This work analyzes the initial value problem in ordinary differential equations with a parametric lexicographic linear program (LP) embedded. The LP is said to be embedded since the dynamics depend on the solution of the LP, which is in turn parameterized by the dynamic states. This problem formulation finds application in dynamic flux balance analysis, which serves as a modeling framework for ...

Metabolic networks are defined as the collection of biochemical reactions within a cell that define the functions of that cell. Due to the growing need to understand the functions of biological organisms for industrial and medical purposes, modeling and simulation of metabolic networks has attracted a lot of attention recently. Traditionally, metabolic networks are modeled such as flux-balance ...

In this work, a Simulated Annealing (SA) algorithm is proposed for a Metabolic Engineering task: the optimization of the set of gene deletions to apply to a microbial strain to achieve a desired production goal. Each mutant strain is evaluated by simulating its phenotype using the Flux-Balance Analysis approach, under the premise that microorganisms have maximized their growth along natural evo...

Despite their topological complexity almost all functional properties of metabolic networks can be derived from steady-state dynamics. Indeed, many theoretical investigations (like flux-balance analysis) rely on extracting function from steady states. This leads to the interesting question, how metabolic networks avoid complex dynamics and maintain a steady-state behavior. Here, we expose metab...