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Other settings of the WRF simulations were the same as the settings of the original simulation described in subsection 2c.
The parameters used in these simulations were the same as those used for the calculation for the inbreeding coefficient described above.
Because the movements of flaps in two MD simulations were the same, the analysis of only one MD simulation is described below.
All remaining evolutionary and epidemiological parameters used in these individual-based simulations were the same as the ones listed in the model parameterization section above.
Initial parameters for all simulations were the same: oxidized cytochrome c 20 μM, reduced cytochrome c 0 μM, and cytochrome bc1 100 nM.
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The configuration of the simulations is the same as described before.
The temperature of 310 K for MD simulations was the same as that used in ITC and CD experiments.
The metabolic network model used for the simulations is the same augmented model developed by Lange [ 51] that was used in [ 50].
The location of the channel determined in these simulations is the same as the one previously reported from simulations of wild-type BR in which D96 was modeled in the deprotonated state.
The ML estimator was derived assuming that all the individuals in the population have the same registration probability, something that translates to p in the simulations is the same for individuals.
The controlling conditions of compositional simulation were the same as those of laboratory WAG coreflood experiments most widely used.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com