Process_Metabolism – Metabolism

Name
WID Process_Metabolism
Name Metabolism
 
Implementation
Initialization order 8 View in model
 
Reactions
Chemical reactions View in model
Complex formation reactions View in model
 
Parameters
Parameters View in model
 
Comments
Comments Transport and metabolism are modeled using the constraint-based method flux-balance analysis (FBA). Briefly, FBA assumes that bacteria have evolved to maximize growth, and poses transport and metabolism as the optimization of cellular building block and energy production subject to available nutrients, and allowed chemical reactions. FBA models are typically constrained by experimentally measured transport and diffusion rates. In addition to these constraints, we constrain constrain our FBA module by our model's predicted enzyme abundances, and by experimentally measured kinetic parameters. These additional constraints yield a more accurate model of transport and metabolism. Furthermore, we use our other modules to obtain a more extensive and accurate metabolic objective than used in earlier FBA models. Flux-balance analysis Computes reaction bounds based on enzyme kinetics, enzyme availability specific transport rate metabolite availability Computes optimal reaction fluxes which maximize biomass production Computes integer-valued production of biomass components Updates amounts of biomass components Variable Units fbaEnzymeBounds molecules/enzyme/s fbaReactionBounds molecules/(gram dry biomass)/s metabolites molecules enzymes molecules simulationStep s lowerBounds reactions/s upperBounds reactions/s growth cell/s biomassComposition molecules/cell metabolismProduction molecules/cell chamberVolume L mediaComposition molecules/chamber growthAssociatedMaintanence  
 
Metadata
Created 2012-10-01 15:07:35
Last updated 2012-10-01 15:14:00