[CHNOSZ-commits] r650 - in pkg/CHNOSZ: . R demo inst inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Mar 16 15:29:58 CET 2021
Author: jedick
Date: 2021-03-16 15:29:58 +0100 (Tue, 16 Mar 2021)
New Revision: 650
Added:
pkg/CHNOSZ/demo/E_coli.R
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/demo/00Index
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
pkg/CHNOSZ/man/examples.Rd
Log:
Add demo/E_coli.R and species to OBIGT/organic_aq.csv (LaRowe and Amend, 2016)
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2021-03-14 14:40:10 UTC (rev 649)
+++ pkg/CHNOSZ/DESCRIPTION 2021-03-16 14:29:58 UTC (rev 650)
@@ -1,6 +1,6 @@
-Date: 2021-03-14
+Date: 2021-03-16
Package: CHNOSZ
-Version: 1.4.0-19
+Version: 1.4.0-20
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2021-03-14 14:40:10 UTC (rev 649)
+++ pkg/CHNOSZ/R/examples.R 2021-03-16 14:29:58 UTC (rev 650)
@@ -34,7 +34,7 @@
"ORP", "findit", "ionize", "buffer", "protbuff", "glycinate",
"mosaic", "copper", "arsenic", "solubility", "gold", "contour", "sphalerite", "zinc",
"Shh", "saturation", "adenine", "DEW", "lambda", "potassium", "TCA", "aluminum",
- "AkDi", "comproportionation", "Pourbaix"), save.png=FALSE) {
+ "AkDi", "comproportionation", "Pourbaix", "E_coli"), save.png=FALSE) {
# run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one
for(i in 1:length(which)) {
# say something so the user sees where we are
Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index 2021-03-14 14:40:10 UTC (rev 649)
+++ pkg/CHNOSZ/demo/00Index 2021-03-16 14:29:58 UTC (rev 650)
@@ -30,3 +30,4 @@
AkDi Henry's constant of dissolved gases
comproportionation Gibbs energy of sulfur comproportionation
Pourbaix Eh-pH diagram for Fe-O-H with equisolubility lines
+E_coli Gibbs energy of biomass synthesis in E. coli
Added: pkg/CHNOSZ/demo/E_coli.R
===================================================================
--- pkg/CHNOSZ/demo/E_coli.R (rev 0)
+++ pkg/CHNOSZ/demo/E_coli.R 2021-03-16 14:29:58 UTC (rev 650)
@@ -0,0 +1,138 @@
+# CHNOSZ/demo/E_coli.R
+# Calculate Gibbs energy of biomass synthesis in E. coli
+# 20210316 jmd version 1
+
+# After LaRowe and Amend (2016): https://doi.org/10.1038/ismej.2015.227
+# Polymerization scheme from Amend et al. (2013): https://doi.org/10.1098/rstb.2012.0255
+
+library(CHNOSZ)
+
+# Concentrations of biomolecules (mol (g cell)-1)
+# (from Table 1 of LaRowe and Amend, 2016)
+concentrations <- c(
+ # Amino acids
+ alanine = 5.43e-04, arginine = 2.81e-04, asparagine = 2.29e-04, aspartate = 2.29e-04,
+ cysteine = 8.70e-05, glutamate = 2.78e-04, glutamine = 2.50e-04, glycine = 5.82e-04,
+ histidine = 9.00e-05, isoleucine = 2.76e-04, leucine = 4.28e-04, lysine = 3.26e-04,
+ methionine = 1.46e-04, phenylalanine = 1.76e-04, proline = 2.10e-04, serine = 2.05e-04,
+ threonine = 2.41e-04, tryptophan = 5.40e-05, tyrosine = 1.31e-04, valine = 4.02e-04,
