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Both the kcat and standard deviation for each enzymatic reaction occurring in solution are selected before the simulation is initiated.
The simulation is initiated by first finding the equilibrium given a constant amount of free neurotransmitter at 500 nM and then goes on for a transitory time of 5 seconds at the predetermined tonic firing rate.
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Each simulation was initiated with maximal diversity (initial genotypes randomly drawn from all possible allelic states) and run for successive generations until the mean within-population expected heterozygosity (HE) reached 0.8 (comparable to levels found in many studies of natural populations using microsatellites).
Each replicate simulation was initiated with 100 individuals.
Each simulation was initiated with a single cell starting with a DM count equal to 1 at time zero.
A simulation was initiated from the crystal structure of ecRNH in the Mg 2+-bound state (PDB ID 1RDD).
Each simulation was initiated with the χ1 angle of the Ser sidechain in one of the three possible stable rotamers.
This atomistic simulation was initiated from the configuration of STX/PM complex from the preceding CMG simulations as described above (see also Figure 3).
The RMD simulation was initiated by using unambiguous NMR distant constraints on the peptide without the presence of the disulfide bond.
The simulation was initiated with the high-resolution (1.9 Å) crystal structure of wildtype AcrB (PDB entry 4DX5), preserving crystallographic water molecules.
Each Monte Carlo simulation was initiated with a random configuration of protonation states, and consists of five cycles of temperature annealing and a subsequent equilibration.
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