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首页> 外文期刊>Chemical Engineering Research & Design: Transactions of the Institution of Chemical Engineers >Computationally efficient dynamic simulation of cellular kinetics via explicit solution of flux balance analysis: xDFBA modelling and its biochemical process applications
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Computationally efficient dynamic simulation of cellular kinetics via explicit solution of flux balance analysis: xDFBA modelling and its biochemical process applications

机译：动态仿真的计算效率通量的细胞动力学通过显式解平衡分析:xDFBA造型及其生化流程应用程序

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摘要

Recent developments in reconstruction of genome scale metabolism have seen their applications in predicting cell's dynamic responses by combining intracellular metabolism with macro-scale kinetic models. This, however, can be computationally prohibitive for genome-scale metabolic models because a large-scale linear program is solved repeatedly between integration time step. In addition, when this model is used to applications such as parameter estimation or optimal control, the resulting problem becomes bi-level optimization problem, which is difficult to solve real-time. This study proposes a novel dynamic flux balance analysis framework, which constructs intracellular fluxes parameterized as functions of boundary conditions a priori. This explicit solution does not require solving linear programs successively and can be readily exploited by macro-scale kinetic models. We refer to the proposed approach as xDFBA meaning dynamic flux balance analysis embedded with explicit solutions. The method is applied to the growth models of Escherichia coli and Saccharomyces cerevisiae and shows identical prediction capability but reduced computational load, compared to the result of existing DFBA schemes. Finally, by applying parameter estimation and optimal control to the kinetic model of E. coli with xDFBA approach, its biochemical applicability is demonstrated. (C) 2016 Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.
机译：最近的事态发展在重建基因组新陈代谢的应用规模结合预测细胞的动态响应细胞内代谢与大规模的动能模型。禁止公司为代谢模型因为大规模线性规划是解决反复之间集成时间步。当该模型用于应用程序参数估计和最优控制等由此产生的问题是双层的优化问题,很难解决实时的。通量平衡分析框架,结构细胞内通量参数化功能先天的边界条件。解决方案不需要求解线性程序先后和很容易利用大规模的动力学模型。建议的方法是xDFBA意义的动态变化平衡分析嵌入式与明确解决方案。大肠杆菌和酿酒的模型酵母和显示相同的预测能力但减少计算负荷,相比现有DFBA计划的结果。最后,通过应用参数估计最优控制大肠杆菌的动力学模型使用xDFBA方法,其生化适用性。化学工程师学会。爱思唯尔帐面价值保留所有权利。

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