Once the model provided the most promising geometrical characteristics for the target operating point, three-dimensional steady RANS analyses are performed to evaluate the actual performance of the compressor for a wide range of mass-flow values.
In agreement with this, both strains showed comparably low, but detectable ribosomal subunit imbalance phenotypes in steady state analyses after shift to restrictive conditions (see above, Fig. 2A, Fig. S1).
Yimod are derived from logical steady state analyses of the logical model assuming galactose present and all other carbon sources absent.
We used the MATLAB toolbox CellNetAnalyzer 7.0 [ 17, 51] to perform structural and functional logical steady state analyses on the established network.
Logical steady states analyses simplify the hypergraph setup, since we do not need to take into consideration the different timescales of different processes.
Next, we performed logical steady state analyses to compute the state of all nodes in the system under all possible environmental conditions (sugars availability), and for all different single gene deletions and some double gene deletions.
(1) It has been shown that a direct application of nanoparticle suspensions to an ICP-MS system does, applying steady state analyses, mostly not provide reliable data for total metal concentrations.
Steady state analyses, where more or less instant convergence to the new attractor state is assumed, will be limited in this regard since they are not able to address the question of developmental timing.
We used the results from the logical steady state analyses for the corresponding conditions in order to calculate the changes in gene expression between the simulated wild-type and the simulated knockout mutant.
Therefore, it is unclear how we can understand transcriptional dynamics in diauxic shift based on knowledge gained from steady state analyses and without a more direct method of measuring cAMP-CRP dynamics in vivo.