+ # Amines
+ ethanolamine = 1.31e-04, `diaminopimelic acid` = 2.79e-05, putrescine = 3.40e-05, spermidine = 6.88e-06,
+ # Nucleotides
+ `AMP2-` = 1.65E-04, `GMP2-` = 1.26E-04, `CMP2-` = 2.03E-04, `UMP2-` = 1.36E-04,
+ `dAMP2-` = 2.46E-05, `dGMP2-` = 2.54E-05, `dCMP2-` = 2.54E-05, `dTMP2-` = 2.46E-05,
+ # Fatty acids
+ palmitate = 1.12e-04, oleate = 6.22e-05, palmitoleate = 8.56e-05, myristate = 1.67e-05, `beta-hydroxymyristate` = 3.37e-05,
+ # Saccharides and more
+ glycerol = 1.61e-04, glucose = 2.50e-05, heptose = 2.52e-05, galactose = 8.33e-06, rhamnose = 8.53e-06,
+ glucoseamine = 1.67e-05, `N-acetylglucosamine` = 3.62e-05, `N-acetylmuramic acid` = 2.76e-05
+)
+# Keep the names of the biomolecules here
+biomolecules <- names(concentrations)
+
+# Set temperature values
+T <- 0:125
+T.K <- convert(T, "K")
+# Convert Eh to pe for oxidizing and reducing conditions
+pe_ox <- convert(0.858, "pe", T = T.K)
+pe_red <- convert(-0.384, "pe", T = T.K)
+pe <- list(pe_ox, pe_red)
+
+# Parameters for [UPBB] in OBIGT are from Kitadai (2014)
+# (https://doi.org/10.1007/s00239-014-9616-1)
+# This command loads "old" parameters for [UPBB]
+# (Dick et al., 2006; https://doi.org/10.5194/bg-3-311-2006)
+# - increases G.P278 by ca. 35-40% (closer to Figure 5 of Amend et al., 2013)
+add.OBIGT("OldAA")
+
+# Calculate polymerization contribution
+# Standard Gibbs energy (J / mol) for AABB -> PBB + H2O
+# (Figure 4 of Amend et al., 2013)
+E.units("J")
+G0.AABB_to_PBB_plus_H2O <- subcrt(c("[AABB]", "[UPBB]", "H2O"), c(-1, 1, 1), T = T)$out$G
+# Standard Gibbs energy for 278 AA -> P[278] + 277H2O
+G0.P278 <- 277 * G0.AABB_to_PBB_plus_H2O
+# logQ for this reaction (decimal logarithm)
+logQ <- log10(8.7e-6) - 278 * log10(6.5e-3)
+# Gibbs energy for this reaction
+# G = G0 + 2.303*RT*logQ
+# (cf. Figure 5 of Amend et al., 2013)
+G.P278 <- G0.P278 + log(10) * 8.3145 * T.K * logQ
+# Gibbs energy (J / peptide bond)
+G.P278_per_bond <- G.P278 / 277 / 6.02e23
+# Gibbs energy of protein polymerization (J / g cell)
+bonds_per_g_cell <- 2.82e21 # Table 2 of Amend et al., 2013
+Gpoly_protein_per_g_cell <- G.P278_per_bond * bonds_per_g_cell
+# The value calculated at 25 degrees C is equal to that given by Amend et al., 2013
+stopifnot(round(Gpoly_protein_per_g_cell[26]) == 191)
+# Calculate energy for non-protein polymerization (J / g cell)
+Gpoly_nonprotein_per_g_cell <- 45 / 55 * Gpoly_protein_per_g_cell
+Gpoly_per_g_cell <- Gpoly_protein_per_g_cell + Gpoly_nonprotein_per_g_cell
+
+# Function to plot Gibbs energy of biomolecule synthesis
+# for a given combination of C-, N- and S-bearing basis species
+plot_G <- function(C, N, S) {
+
+ # Retrieve logarithm of activity for given basis species
+ # (from Table 2 of LaRowe and Amend, 2016)
+ loga_C <- switch(C, "CO2" = -3, "CH3COO-" = -5, "CH4" = -6)
