1. Distributed flux balance analysis simulations of serial biomass fermentation by two organisms
- Author
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Zohar Yakhini, Edward Vitkin, Alexander Golberg, Mark Polikovsky, Amichai Gillis, and Barak Bender
- Subjects
Metabolic Processes ,Biomass ,Yeast and Fungal Models ,02 engineering and technology ,Ethanol fermentation ,Biochemistry ,Ulva ,0202 electrical engineering, electronic engineering, information engineering ,Ethanol fuel ,Bioenergy ,0303 health sciences ,Multidisciplinary ,Organic Compounds ,Hydrolysis ,Monosaccharides ,food and beverages ,Eukaryota ,Plants ,Pulp and paper industry ,Flux balance analysis ,Chemistry ,Experimental Organism Systems ,Scientific method ,Physical Sciences ,Bioenergy Feedstock ,Medicine ,Engineering and Technology ,Computer-Aided Design ,Research Article ,Chemical Elements ,Computer and Information Sciences ,Science ,020209 energy ,Carbohydrates ,Saccharomyces cerevisiae ,Raw material ,Research and Analysis Methods ,complex mixtures ,Models, Biological ,Zea mays ,03 medical and health sciences ,Saccharomyces ,Model Organisms ,Plant and Algal Models ,Escherichia coli ,Computer Simulation ,Grasses ,030304 developmental biology ,Ethanol ,Organic Chemistry ,Chemical Compounds ,Organisms ,Fungi ,Biology and Life Sciences ,Cloud Computing ,Biorefinery ,Computing Methods ,Yeast ,Maize ,Energy and Power ,Oxygen ,Metabolism ,Glucose ,Alcohols ,Fermentation ,Rhodophyta ,Animal Studies ,Environmental science - Abstract
Intelligent biorefinery design that addresses both the composition of the biomass feedstock as well as fermentation microorganisms could benefit from dedicated tools for computational simulation and computer-assisted optimization. Here we present the BioLego Vn2.0 framework, based on Microsoft Azure Cloud, which supports large-scale simulations of biomass serial fermentation processes by two different organisms. BioLego enables the simultaneous analysis of multiple fermentation scenarios and the comparison of fermentation potential of multiple feedstock compositions. Thanks to the effective use of cloud computing it further allows resource intensive analysis and exploration of media and organism modifications. We use BioLego to obtain biological and validation results, including (1) exploratory search for the optimal utilization of corn biomasses-corn cobs, corn fiber and corn stover-in fermentation biorefineries; (2) analysis of the possible effects of changes in the composition of K. alvarezi biomass on the ethanol production yield in an anaerobic two-step process (S. cerevisiae followed by E. coli); (3) analysis of the impact, on the estimated ethanol production yield, of knocking out single organism reactions either in one or in both organisms in an anaerobic two-step fermentation process of Ulva sp. into ethanol (S. cerevisiae followed by E. coli); and (4) comparison of several experimentally measured ethanol fermentation rates with the predictions of BioLego.
- Published
- 2020