dorsal/arxiv
View SchemaA Modified Iterative IOM Approach for Optimization of Biochemical Systems
| Authors | Gongxian Xu, Cheng Shao, Zhilong Xiu |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0508038 |
| URL | https://arxiv.org/abs/q-bio/0508038 |
Abstract
The presented previously indirect optimization method (IOM) developed within biochemical systems theory (BST) provides a versatile and mathematically tractable optimization strategy for biochemical systems. However, due to the local approximations nature of the BST formalism, the iterative version of this technique possibly does not yield the true optimum solution. In this work, an algorithm is proposed to obtain the correct and consistent optimum steady-state operating point of biochemical systems. The existing linear optimization problem of the direct IOM approach is modified by adding an equality constraint of describing the consistency of solutions between the S-system and the original model. Lagrangian analysis is employed to derive the first order necessary optimality conditions for the above modified optimization problem. This leads to a procedure that may be regarded as a modified iterative IOM approach in which the optimization objective function includes an extra linear term. The extra term contains a comparison of metabolite concentration derivatives with respect to the enzyme activities between the S-system and the original model and ensures that the new algorithm is still carried out within linear programming techniques. The presented framework is applied to several biochemical systems and shown to the tractability and effectiveness of the method. The simulation is also studied to investigate the convergence properties of the algorithm and to give a performance comparison of standard and modified iterative IOM approach.
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"abstract": "The presented previously indirect optimization method (IOM) developed within\nbiochemical systems theory (BST) provides a versatile and mathematically\ntractable optimization strategy for biochemical systems. However, due to the\nlocal approximations nature of the BST formalism, the iterative version of this\ntechnique possibly does not yield the true optimum solution. In this work, an\nalgorithm is proposed to obtain the correct and consistent optimum steady-state\noperating point of biochemical systems. The existing linear optimization\nproblem of the direct IOM approach is modified by adding an equality constraint\nof describing the consistency of solutions between the S-system and the\noriginal model. Lagrangian analysis is employed to derive the first order\nnecessary optimality conditions for the above modified optimization problem.\nThis leads to a procedure that may be regarded as a modified iterative IOM\napproach in which the optimization objective function includes an extra linear\nterm. The extra term contains a comparison of metabolite concentration\nderivatives with respect to the enzyme activities between the S-system and the\noriginal model and ensures that the new algorithm is still carried out within\nlinear programming techniques. The presented framework is applied to several\nbiochemical systems and shown to the tractability and effectiveness of the\nmethod. The simulation is also studied to investigate the convergence\nproperties of the algorithm and to give a performance comparison of standard\nand modified iterative IOM approach.",
"arxiv_id": "q-bio/0508038",
"authors": [
"Gongxian Xu",
"Cheng Shao",
"Zhilong Xiu"
],
"categories": [
"q-bio.QM"
],
"title": "A Modified Iterative IOM Approach for Optimization of Biochemical Systems",
"url": "https://arxiv.org/abs/q-bio/0508038"
},
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