Page 204 - Thermodynamics of Biochemical Reactions

204 Mathematica Solutions to Problems

1iStfnpHi.S = (acetaldehyde, acetate, acetone, acetylcoA, acetylphos, aconitatecis, adenine,
adenosine, adp, alanine, ammonia, amp, arabinose, asparaginel, aspartate, atp, bpg.
butanoln, butyrate, citrate, citrateiso, COA, collglutathione, c02g, coatot, coag,
cog, creatine, creatinine, cysteinel, cystinel, cytochromecox, cytochramecred,
dihydroxyacetonephos, ethanol, ethylacetate, fadox, fadred, fadenzox, fadenzred.
ferredoxinox, ferredoxinred, fmnox, fmnred, formate, fructose, fructose6phos.
fructosel6phos, fumarate, galactose, galactoselphos, glucose, glucoselphos,
glucose6phos, glutamate, glutamine, glutathioneox, glutathionered, glyceraldehydephos,
glycerol, glycerol3phos, glycine, glycolate, glycylglycine, glyoxylate, h2ag,
h2g, h20, h202aq, hydroxypropionateb, hypoxanthine, indole, ketoglutarate, lactate,
lactose, leucineisol, leucinel, lyxose, malate, maltose, mannitolD, mannose,
methaneaq, methaneg, methanol, methioninel, methylamineion, n2ag, nZg, nadox,
nadred, nadpox, nadpred, 02agr 02g, oxalate, oxaloacetate, oxalosuccinate, palmitate,
pep, pg2, pg3, phenylalaninel, pi, pgi, propanola, propanoh, pyruvate, retinal,
retinol, ribose, riboselphos, ribose5pho6, ribulose, serinel, sorbose, succinate,
succinylcoll, sucrose, thioredoxinox, thioredoxinred, tryptophanel, tyrosinel,
ubiquinoneox, ubiquinonered, urate, urea, uricacid, valinel, xylose, xylulose};
The following is a list of names of the entries in the basic thermodynamic data on species making up a reactant.

listspeciesdata = {acetaldehydesp, acetatesp, acetonesp, acetylcollsp, acetylphossp,
aconitatecissp, adeninesp, adenosinesp, adpsp, alaninesp, ammoniasp, ampsp,
arabinosesp, asparaginelsp, aspartatesp, atpsg, bpgsp, butanolnsp, butyratesp,
citratesp, citrateisosp, coAsp, collglutathionesp, coagsp, co2totsg, coaqsp,
cogsp, creatinesp, creatininesp, cysteinelsp, cystinelsg, cytochromecoxsp,
cytochramecredsp, dihydroxyacetonephossp, ethanolsp, ethylacetatesp, fadoxsp,
fadredsp, fadenzoxsp, fadenzredsp, ferredoxinoxsp, ferredoxinredsp, fmnoxsp,
fmnredsp, formatesp, fructosesp, fructose6phossp, fructosel6phossp, fumaratesp,
galactosesp, galactoselphossp, glucosesp, glucoselphossp, glucose6phossp,
glutamatesp, glutaminesp, glutathioneoxsg, glutathioneredsp, glyceraldehydephossp,
glycerolsp, glycerol3phossp, glycinesp, glycolatesp, glycylglycinesp, glyoxylatesp,
haaqsp, hagsp, h2osp, h202aqsp, hydroxypropionatebsp, hypoxanthinesp, indolesp,
ketoglutaratesp, lactatesp, lactosesp, leucineisolsp, leucinelsp, lyxosesp,
malatesp,maltosesp, mannitolDsp, ma~osesp,methaneagsp, methanegsp, methanolsp,
methioninelsp, methylamineionsp, naagsp, n2gsp, nadoxsp, nadredsp, nadpoxsp,
nadpredsp, olagsp, 02gsp, oxalatesp, oxaloacetatesp, oxalosuccinatesp, palmitatesp,
pepsp, pgasp, gg3sp, phenylalaninelsp, pisp, ppisp, propanol2sp, propanolnsp,
pyruvatesp, retinalsp, retinolsp, ribosesp. riboselphossp, ribose5phossp.
ribulosesp, serinelsp, sorbosesp, succinatesp, succinylcollsp, sucrosesp,
thioredoxinoxsp, thioredoxinredsp, tryptophanelsp, tyrosinelsp, ubiquinoneoxsp,
ubiguinoneredsp, uratesp, ureasp, uricacidsp, valinelsp, xylosesp, xylulosesp};

Now Map is used to apply calcdGmat to each of the matrices of species data.