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For investigation of the shape of the predicted response surfaces and for model optimization, the canonical analysis was applied.
The program will also print out the execution time required for model optimization, the execution time of one SPR cycle, and the overall execution time.
For model optimization, the backbone atoms of the structures were initially frozen and only the side chains were allowed to move for a selective minimization by conjugate gradient method.
Because branch lengths play a crucial role in model optimization, the analysis was repeated on an alternative version of the reference tree in which branch lengths were transformed using a rate smoothing approach.
Moreover, during model optimization, the inability to obtain good fits from experimental measurements indicated that the initial, core model design, focusing on pathway dynamics, required integration of the autophagic process with the cellular nutrient levels.
As part of the model optimization, the Kp value for each tissue was subsequently tested at 10, 100, and a maximum value of 1,000 as an initial setting for screening purposes to identify the tissue most contributing to sirolimus volume of distribution.
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For the pore model, optimization of the side chain rotamers was done using SCWRL (Krivov et al., 2009) prior to the calculation of the electrostatic potential.
This study introduces another parameter for model optimization: defining the relationship among groups in the CMLM.
After the model optimization, three different concentrations of the grey water were used to run the proposed mathematical model.
Based on the validated model, optimizations of the overall system performance were carried out.
The results of the model optimization are confirmed by AFM.
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