+ loga_N <- switch(N, "NO3-" = -5, "NH4+" = -6)
+ loga_S <- switch(S, "SO4-2" = -3, "HS-" = -6)
+ # Set basis species
+ # (Note: we set activity of e- in affinity())
+ basis(c(C, N, S, "HPO4-2", "H2O", "H+", "e-"), c(loga_C, loga_N, loga_S, -5, 0, -7, 0))
+ # Load formed species
+ species(biomolecules, -9)
+
+ # Start plot
+ ylab <- quote(list(Delta*italic(G[synth]), kJ*(dry~g~cells)^-1))
+ plot(c(0, 125), c(-15, 30), xlab = axis.label("T"), ylab = ylab, type = "n", xaxs = "i", yaxs = "i")
+ axis(3, labels = FALSE)
+ axis(4, labels = FALSE)
+ # Loop over oxidizing/reducing conditions
+ for(ipe in 1:2) {
+ # Calculate dimensionless affinity (A/2.303RT) from 0 to 125 degC at 1 bar
+ a <- affinity(T = T, `e-` = -pe[[ipe]])
+ # Convert affinity to Gibbs energy (kJ/mol)
+ G.cal <- lapply(a$values, convert, "G", T = T.K)
+ G.J <- lapply(G.cal, convert, "J")
+ G.kJ <- lapply(G.J, "*", 1e-3)
+ # Calculate Gibbs energy (kJ (g cell)-1) for each biomolecule
+ G.kJ.g_cell <- Map("*", G.kJ, concentrations)
+ # Sum Gibbs energy for all biomolecules
+ sum.G.kJ.g_cell <- Reduce("+", G.kJ.g_cell)
+ # Add polymerization contribution
+ total.G.kJ.g_cell <- sum.G.kJ.g_cell + Gpoly_per_g_cell / 1000
+ # Add line to plot
+ # (Note: ipe * 2 = 2 (red) or 4 (blue))
+ lines(T, total.G.kJ.g_cell, col = ipe * 2, lwd = 2)
+ # Add label
+ dy_ox <- 3
+ dy_red <- ifelse(C == "CH4", 3, -3)
+ if(ipe == 1) text(T[25], total.G.kJ.g_cell[25] + dy_ox, "Oxidizing")
+ if(ipe == 2) text(T[25], total.G.kJ.g_cell[25] + dy_red, "Reducing")
+ }
+ # Add legend
+ Cexpr <- expr.species(C)
+ Nexpr <- expr.species(N)
+ Sexpr <- expr.species(S)
+ legend <- bquote(list(.(Cexpr), .(Nexpr), .(Sexpr)))
+ x <- ifelse(C == "CO2", "bottomright", "topright")
+ legend(x, legend = legend, bty = "n")
+
+}
+
+# Make plots with different combinations of basis species
+par(mfrow = c(3, 2))
+par(mar = c(2.5, 3, 1.5, 1), mgp = c(1.5, 0.3, 0))
+par(tcl = 0.25)
+par(cex = 1)
+plot_G("CO2", "NO3-", "SO4-2")
+plot_G("CO2", "NH4+", "HS-")
+plot_G("CH3COO-", "NO3-", "SO4-2")
+plot_G("CH3COO-", "NH4+", "HS-")
+plot_G("CH4", "NO3-", "SO4-2")
+plot_G("CH4", "NH4+", "HS-")
+
+# Reset CHNOSZ settings (units and OBIGT database)
+reset()
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2021-03-14 14:40:10 UTC (rev 649)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2021-03-16 14:29:58 UTC (rev 650)
@@ -10,7 +10,7 @@
\newcommand{\s}{\ifelse{latex}{\eqn{_{#1}}}{\ifelse{html}{\out{<sub>#1</sub>}}{#1}}}
\newcommand{\S}{\ifelse{latex}{\eqn{^{#1}}}{\ifelse{html}{\out{<sup>#1</sup>}}{^#1}}}
-\section{Changes in CHNOSZ version 1.4.0-19 (2021-03-08)}{
+\section{Changes in CHNOSZ version 1.4.0-20 (2021-03-16)}{
\subsection{NEW FEATURES}{
\itemize{
@@ -61,6 +61,11 @@
\href{https://www.uniprot.org/uniprot/P06493}{P06493}) in
thermo/protein.csv.
