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To summarize, the hill-finding approach, which is the second phase of the ModuLand methods, gives an additional layer of flexibility, where the relatively inaccurate results of simpler hill definitions, and the large computational costs of more accurate optimization processes can be tailored to the network and to the experimenter's needs and possibilities.
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Why does the very simple Hill equation match so well to the range of observed input-output relations?
We show that a simple Hill kinetic model is the most efficient way to model RNA interference.
TMEM16A 0) data could be fitted with a simple Hill equation giving a Kd of 371 nM for Ca2+.
Coefficients λ1 and λ2 were estimated by maximizing the training-partition classification accuracy via simple hill climbing.
For well-mixed reaction systems a simple Hill function is often employed to model cooperative behavior in a 'generic' way.
We thus compared our approach to a simple hill climbing search algorithm on the Yu et al. data set (see Methods).
In contrast, in the limiting case of a simple Hill activation, the formation of inward propagating waves is suppressed by a Turing instability.
Our findings show that the simple Hill function described by Model 4 is sufficient to quantitatively describe the effect of RNA interference, at the mRNA and protein level, in mammalian cells in vitro, for varying concentration of siRNA oligomers.
Despite this complexity, the dose-response is deceptively simple: it often takes the form of a simple Hill function with a coefficient of unity, which has traditionally been interpreted to imply that ligand-binding is the only rate-limiting step in the activation pathway (Ong et al., 2010).
Specifically, we address the question whether the symmetry model of Monod, Wyman and Changeux (MWC) [ 37], as employed in the Goldbeter model, is necessary to generate inward propagating waves or whether a more simple Hill kinetics, as it was used by Sel'kov [ 12] to model the PFK activation, is suffcient.
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