Simulation and optimization of dynamic flux balance analysis models using an interior point method reformulation

Felipe Scott, Pamela Wilson, Raúl Conejeros, Vassilios S. Vassiliadis*

*Autor correspondiente de este trabajo

Resultado de la investigación: Contribución a una revistaArtículorevisión exhaustiva

11 Citas (Scopus)

Resumen

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.
Idioma originalInglés
Páginas (desde-hasta)152-170
Número de páginas19
PublicaciónComputers and Chemical Engineering
Volumen119
DOI
EstadoPublicada - 2 nov. 2018

Nota bibliográfica

Publisher Copyright:
© 2018

Palabras clave

  • Dynamic flux balance analysis
  • Genome-scale metabolic network
  • Linear programming
  • Ordinary differential equations with embedded optimization

Huella

Profundice en los temas de investigación de 'Simulation and optimization of dynamic flux balance analysis models using an interior point method reformulation'. En conjunto forman una huella única.

Citar esto