+ \item Add properties of some aqueous species to
+ \samp{OBIGT/organic_aq.csv} and associated \samp{demo/E_coli.R} (Gibbs
+ energy of biomass synthesis in E. coli, after
+ \href{https://doi.org/10.1038/ismej.2015.227}{LaRowe and Amend, 2016}).
+
}
}
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv 2021-03-14 14:40:10 UTC (rev 649)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv 2021-03-16 14:29:58 UTC (rev 650)
@@ -197,7 +197,7 @@
"azelaic acid",NA,C9H16O4,aq,Sho95,NA,1992-06-16,cal,-163660,-240700,101.6,143.8,161.8,23.9348,47.5253,-6.2031,-4.7436,125.8045,9.2464,0.0862,0
"sebacic acid",NA,C10H18O4,aq,Sho95,NA,1992-06-16,cal,-161240,-246000,108.3,165,177.6,26.1119,52.4558,-7.3146,-4.9474,143.1573,11.341,0.1306,0
formate,NA,HCO2-,aq,Sho95,NA,1992-02-28,cal,-83862,-101680,21.7,-22,26.16,5.7842,4.7242,7.363,-2.9742,17,-12.4,1.3003,-1
-acetate,NA,C2H3O2-,aq,Sho95,NA,1992-02-28,cal,-88270,-116160,20.6,6.2,40.5,7.7525,8.6996,7.5825,-3.1385,26.3,-3.86,1.3182,-1
+acetate,CH3COO-,C2H3O2-,aq,Sho95,NA,1992-02-28,cal,-88270,-116160,20.6,6.2,40.5,7.7525,8.6996,7.5825,-3.1385,26.3,-3.86,1.3182,-1
propanoate,NA,C3H5O2-,aq,Sho95,NA,1992-02-28,cal,-86780,-122630,26.5,30.9,54.95,9.6992,12.1344,9.0612,-3.2805,52.3,-4.2,1.2276,-1
n-butanoate,NA,C4H7O2-,aq,Sho95,NA,1992-06-17,cal,-84650,-128630,31.8,44.5,70.3,11.7724,17.0492,7.4458,-3.4837,62.3135,-3.5666,1.1469,-1
n-pentanoate,NA,C5H9O2-,aq,Sho95,NA,1992-06-17,cal,-82630,-134380,38.3,70.3,86.31,13.9304,24.8456,-1.0403,-3.806,86.5816,-3.2539,1.0496,-1
@@ -680,3 +680,18 @@
phloroglucinol,NA,C6H6O3,aq,LA19,NA,2019-05-30,J,-421100,-558200,274.1,193.1,93.33,61.16,151,-108.6,-17.87,245.7,-21.74,0.9125,0
"cyclohexane carboxylate",NA,C7H11O2-,aq,LA19,NA,2019-05-30,J,-299800,-562900,146.8,292.7,110.1,170.96,12.91,-471.5,8.765,328,5.707,5.142,-1
"cyclohexane carboxylic acid",NA,C7H12O2,aq,LA19,NA,2019-05-30,J,-323700,-563300,225.9,449.4,122.2,175.86,24.31,-474.8,8.294,372.8,36.31,-0.3117,0
+palmitate,NA,C16H31O2-,aq,LA16,NA,2021-03-16,J,-241200,-821500,441,NA,NA,230.4,183.5,166,-106.8,1089,107.5,5.1,-1
+oleate,NA,C18H35O2-,aq,LA16,NA,2021-03-16,J,-140300,-740000,517.9,NA,NA,211.8,295.3,35.2,-81.3,1008,202.1,1.1,-1
+palmitoleate,NA,C16H29O2-,aq,LA16,NA,2021-03-16,J,-159000,-950400,415,NA,NA,278.3,89.6,322.6,-146.6,1304,32.2,9.2,-1
+myristate,NA,C14H27O2-,aq,LA16,NA,2021-03-16,J,-260000,-774000,390.2,NA,NA,201.2,165.5,140.1,-92.6,955,88.3,5.1,-1
