A Newton Cooperative Genetic Algorithm Method for In Silico Optimization of Metabolic Pathway Production
This paper presents an in silico optimization method of metabolic pathway production. The metabolic pathway can be represented by a mathematical model known as the generalized mass action model, which leads to a complex nonlinear equations system. The optimization process becomes difficult when stea...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science
2015
|
| Subjects: | |
| Online Access: | http://umpir.ump.edu.my/id/eprint/11777/ http://umpir.ump.edu.my/id/eprint/11777/1/A%20Newton%20Cooperative%20Genetic%20Algorithm%20Method%20for%20In%20Silico%20Optimization%20of%20Metabolic%20Pathway%20Production.pdf |
| _version_ | 1848819075822649344 |
|---|---|
| author | Mohd Arfian, Ismail Safaai, Deris Mohd Saberi, Mohamad Afnizanfaizal, Abdullah |
| author_facet | Mohd Arfian, Ismail Safaai, Deris Mohd Saberi, Mohamad Afnizanfaizal, Abdullah |
| author_sort | Mohd Arfian, Ismail |
| building | UMP Institutional Repository |
| collection | Online Access |
| description | This paper presents an in silico optimization method of metabolic pathway production. The metabolic pathway can be represented by a mathematical model known as the generalized mass action model, which leads to a complex nonlinear equations system. The optimization process becomes difficult when steady state and the constraints of the components in the metabolic pathway are involved. To deal with this situation, this paper presents an in silico optimization method, namely the Newton Cooperative Genetic Algorithm (NCGA). The NCGA used Newton method in dealing with the metabolic pathway, and then integrated genetic algorithm and cooperative co-evolutionary algorithm. The proposed method was experimentally applied on the benchmark metabolic pathways, and the results showed that the NCGA achieved better results compared to the existing methods. |
| first_indexed | 2025-11-15T01:47:48Z |
| format | Article |
| id | ump-11777 |
| institution | Universiti Malaysia Pahang |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T01:47:48Z |
| publishDate | 2015 |
| publisher | Public Library of Science |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | ump-117772018-03-27T03:45:30Z http://umpir.ump.edu.my/id/eprint/11777/ A Newton Cooperative Genetic Algorithm Method for In Silico Optimization of Metabolic Pathway Production Mohd Arfian, Ismail Safaai, Deris Mohd Saberi, Mohamad Afnizanfaizal, Abdullah QA75 Electronic computers. Computer science QD Chemistry This paper presents an in silico optimization method of metabolic pathway production. The metabolic pathway can be represented by a mathematical model known as the generalized mass action model, which leads to a complex nonlinear equations system. The optimization process becomes difficult when steady state and the constraints of the components in the metabolic pathway are involved. To deal with this situation, this paper presents an in silico optimization method, namely the Newton Cooperative Genetic Algorithm (NCGA). The NCGA used Newton method in dealing with the metabolic pathway, and then integrated genetic algorithm and cooperative co-evolutionary algorithm. The proposed method was experimentally applied on the benchmark metabolic pathways, and the results showed that the NCGA achieved better results compared to the existing methods. Public Library of Science 2015 Article PeerReviewed application/pdf en cc_by http://umpir.ump.edu.my/id/eprint/11777/1/A%20Newton%20Cooperative%20Genetic%20Algorithm%20Method%20for%20In%20Silico%20Optimization%20of%20Metabolic%20Pathway%20Production.pdf Mohd Arfian, Ismail and Safaai, Deris and Mohd Saberi, Mohamad and Afnizanfaizal, Abdullah (2015) A Newton Cooperative Genetic Algorithm Method for In Silico Optimization of Metabolic Pathway Production. PLoS ONE, 10 (5). pp. 1-19. ISSN 1932-6203. (Published) http://dx.doi.org/10.1371/journal.pone.0126199 DOI: 10.1371/journal.pone.0126199 |
| spellingShingle | QA75 Electronic computers. Computer science QD Chemistry Mohd Arfian, Ismail Safaai, Deris Mohd Saberi, Mohamad Afnizanfaizal, Abdullah A Newton Cooperative Genetic Algorithm Method for In Silico Optimization of Metabolic Pathway Production |
| title | A Newton Cooperative Genetic Algorithm Method for In Silico Optimization of Metabolic Pathway Production |
| title_full | A Newton Cooperative Genetic Algorithm Method for In Silico Optimization of Metabolic Pathway Production |
| title_fullStr | A Newton Cooperative Genetic Algorithm Method for In Silico Optimization of Metabolic Pathway Production |
| title_full_unstemmed | A Newton Cooperative Genetic Algorithm Method for In Silico Optimization of Metabolic Pathway Production |
| title_short | A Newton Cooperative Genetic Algorithm Method for In Silico Optimization of Metabolic Pathway Production |
| title_sort | newton cooperative genetic algorithm method for in silico optimization of metabolic pathway production |
| topic | QA75 Electronic computers. Computer science QD Chemistry |
| url | http://umpir.ump.edu.my/id/eprint/11777/ http://umpir.ump.edu.my/id/eprint/11777/ http://umpir.ump.edu.my/id/eprint/11777/ http://umpir.ump.edu.my/id/eprint/11777/1/A%20Newton%20Cooperative%20Genetic%20Algorithm%20Method%20for%20In%20Silico%20Optimization%20of%20Metabolic%20Pathway%20Production.pdf |