An increasing number of industrial bioprocesses capitalize on living cells by using them as
cell factories that convert sugars into chemicals. These processes range from the production …

Biochemical systems theory (BST) is the foundation for a set of analytical andmodeling tools
that facilitate the analysis of dynamic biological systems. This paper depicts major …

In contrast to stoichiometric-based models, the development of large-scale kinetic models of
metabolism has been hindered by the challenge of identifying kinetic parameter values and …

Highlights•We now have metabolic network models; the metabolome is represented by their
nodes.•Metabolite levels are sensitive to changes in enzyme activities.•Drugs hitchhike on …

Computational strain design protocols aim at the system-wide identification of intervention
strategies for the enhanced production of biochemicals in microorganisms. Existing …

Mathematical modeling is a key process to describe the behavior of biological networks.
One of the most difficult challenges is to build models that allow quantitative predictions of …

Genome-scale metabolic models are increasingly becoming available for a variety of
microorganisms. This has spurred the development of a wide array of computational tools …

Microorganisms evolved adaptive responses to survive stressful challenges in ever-
changing environments. Understanding the relationships between the physiological …

Biological networks are currently being studied with approaches derived from the
mathematical and physical sciences. Their structural analysis enables to highlight nodes …

This paper describes and validates an algorithm to solve optimal control problems for agent-
based models (ABMs). For a given ABM and a given optimal control problem, the algorithm …