+β-hydroxymyristate,beta-hydroxymyristate,C14H27O3-,aq,LA16,NA,2021-03-16,J,-409200,-945500,418.3,NA,NA,201.4,165.9,140,-92.6,970,88.5,4.7,-1
+glycerol,NA,C3H8O3,aq,LA16,NA,2021-03-16,J,-502700,-684400,238.5,NA,NA,64.9,26.4,34.4,-20.7,264,13,-0.4,0
+heptose,NA,C7H14O7,aq,LA16,NA,2021-03-16,J,-1238400,-1698300,382.1,NA,NA,147.6,10.6,41.6,-23.2,488,-8.2,-4.9,0
+rhamnose,NA,C6H12O5,aq,LA16,NA,2021-03-16,J,-751300,-1076700,238.9,NA,NA,108.8,32.8,47.8,-27.2,508,-49.4,0.8,0
+glucoseamine,NA,C6H13NO5,aq,LA16,NA,2021-03-16,J,-712700,-1076600,271,NA,NA,108.8,33.3,71,-30.3,484,-67.8,0.3,0
+N-acetylglucosamine,NA,C8H15NO6,aq,LA16,NA,2021-03-16,J,-918200,-1329000,358.2,NA,NA,144.1,40.5,36.1,-33.7,570,-58.6,0.8,0
+"N-acetylmuramic acid",NA,C11H17NO8,aq,LA16,NA,2021-03-16,J,-1272400,-1789500,485.4,NA,NA,185.8,57.1,64.7,-48,685,-55.7,0.3,0
+ethanolamine,NA,C2H7NO,aq,LA16,NA,2021-03-16,J,-138300,-281000,173.2,NA,NA,47.7,26.4,52.4,-18.3,218,-6.7,-1,0
+"diaminopimelic acid",NA,C7H14N2O4,aq,LA16,NA,2021-03-16,J,-673500,-925900,347.2,NA,NA,59.7,145.2,-10.5,-13.3,215,-6.6,-0.4,0
+putrescine,NA,C4H12N2,aq,LA16,NA,2021-03-16,J,48200,-99500,140.5,NA,NA,52.4,33.5,65.6,-25.4,242,8.8,-0.8,0
+spermidine,NA,C7H19N3,aq,LA16,NA,2021-03-16,J,114900,-170500,248.7,NA,NA,96.2,61,127.5,-49.8,420,19.2,-1.4,0
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2021-03-14 14:40:10 UTC (rev 649)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2021-03-16 14:29:58 UTC (rev 650)
@@ -117,6 +117,10 @@
"OBIGT",853,"Zn(CO3)2-2","aq","cal",,,-4724
"OBIGT",854,"Cu(CO3)2-2","aq","cal",,,-4929
"OBIGT",855,"Pb(CO3)2-2","aq","cal",,,-6676
+"OBIGT",857,"KCO3-","aq","cal",,,4996
+"OBIGT",859,"RbCO3-","aq","cal",,,-533
+"OBIGT",862,"MnHCO3+","aq","cal",,,945
+"OBIGT",870,"KHCO3","aq","cal",,,3759
"OBIGT",872,"CH4","aq","cal",-2.61,,
"OBIGT",877,"hexane","aq","cal",1.43,3.21,
"OBIGT",880,"ethylene","aq","cal",6.12,-3.82,
@@ -229,51 +233,59 @@
"OBIGT",1522,"n-butanethiol","aq","cal",2.19,,
"OBIGT",1544,"methyldiethanolamine","aq","cal",1.61,,
"OBIGT",1547,"dimethylamine","aq","J",-8.05,,
-"OBIGT",1561,"cysteinate","aq","cal",-1,,
-"OBIGT",1587,"glucose","aq","cal",1.11,,
-"OBIGT",1615,"guanine","aq","cal",-4.26,,
-"OBIGT",1659,"dHUMP-","aq","cal",-3.13,,
-"OBIGT",1756,"MgADP-","aq","cal",-1.01,,
-"OBIGT",1767,"HNicMP(ox)","aq","cal",,9.4,
-"OBIGT",1775,"ribose-5-phosphate","aq","cal",,7.48,
