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In the canonical model, we used a typical Michaelis Menten kinetic model to describe the promoting activities of GEFs (reaction 4 in Figure 1A and C) and GAPs (reaction 5 in Figure 1A and D) towards the Rho GTPases.
We used the non-competitive inhibition model of Michaelis Menten kinetics to describe the reactions in which GDIs inhibit the actions of GEFs (reaction 4 in Figure 1B and D) and GAPs (reaction 5 in Figure 1B and C), because in the non-competitive inhibition model the inhibitor and substrate can simultaneously bind the enzyme.
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Agarwal et al. had studied the same reaction by other approaches with an energy gap reaction coordinate, and the recrossing transmission coefficients from the two treatments are similar, showing the suitability of both reaction coordinates.
SMILEY was run on 166 false negative cases and 49 gap reactions (Additional file 2).
GAP reactions were started by the addition of GAP to 1 µM Rab in 50 µl final volume as specified in the figures.
The SMILEY algorithm was then used to predict gap-filling reactions and reactions that correct false negative model predictions.
The variables included current density, inter-electrode gap and reaction time.
The degradation kinetics of d-GAP under reaction conditions was investigated and a reaction kinetics model defining the entire cascade was developed.
The inter-disk gap, the reaction temperature, and the surface topology of the disks were the most important factors influencing reactor performance.
In the current work, a novel reactive distillation column with several liquid-holdup regions was designed, since it allows long residence time and provides flexibility for narrowing the efficiency gap between reaction and distillation.
DNA ligases from viruses, bacteriophage, archaea and eukaryotes couple the strand-joining, or "gap-sealing," reaction to cleavage of the α−β phosphodiester bond of ATP in a three-step mechanism (Fig. 2A) [20], [20].
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