2022
DOI: 10.1016/j.ymben.2021.10.012
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Quantifying the propagation of parametric uncertainty on flux balance analysis

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Cited by 16 publications
(22 citation statements)
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“…ATP maintenance rate parameters, GAM and NGAM are necessary to accurately account for the fraction of glucose uptake apportioned towards energy production and ultimately growth 77 .We estimated GAM and NGAM parameters values using an ATP synthase proton/ATP ratio of 10/3. This reflects the fact that the S. cerevisiae ATP synthase consists of 10 c-ring for every 3 F 1 F 0 subunits 113 resulting in 10 proton molecules translocated across mitochondrial membrane per 3 ATP molecules produced.…”
Section: Resultsmentioning
confidence: 99%
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“…ATP maintenance rate parameters, GAM and NGAM are necessary to accurately account for the fraction of glucose uptake apportioned towards energy production and ultimately growth 77 .We estimated GAM and NGAM parameters values using an ATP synthase proton/ATP ratio of 10/3. This reflects the fact that the S. cerevisiae ATP synthase consists of 10 c-ring for every 3 F 1 F 0 subunits 113 resulting in 10 proton molecules translocated across mitochondrial membrane per 3 ATP molecules produced.…”
Section: Resultsmentioning
confidence: 99%
“…Instead of reconstructing multiple models with different biomass coefficients at different growth rates, the biomass reaction is recast as a set of precursor sink reactions whose fluxes are equal to the coefficients multiplied by the growth rate. We ensure that the biomass molecular weight is always 1 g mmol -1 so that growth yield and rate predictions are consistent 76,77 . Detailed biomass formulation is provided in the Supplementary Methods and Supplementary Data 1.…”
Section: Rba Model Reconstructionmentioning
confidence: 99%
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“…Consequently, the reaction boundaries of both reactions can directly contribute to shape the solution space, as the main criteria in FBA is maximizing the growth-associated ATP production (assuming that the objective function is the biomass reaction). As a parameter, ATPm has been shown to be important for the result of FBA and has a pronounced impact on the consistency of biomass production [17].…”
Section: The Influence Of Atp Maintenance On the Solution Spacementioning
confidence: 99%
“…To name one, coordinated hit-and-run with rounding (CHRR) is reportedly a very efficient method and has been used to study the properties of genome-scale models of bacterial systems [15,16]. Sampling methods have also been used to study the effect of a change in biomass precursors, ATP maintenance (ATPm) and the uptake/production rates of metabolites in response to temporal fluctuations in environments, leading to the conclusion that incorporation of such constraints considerably increases the accuracy of flux distribution [17].…”
Section: Introductionmentioning
confidence: 99%