-"OBIGT",1777,"ribose-5-phosphate-2","aq","cal",1.53,,
-"OBIGT",1778,"H4NADP(red)","aq","cal",1.73,,
-"OBIGT",1779,"H3NADP(red)-","aq","cal",2.41,,
-"OBIGT",1780,"H2NADP(red)-2","aq","cal",1.28,,
-"OBIGT",1781,"HNADP(red)-3","aq","cal",2.09,,
-"OBIGT",1782,"NADP(red)-4","aq","cal",1.09,,
-"OBIGT",1784,"H3NADP(ox)","aq","cal",1.05,,
-"OBIGT",1855,"diglycine+","aq","cal",-177.69,,
-"OBIGT",1856,"diglycine-","aq","cal",-49.22,,565
-"OBIGT",1857,"triglycine+","aq","cal",,1.75,
-"OBIGT",1858,"triglycine-","aq","cal",,1.78,
-"OBIGT",1917,"hydromagnesite","cr","cal",,,-2569
-"OBIGT",1994,"jarosite","cr","cal",,,20697
-"OBIGT",1995,"natrojarosite","cr","cal",,,17554
-"OBIGT",2003,"realgar,alpha","cr","J",,,768
-"OBIGT",2004,"realgar,beta","cr","J",,,989
-"OBIGT",2005,"orpiment","cr","J",,,-1036
-"OBIGT",2013,"dawsonite","cr","J",,,19466
-"OBIGT",2015,"ferberite","cr","J",1.21,,
-"OBIGT",2028,"Co-pentlandite","cr","cal",,,-3630
-"OBIGT",2049,"octadecane","cr","cal",-2.63,,
-"OBIGT",2050,"nonadecane","cr","cal",-13.32,,
-"OBIGT",2051,"eicosane","cr","cal",-2.79,,
-"OBIGT",2052,"heneicosane","cr","cal",-8.61,,
-"OBIGT",2053,"docosane","cr","cal",-2.63,,
-"OBIGT",2054,"tricosane","cr","cal",-5.22,,
-"OBIGT",2055,"tetracosane","cr","cal",-2.02,,
-"OBIGT",2056,"pentacosane","cr","cal",-2.93,,
-"OBIGT",2057,"hexacosane","cr","cal",-1.29,,
-"OBIGT",2058,"heptacosane","cr","cal",-1.23,,
-"OBIGT",2110,"carbazole","cr","cal",-43.39,,
-"OBIGT",2151,"triphenylene","cr","cal",,,541
-"OBIGT",2464,"deoxyadenosine","cr","cal",,,-2977
-"OBIGT",2622,"ethylene","gas","cal",-4.59,,
-"OBIGT",2632,"3,5-dimethylphenol","gas","cal",,,628
-"OBIGT",2942,"nonacontane","liq","cal",,,635
-"OBIGT",2949,"2-methyloctane","liq","cal",10,,
-"OBIGT",3362,"5,6-dithiadecane","liq","cal",2,,
+"OBIGT",1554,"oleate","aq","J",,,39179
+"OBIGT",1555,"palmitoleate","aq","J",,,-242150
+"OBIGT",1559,"heptose","aq","J",,,-75027
+"OBIGT",1563,"N-acetylmuramic acid","aq","J",,,-38589
+"OBIGT",1564,"ethanolamine","aq","J",,,4598
+"OBIGT",1565,"diaminopimelic acid","aq","J",,,108258
+"OBIGT",1566,"putrescine","aq","J",,,108157
+"OBIGT",1567,"spermidine","aq","J",,,108263
+"OBIGT",1576,"cysteinate","aq","cal",-1,,
+"OBIGT",1602,"glucose","aq","cal",1.11,,
+"OBIGT",1630,"guanine","aq","cal",-4.26,,
+"OBIGT",1674,"dHUMP-","aq","cal",-3.13,,
+"OBIGT",1771,"MgADP-","aq","cal",-1.01,,
+"OBIGT",1782,"HNicMP(ox)","aq","cal",,9.4,
+"OBIGT",1790,"ribose-5-phosphate","aq","cal",,7.48,
