Simulation and optimization of dynamic flux balance analysis models using an interior point method reformulation
Computers and Chemical Engineering
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Scott, F., Wilson, P., Conejeros, R., & Vassiliadis, V. (2018). Simulation and optimization of dynamic flux balance analysis models using an interior point method reformulation. Computers and Chemical Engineering, 119 152-170. https://doi.org/10.1016/j.compchemeng.2018.08.041
This work presents a novel, diﬀerentiable, way of solving dynamic Flux Balance Analysis (dFBA) problems by embedding ﬂux balance analysis of metabolic network models within lumped bulk kinetics for biochemical processes. The proposed methodology utilizes transformation of the bounds of the embedded linear programming problem of ﬂux balance analysis via a logarithmic barrier (interior point) approach. By exploiting the ﬁrst-order optimality conditions of the interior-point problem, and with further transformations, the approach results in a system of implicit ordinary diﬀerential equations. Results from four case studies, show that the CPU and wall-times obtained using the proposed method are competitive with existing state-of-the-art approaches for solving dFBA simulations, for problem sizes up to genome-scale. The diﬀerentiability of the proposed approach allows, using existing commercial packages, its application to the optimal control of dFBA problems at a genome-scale size, thus outperforming existing formulations as shown by two dynamic optimization case studies.
• R. Conejeros would like to thank CONICYT’s research grant FONDECYT 1151295 for funding this research. • F. Scott gratefully acknowledges ﬁnancial support from CONICYT (Proyectos REDES ETAPA INICIAL, Convocatoria 2017, REDI170254).
External DOI: https://doi.org/10.1016/j.compchemeng.2018.08.041
This record's URL: https://www.repository.cam.ac.uk/handle/1810/285147