola Nuno F. Azevedo Anália Lourenco |
author2_role |
author author author author author |
dc.contributor.author.fl_str_mv |
Gael Pérez Rodríguez Martín Pérez Pérez Daniel Glez Peña Florentino Fdez Riverola Nuno F. Azevedo Anália Lourenco |
dc.subject.por.fl_str_mv |
Outras ciências médicas Other medical sciences |
topic |
Outras ciências médicas Other medical sciences |
description |
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. |
publishDate |
2015 |
dc.date.none.fl_str_mv |
2015 2015-01-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://hdl.handle.net/10216/104894 |
url |
https://hdl.handle.net/10216/104894 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
2314-6133 10.1155/2015/769471 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
|
_version_ |
1799135518316822528 |