+"OBIGT",1792,"ribose-5-phosphate-2","aq","cal",1.53,,
+"OBIGT",1793,"H4NADP(red)","aq","cal",1.73,,
+"OBIGT",1794,"H3NADP(red)-","aq","cal",2.41,,
+"OBIGT",1795,"H2NADP(red)-2","aq","cal",1.28,,
+"OBIGT",1796,"HNADP(red)-3","aq","cal",2.09,,
+"OBIGT",1797,"NADP(red)-4","aq","cal",1.09,,
+"OBIGT",1799,"H3NADP(ox)","aq","cal",1.05,,
+"OBIGT",1870,"diglycine+","aq","cal",-177.69,,
+"OBIGT",1871,"diglycine-","aq","cal",-49.22,,565
+"OBIGT",1872,"triglycine+","aq","cal",,1.75,
+"OBIGT",1873,"triglycine-","aq","cal",,1.78,
+"OBIGT",1932,"hydromagnesite","cr","cal",,,-2569
+"OBIGT",2009,"jarosite","cr","cal",,,20697
+"OBIGT",2010,"natrojarosite","cr","cal",,,17554
+"OBIGT",2018,"realgar,alpha","cr","J",,,768
+"OBIGT",2019,"realgar,beta","cr","J",,,989
+"OBIGT",2020,"orpiment","cr","J",,,-1036
+"OBIGT",2028,"dawsonite","cr","J",,,19466
+"OBIGT",2030,"ferberite","cr","J",1.21,,
+"OBIGT",2043,"Co-pentlandite","cr","cal",,,-3630
+"OBIGT",2064,"octadecane","cr","cal",-2.63,,
+"OBIGT",2065,"nonadecane","cr","cal",-13.32,,
+"OBIGT",2066,"eicosane","cr","cal",-2.79,,
+"OBIGT",2067,"heneicosane","cr","cal",-8.61,,
+"OBIGT",2068,"docosane","cr","cal",-2.63,,
+"OBIGT",2069,"tricosane","cr","cal",-5.22,,
+"OBIGT",2070,"tetracosane","cr","cal",-2.02,,
+"OBIGT",2071,"pentacosane","cr","cal",-2.93,,
+"OBIGT",2072,"hexacosane","cr","cal",-1.29,,
+"OBIGT",2073,"heptacosane","cr","cal",-1.23,,
+"OBIGT",2125,"carbazole","cr","cal",-43.39,,
+"OBIGT",2166,"triphenylene","cr","cal",,,541
+"OBIGT",2479,"deoxyadenosine","cr","cal",,,-2977
+"OBIGT",2637,"ethylene","gas","cal",-4.59,,
+"OBIGT",2647,"3,5-dimethylphenol","gas","cal",,,628
+"OBIGT",2957,"nonacontane","liq","cal",,,635
+"OBIGT",2964,"2-methyloctane","liq","cal",10,,
+"OBIGT",3377,"5,6-dithiadecane","liq","cal",2,,
"DEW",8,"AlO2(SiO2)-","aq","cal",,,-897
"DEW",17,"BO(OH)","aq","cal",,,-1111
"DEW",19,"Ca(HCO3)+","aq","cal",,,-2971
Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2021-03-14 14:40:10 UTC (rev 649)
+++ pkg/CHNOSZ/man/examples.Rd 2021-03-16 14:29:58 UTC (rev 650)
@@ -18,7 +18,7 @@
"glycinate", "mosaic", "copper", "arsenic", "solubility", "gold",
"contour", "sphalerite", "zinc", "Shh", "saturation",
"adenine", "DEW", "lambda", "potassium", "TCA", "aluminum", "AkDi",
- "comproportionation", "Pourbaix"),
+ "comproportionation", "Pourbaix", "E_coli"),
save.png=FALSE)
}
@@ -63,6 +63,7 @@
