Optimization strategies for metabolic networks

Bibliographic Details
Main Author: Domingues, Alexandre
Publication Date: 2010
Other Authors: Vinga, Susana, Lemos, João M.
Format: Article
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: http://hdl.handle.net/10362/41816
Summary: The work reported in this paper was performed within the project DynaMo - Dynamical modeling, control and optimization of metabolic networks, supported by FCT (Portugal) under contract PTDC/EEA-ACR/69530/2006.
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spelling Optimization strategies for metabolic networkssystemsThe work reported in this paper was performed within the project DynaMo - Dynamical modeling, control and optimization of metabolic networks, supported by FCT (Portugal) under contract PTDC/EEA-ACR/69530/2006.Background: The increasing availability of models and data for metabolic networks poses new challenges in what concerns optimization for biological systems. Due to the high level of complexity and uncertainty associated to these networks the suggested models often lack detail and liability, required to determine the proper optimization strategies. A possible approach to overcome this limitation is the combination of both kinetic and stoichiometric models. In this paper three control optimization methods, with different levels of complexity and assuming various degrees of process information, are presented and their results compared using a prototype network. Results: The results obtained show that Bi-Level optimization lead to a good approximation of the optimum attainable with the full information on the original network. Furthermore, using Pontryagin's Maximum Principle it is shown that the optimal control for the network in question, can only assume values on the extremes of the interval of its possible values. Conclusions: It is shown that, for a class of networks in which the product that favors cell growth competes with the desired product yield, the optimal control that explores this trade-off assumes only extreme values. The proposed Bi-Level optimization led to a good approximation of the original network, allowing to overcome the limitation on the available information, often present in metabolic network models. Although the prototype network considered, it is stressed that the results obtained concern methods, and provide guidelines that are valid in a wider context.NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)RUNDomingues, AlexandreVinga, SusanaLemos, João M.2018-07-17T22:04:34Z2010-08-132010-08-13T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article8application/pdfhttp://hdl.handle.net/10362/41816eng1752-0509PURE: 388857https://doi.org/10.1186/1752-0509-4-113info:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2024-05-22T17:33:53Zoai:run.unl.pt:10362/41816Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-28T17:04:50.102450Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
dc.title.none.fl_str_mv Optimization strategies for metabolic networks
title Optimization strategies for metabolic networks
spellingShingle Optimization strategies for metabolic networks
Domingues, Alexandre
systems
title_short Optimization strategies for metabolic networks
title_full Optimization strategies for metabolic networks
title_fullStr Optimization strategies for metabolic networks
title_full_unstemmed Optimization strategies for metabolic networks
title_sort Optimization strategies for metabolic networks
author Domingues, Alexandre
author_facet Domingues, Alexandre
Vinga, Susana
Lemos, João M.
author_role author
author2 Vinga, Susana
Lemos, João M.
author2_role author
author
dc.contributor.none.fl_str_mv NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)
RUN
dc.contributor.author.fl_str_mv Domingues, Alexandre
Vinga, Susana
Lemos, João M.
dc.subject.por.fl_str_mv systems
topic systems
description The work reported in this paper was performed within the project DynaMo - Dynamical modeling, control and optimization of metabolic networks, supported by FCT (Portugal) under contract PTDC/EEA-ACR/69530/2006.
publishDate 2010
dc.date.none.fl_str_mv 2010-08-13
2010-08-13T00:00:00Z
2018-07-17T22:04:34Z
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 http://hdl.handle.net/10362/41816
url http://hdl.handle.net/10362/41816
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 1752-0509
PURE: 388857
https://doi.org/10.1186/1752-0509-4-113
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 8
application/pdf
dc.source.none.fl_str_mv reponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron:RCAAP
instname_str FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron_str RCAAP
institution RCAAP
reponame_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
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