[CHNOSZ-commits] r191 - in pkg/CHNOSZ: . inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Apr 29 07:40:55 CEST 2017
Author: jedick
Date: 2017-04-29 07:40:54 +0200 (Sat, 29 Apr 2017)
New Revision: 191
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/vig.bib
Log:
anintro.Rmd: add Sabatini et al., 2012 reference
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-04-28 08:30:51 UTC (rev 190)
+++ pkg/CHNOSZ/DESCRIPTION 2017-04-29 05:40:54 UTC (rev 191)
@@ -1,6 +1,6 @@
-Date: 2017-04-28
+Date: 2017-04-29
Package: CHNOSZ
-Version: 1.0.8-79
+Version: 1.0.8-80
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-04-28 08:30:51 UTC (rev 190)
+++ pkg/CHNOSZ/inst/NEWS 2017-04-29 05:40:54 UTC (rev 191)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-79 (2017-04-28)
+CHANGES IN CHNOSZ 1.0.8-80 (2017-04-29)
---------------------------------------
DOCUMENTATION:
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2017-04-28 08:30:51 UTC (rev 190)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2017-04-29 05:40:54 UTC (rev 191)
@@ -558,7 +558,7 @@
Given values of affinity, the <span style="color:green">`diagram()`</span> function uses the maximum affinity method to make a potential diagram (i.e. a Pourbaix diagram).
Areas corresponding to Eh-pH conditions beyond the stability limits of water are colored slate gray.
-A second function, <span style="color:green">`water.lines()`</span>, is used to draw lines at the water stability limits:
+Another function, <span style="color:green">`water.lines()`</span>, is used to draw lines at the water stability limits:
```{r EhpH_plot, echo=-1, eval=FALSE}
```
@@ -1642,8 +1642,12 @@
</p>
We have calculated the distribution of ATP species and average binding number of H<sup>+</sup> and Mg<sup>+2</sup> for given pH, pMg, ionic strength, and temperature.
-Apparent equilibrium constants tabulated for specified ionic strength make an algebraic solution of the equilibrium distribution of species feasible, as demonstrated by the Mathematica code in Alberty (2003).
-The required calculations can be performed "on the fly" in CHNOSZ by using the `IS` argument in <span style="color:green">`subcrt()`</span> or <span style="color:green">`affinity()`</span> to invoke the nonideality model on top of the standard Gibbs energies of species.
+Accounting for the distribution of chemical species lends itself to thermodynamic models for reactions between reactants that have multiple possibly ionized and bound states.
+In contrast, Alberty (2003) and others propose models for biochemical reactions where the ionized and complexed species are combined into a single representation.
+Those models invoke Legendre-transformed thermodynamic properties, such as transformed Gibbs energies that are tabulated for specified pH, pMg, and ionic strength.
+Although the conceptual pathways are different, the two approaches lead to equivalent results concerning the energetics of the overall reactions and the conditions for equilibrium [@SVI12].
+The example here shows how the required calculations can be performed at the species level using conventional standard Gibbs energies for species referenced to infinite dilution (zero ionic strength).
+The effects of ionic strength are modeled "on the fly" in CHNOSZ by setting the `IS` argument in <span style="color:green">`subcrt()`</span> or <span style="color:green">`affinity()`</span> to invoke the nonideality model on top of the standard Gibbs energies of species.
## Optimization of chemical activities
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2017-04-28 08:30:51 UTC (rev 190)
+++ pkg/CHNOSZ/vignettes/vig.bib 2017-04-29 05:40:54 UTC (rev 191)
@@ -237,14 +237,14 @@
}
@Article{MSS13,
- author = {Manning, Craig E. and Shock, Everett L. and Sverjensky, Dimitri A.},
- journal = {Reviews in Mineralogy and Geochemistry},
- title = {The chemistry of carbon in aqueous fluids at crustal and upper-mantle conditions: {E}xperimental and theoretical constraints},
- year = {2013},
- volume = {75},
- number = {1},
- pages = {109--148},
- doi = {10.2138/rmg.2013.75.5},
+ author = {Manning, Craig E. and Shock, Everett L. and Sverjensky, Dimitri A.},
+ journal = {Reviews in Mineralogy and Geochemistry},
+ title = {{T}he chemistry of carbon in aqueous fluids at crustal and upper-mantle conditions: {E}xperimental and theoretical constraints},
+ year = {2013},
+ volume = {75},
+ number = {1},
+ pages = {109--148},
+ doi = {10.2138/rmg.2013.75.5},
}
@InProceedings{NPW_79,
@@ -530,12 +530,12 @@
url = {http://www.worldcat.org/oclc/18559968},
}
- at Article{Dic17,
- author = {Dick, Jeffrey M.},
- journal = {bioRxiv},
- title = {{C}hemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress},
- year = {2017},
- doi = {10.1101/097667},
+ at Article{Dic17a,
+ author = {Dick, Jeffrey M.},
+ journal = {bioRxiv},
+ title = {{C}hemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress},
+ year = {2017},
+ doi = {10.1101/097667},
}
@Article{HW97,
@@ -638,3 +638,26 @@
number = {UCRL-MA-110662 PT I},
}
+ at Article{Dic17,
+ author = {Dick, Jeffrey M.},
+ journal = {PeerJ},
+ title = {{C}hemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress},
+ year = {2017},
+}
+
+ at Article{SVI12,
+ author = {Sabatini, Antonio and Vacca, Alberto and Iotti, Stefano},
+ journal = {PLoS ONE},
+ title = {{B}alanced biochemical reactions: {A} new approach to unify chemical and biochemical thermodynamics},
+ year = {2012},
+ volume = {7},
+ number = {1},
+ pages = {e29529},
+ doi = {10.1371/journal.pone.0029529},
+ sn = {1932-6203},
+ z8 = {0},
+ z9 = {0},
+ zb = {0},
+ zs = {0},
+}
+
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