IDEAS home Printed from https://ideas.repec.org/a/spr/jglopt/v62y2015i4p791-810.html
   My bibliography  Save this article

Parameter identification for a nonlinear enzyme-catalytic dynamic system with time-delays

Author

Listed:
  • Jinlong Yuan
  • Lei Wang
  • Xu Zhang
  • Enmin Feng
  • Hongchao Yin
  • Zhilong Xiu

Abstract

In this paper, we consider a nonlinear enzyme-catalytic dynamical system with uncertain system parameters and state-delays for describing the process of batch culture. Some important properties of the time-delay system are discussed. Taking account of the difficulty in accurately measuring the concentrations of intracellular substances and the absence of equilibrium points for the time-delay system, we define quantitatively biological robustness of the intracellular substance concentrations for the entire process of batch culture to identify the uncertain system parameters and state-delays. Taking the defined biological robustness as a cost function, we establish an identification model subject to the time-delay system, continuous state inequality constraints and parameter constraints. By a penalty approach, this model can be converted into a sequence of nonlinear programming submodels. In consideration of both the difficulty in finding analytical solutions and the complexity of numerical solution to the nonlinear system, based on an improved simulated annealing, we develop a parallelized synchronous algorithm to solve these nonlinear programming submodels. An illustrative numerical example shows the appropriateness of the optimal system parameters and state-delays as well as the validity of the parallel algorithm. Copyright Springer Science+Business Media New York 2015

Suggested Citation

  • Jinlong Yuan & Lei Wang & Xu Zhang & Enmin Feng & Hongchao Yin & Zhilong Xiu, 2015. "Parameter identification for a nonlinear enzyme-catalytic dynamic system with time-delays," Journal of Global Optimization, Springer, vol. 62(4), pages 791-810, August.
  • Handle: RePEc:spr:jglopt:v:62:y:2015:i:4:p:791-810
    DOI: 10.1007/s10898-014-0245-4
    as

    Download full text from publisher

    File URL: http://hdl.handle.net/10.1007/s10898-014-0245-4
    Download Restriction: Access to full text is restricted to subscribers.