\code{AkDi} \tab Henry's constant of dissolved gases (Akinfiev and Diamond, 2003) \cr
\code{comproportionation} \tab Gibbs energy of sulfur comproportionation (Amend et al., 2020) \cr
\code{Pourbaix} \tab Eh-pH diagram for Fe-O-H with equisolubility lines (Pourbaix, 1974) \cr
+ \code{E_coli} \tab Gibbs energy of biomass synthesis in \emph{E. coli} (LaRowe and Amend, 2016) \cr
}
For either function, if \code{save.png} is TRUE, the plots are saved in \code{\link{png}} files whose names begin with the names of the help topics or demos.
@@ -98,7 +99,7 @@
Amend, J. P. and Shock, E. L. (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. \emph{FEMS Microbiol. Rev.} \bold{25}, 175--243. \url{https://doi.org/10.1016/S0168-6445(00)00062-0}
-Amend, J. P., Aronson, H. S., Macalady, J. and LaRowe, D. E. (2020) Another chemolithotrophic metabolism missing in nature: sulfur comproportionation. \emph{Environ. Microbiol.} \url{https://doi.org/10.1111/1462-2920.14982}
+Amend, J. P., Aronson, H. S., Macalady, J. and LaRowe, D. E. (2020) Another chemolithotrophic metabolism missing in nature: sulfur comproportionation. \emph{Environ. Microbiol.} \bold{22}, 1971--1976. \url{https://doi.org/10.1111/1462-2920.14982}
Azadi, M. R., Karrech, A., Attar, M. and Elchalakani, M. (2019) Data analysis and estimation of thermodynamic properties of aqueous monovalent metal-glycinate complexes. \emph{Fluid Phase Equilib.} \bold{480}, 25-40. \url{https://doi.org/10.1016/j.fluid.2018.10.002}
@@ -116,6 +117,8 @@
Johnson, J. W., Oelkers, E. H. and Helgeson, H. C. (1992) SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000\degC. \emph{Comp. Geosci.} \bold{18}, 899--947. \url{https://doi.org/10.1016/0098-3004(92)90029-Q}
+LaRowe, D. E. and Amend, J. P. (2016) The energetics of anabolism in natural settings. \emph{ISME J.} \bold{10}, 1285--1295. \url{https://doi.org/10.1038/ismej.2015.227}
+
Lowe, A. R., Cox, J. S. and Tremaine, P. R. (2017) Thermodynamics of aqueous adenine: Standard partial molar volumes and heat capacities of adenine, adeninium chloride, and sodium adeninate from \emph{T} = 278.15 K to 393.15 K. \emph{J. Chem. Thermodyn.} \bold{112}, 129--145. \url{https://doi.org/10.1016/j.jct.2017.04.005}
Lu, P. and Zhu, C. (2011) Arsenic Eh--pH diagrams at 25\degC and 1 bar. \emph{Environ. Earth Sci.} \bold{62}, 1673--1683. \url{https://doi.org/10.1007/s12665-010-0652-x}
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