Multi-scale approach for simulating time-delay biochemical reaction systems

This study presents a multi-scale approach for simulating time-delay biochemical reaction systems when there are wide ranges of molecular numbers. The authors construct a new efficient approach based on partitioning into slow and fast subsets in conjunction with predictor–corrector methods. This mul...

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Vydáno v:IET systems biology Ročník 9; číslo 1; s. 31 - 38
Hlavní autoři: Niu, Yuanling, Burrage, Kevin, Zhang, Chengjian
Médium: Journal Article
Jazyk:angličtina
Vydáno: England The Institution of Engineering and Technology 01.02.2015
Témata:
Algorithms
Biochemistry
biological techniques
Biology
Computational efficiency
Computer Simulation
Delay
delay stochastic simulation algorithm
delays
Mathematical models
method accuracy
Models, Biological
Models, Chemical
modified next reaction method
multiscale approach
numerical testing
Partitioning
predictor‐corrector methods
Proteins - chemistry
Proteins - metabolism
Signal Transduction - physiology
systems biology
time‐delay biochemical reaction systems
systems biology
numerical testing
modified next reaction method
time-delay biochemical reaction systems
computational efficiency
multiscale approach
predictor–corrector methods
delays
biochemistry
method accuracy
delay stochastic simulation algorithm
biological techniques
predictor-corrector methods
ISSN:1751-8849, 1751-8857
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Abstract This study presents a multi-scale approach for simulating time-delay biochemical reaction systems when there are wide ranges of molecular numbers. The authors construct a new efficient approach based on partitioning into slow and fast subsets in conjunction with predictor–corrector methods. This multi-scale approach is shown to be much more efficient than existing methods such as the delay stochastic simulation algorithm and the modified next reaction method. Numerical testing on several important problems in systems biology confirms the accuracy and computational efficiency of this approach.
AbstractList This study presents a multi-scale approach for simulating time-delay biochemical reaction systems when there are wide ranges of molecular numbers. The authors construct a new efficient approach based on partitioning into slow and fast subsets in conjunction with predictor–corrector methods. This multi-scale approach is shown to be much more efficient than existing methods such as the delay stochastic simulation algorithm and the modified next reaction method. Numerical testing on several important problems in systems biology confirms the accuracy and computational efficiency of this approach.
This study presents a multi-scale approach for simulating time-delay biochemical reaction systems when there are wide ranges of molecular numbers. The authors construct a new efficient approach based on partitioning into slow and fast subsets in conjunction with predictor-corrector methods. This multi-scale approach is shown to be much more efficient than existing methods such as the delay stochastic simulation algorithm and the modified next reaction method. Numerical testing on several important problems in systems biology confirms the accuracy and computational efficiency of this approach.This study presents a multi-scale approach for simulating time-delay biochemical reaction systems when there are wide ranges of molecular numbers. The authors construct a new efficient approach based on partitioning into slow and fast subsets in conjunction with predictor-corrector methods. This multi-scale approach is shown to be much more efficient than existing methods such as the delay stochastic simulation algorithm and the modified next reaction method. Numerical testing on several important problems in systems biology confirms the accuracy and computational efficiency of this approach.
Author Burrage, Kevin
Niu, Yuanling
Zhang, Chengjian
AuthorAffiliation 4 Department of Computer Science Oxford University Wolfson Building, Parks Road Oxford OX1 3QD UK
3 Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai 200031 People's Republic of China
2 School of Mathematics and Statistics, Huazhong University of Science and Technology Wuhan 430074 People's Republic of China
1 School of Mathematics and Statistics, Central South University Changsha 410083 People's Republic of China
5 School of Mathematical Sciences, Queensland University of Technology Brisbane QLD 4001 Australia
AuthorAffiliation_xml – name: 2 School of Mathematics and Statistics, Huazhong University of Science and Technology Wuhan 430074 People's Republic of China
– name: 1 School of Mathematics and Statistics, Central South University Changsha 410083 People's Republic of China
– name: 5 School of Mathematical Sciences, Queensland University of Technology Brisbane QLD 4001 Australia
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  surname: Niu
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  fullname: Zhang, Chengjian
  organization: 2School of Mathematics and Statistics, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
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Issue 1
Keywords systems biology
numerical testing
modified next reaction method
time-delay biochemical reaction systems
computational efficiency
multiscale approach
predictor–corrector methods
delays
biochemistry
method accuracy
delay stochastic simulation algorithm
biological techniques
predictor-corrector methods
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Snippet This study presents a multi-scale approach for simulating time-delay biochemical reaction systems when there are wide ranges of molecular numbers. The authors...
This study presents a multi‐scale approach for simulating time‐delay biochemical reaction systems when there are wide ranges of molecular numbers. The authors...
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wiley
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SubjectTerms Algorithms
Biochemistry
biological techniques
Biology
Computational efficiency
Computer Simulation
Delay
delay stochastic simulation algorithm
delays
Mathematical models
method accuracy
Models, Biological
Models, Chemical
modified next reaction method
multiscale approach
numerical testing
Partitioning
predictor‐corrector methods
Proteins - chemistry
Proteins - metabolism
Signal Transduction - physiology
systems biology
time‐delay biochemical reaction systems
Title Multi-scale approach for simulating time-delay biochemical reaction systems
URI http://digital-library.theiet.org/content/journals/10.1049/iet-syb.2013.0023
https://onlinelibrary.wiley.com/doi/abs/10.1049%2Fiet-syb.2013.0023
https://www.ncbi.nlm.nih.gov/pubmed/25569862
https://www.proquest.com/docview/1645776399
https://www.proquest.com/docview/1808095409
https://pubmed.ncbi.nlm.nih.gov/PMC8687155
Volume 9
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