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All computations needed for controller design and system analysis were implemented using a freely available software toolbox.

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In practice, the DDD analysis is implemented using a regression framework.

The cortical analysis is implemented using a bank of modulation filters operating in the Fourier domain.

SEM analysis was carried out with the aid of Hitachi model S-4160 AFM analysisysis was implemented using a Park Scientific Instrument model auto probe CP, the optical transmittance spectra of films in the UV Vis NIR region were recorded by a spectrophotometer (Cary 500 Scan).

In practice, the DD analysis is implemented using a regression framework.20 We estimate several unique model specification that take the general form of the following OLS model: {LPE}_{it}=a+{beta}_1{Treat}_{it}+{beta}_2mathit{operatorname{Re}}{form}_t+{beta}_3{Treat}_{it}ast mathit{operatorname{Re}}{form}_t+{varepsilon}_{it} (1).

This analysis was implemented using an in-house Python script that utilizes PHYLIP package command line programs PROTDIST, NEIGHBOR and TREEDIST [ 23].

The complete method and subsequent analysis were implemented using MATLAB software (version R2009b, Mathworks, Natick, MA).

The analysis were implemented using the GLM function in R [ 9].

ML-based analysis were implemented using CODEML of PAML package v4.0b [ 20].

Clustering and PCA analysis were implemented using Partek Genomics Suite version 6.5.

Stepwise multiple regression analysis were implemented using the REG procedure of SAS 9.2 (SAS Institute Inc., Cary, NC), and the resulting models were evaluated for goodness of fit based on standard regression analysis procedures [ 23].

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