    File URL: https://libkey.io/10.1007/s10898-014-0245-4?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Ishibuchi, Hisao & Misaki, Shinta & Tanaka, Hideo, 1995. "Modified simulated annealing algorithms for the flow shop sequencing problem," European Journal of Operational Research, Elsevier, vol. 81(2), pages 388-398, March.
    2. U. Alon & M. G. Surette & N. Barkai & S. Leibler, 1999. "Robustness in bacterial chemotaxis," Nature, Nature, vol. 397(6715), pages 168-171, January.
    3. A. Ferreiro & J. García & J. López-Salas & C. Vázquez, 2013. "An efficient implementation of parallel simulated annealing algorithm in GPUs," Journal of Global Optimization, Springer, vol. 57(3), pages 863-890, November.
    4. Ahonen, H. & de Alvarenga, A.G. & Amaral, A.R.S., 2014. "Simulated annealing and tabu search approaches for the Corridor Allocation Problem," European Journal of Operational Research, Elsevier, vol. 232(1), pages 221-233.
    5. N. Barkai & S. Leibler, 1997. "Robustness in simple biochemical networks," Nature, Nature, vol. 387(6636), pages 913-917, June.
    6. Yuan, Jinlong & Zhu, Xi & Zhang, Xu & Yin, Hongchao & Feng, Enmin & Xiu, Zhilong, 2014. "Robust identification of enzymatic nonlinear dynamical systems for 1,3-propanediol transport mechanisms in microbial batch culture," Applied Mathematics and Computation, Elsevier, vol. 232(C), pages 150-163.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Jae Kyoung Kim & Trachette L Jackson, 2013. "Mechanisms That Enhance Sustainability of p53 Pulses," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-11, June.
    2. Deyan Luan & Michael Zai & Jeffrey D Varner, 2007. "Computationally Derived Points of Fragility of a Human Cascade Are Consistent with Current Therapeutic Strategies," PLOS Computational Biology, Public Library of Science, vol. 3(7), pages 1-13, July.
    3. Jasmin Fisher & Nir Piterman & Alex Hajnal & Thomas A Henzinger, 2007. "Predictive Modeling of Signaling Crosstalk during C. elegans Vulval Development," PLOS Computational Biology, Public Library of Science, vol. 3(5), pages 1-12, May.
    4. Diana Clausznitzer & Olga Oleksiuk & Linda Løvdok & Victor Sourjik & Robert G Endres, 2010. "Chemotactic Response and Adaptation Dynamics in Escherichia coli," PLOS Computational Biology, Public Library of Science, vol. 6(5), pages 1-11, May.
    5. Guillermo Rodrigo & Santiago F Elena, 2011. "Structural Discrimination of Robustness in Transcriptional Feedforward Loops for Pattern Formation," PLOS ONE, Public Library of Science, vol. 6(2), pages 1-7, February.
    6. Nikita Vladimirov & Linda Løvdok & Dirk Lebiedz & Victor Sourjik, 2008. "Dependence of Bacterial Chemotaxis on Gradient Shape and Adaptation Rate," PLOS Computational Biology, Public Library of Science, vol. 4(12), pages 1-17, December.
    7. Robert J Prill & Pablo A Iglesias & Andre Levchenko, 2005. "Dynamic Properties of Network Motifs Contribute to Biological Network Organization," PLOS Biology, Public Library of Science, vol. 3(11), pages 1-1, October.
    8. Robert M Cooper & Ned S Wingreen & Edward C Cox, 2012. "An Excitable Cortex and Memory Model Successfully Predicts New Pseudopod Dynamics," PLOS ONE, Public Library of Science, vol. 7(3), pages 1-12, March.
    9. Önder Kartal & Oliver Ebenhöh, 2009. "Ground State Robustness as an Evolutionary Design Principle in Signaling Networks," PLOS ONE, Public Library of Science, vol. 4(12), pages 1-8, December.
    10. Junjie Luo & Jun Wang & Ting Martin Ma & Zhirong Sun, 2010. "Reverse Engineering of Bacterial Chemotaxis Pathway via Frequency Domain Analysis," PLOS ONE, Public Library of Science, vol. 5(3), pages 1-8, March.
    11. Miri Adler & Avi Mayo & Uri Alon, 2014. "Logarithmic and Power Law Input-Output Relations in Sensory Systems with Fold-Change Detection," PLOS Computational Biology, Public Library of Science, vol. 10(8), pages 1-14, August.
    12. Kirstin Meyer & Nicholas C. Lammers & Lukasz J. Bugaj & Hernan G. Garcia & Orion D. Weiner, 2023. "Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    13. Gabriele Micali & Gerardo Aquino & David M Richards & Robert G Endres, 2015. "Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation," PLOS Computational Biology, Public Library of Science, vol. 11(6), pages 1-21, June.
    14. Zeina Shreif & Vipul Periwal, 2014. "A Network Characteristic That Correlates Environmental and Genetic Robustness," PLOS Computational Biology, Public Library of Science, vol. 10(2), pages 1-23, February.
    15. Kazunari Kaizu & Hisao Moriya & Hiroaki Kitano, 2010. "Fragilities Caused by Dosage Imbalance in Regulation of the Budding Yeast Cell Cycle," PLOS Genetics, Public Library of Science, vol. 6(4), pages 1-12, April.
    16. Burton W Andrews & Tau-Mu Yi & Pablo A Iglesias, 2006. "Optimal Noise Filtering in the Chemotactic Response of Escherichia coli," PLOS Computational Biology, Public Library of Science, vol. 2(11), pages 1-12, November.
    17. Diana Clausznitzer & Gabriele Micali & Silke Neumann & Victor Sourjik & Robert G Endres, 2014. "Predicting Chemical Environments of Bacteria from Receptor Signaling," PLOS Computational Biology, Public Library of Science, vol. 10(10), pages 1-14, October.
    18. Robyn P. Araujo & Lance A. Liotta, 2023. "Universal structures for adaptation in biochemical reaction networks," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    19. Andrew C Ahn & Muneesh Tewari & Chi-Sang Poon & Russell S Phillips, 2006. "The Limits of Reductionism in Medicine: Could Systems Biology Offer an Alternative?," PLOS Medicine, Public Library of Science, vol. 3(6), pages 1-1, May.
    20. Silke Neumann & Linda Løvdok & Kajetan Bentele & Johannes Meisig & Ekkehard Ullner & Ferencz S Paldy & Victor Sourjik & Markus Kollmann, 2014. "Exponential Signaling Gain at the Receptor Level Enhances Signal-to-Noise Ratio in Bacterial Chemotaxis," PLOS ONE, Public Library of Science, vol. 9(4), pages 1-11, April.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:spr:jglopt:v:62:y:2015:i:4:p:791-810. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.