This seems like a really roundabout way to research manufacturing processes. There are much simpler factory designs than a biological cell, which have a higher efficiency (as measured by useful output per useful unit input). Those are what should be modeled, researched, and optimized, not these labyrinthine mechanisms.
"A Whole-Cell Computational Model Predicts Phenotype from Genotype" by Jonathan Karr et al.
This paper appeared a few days ago in Cell, and describes a computational simulation of the bacterium Mycoplasma genitalium, conducted at this lab. The paper is behind a paywall, but is blogged about here. The simulation software is freely available from the project web site.
From the abstract: "Here, we present a ‘‘whole-cell’’ model of the bacterium Mycoplasma genitalium, a human urogenital parasite whose genome contains 525 genes. Our model attempts to: (1) describe the life cycle of a single cell from the level of individual molecules and their interactions; (2) account for the specific function of every annotated gene product; and (3) accurately predict a wide range of observable cellular behaviors."
According to an editorial commentary in the same issue, this is the first simulation of a complete free-living microbe.