examples: Run Examples from the Documentation

Description Usage Arguments Details References Examples

View source: R/examples.R

Description

Run the examples contained in each of the documentation topics.

Usage

1
2
3
4
5
6
7
  examples(save.png = FALSE)
  demos(which = c("sources", "protein.equil", "affinity", "NaCl",
    "density", "ORP", "revisit", "findit", "ionize", "buffer",
    "protbuff", "yeastgfp", "mosaic", "copper", "solubility",
    "wjd", "bugstab", "Shh", "activity_ratios", "adenine",
    "DEW", "lambda", "TCA", "go-IU"),
    save.png=FALSE)

Arguments

save.png

logical, generate PNG image files for the plots?

which

character, which example to run

Details

examples runs all the examples in the documentation for the package. example is called for each topic with ask set to FALSE (so all of the figures are shown without prompting the user).

demos runs all the demos in the package. The demo(s) to run is/are specified by which; the default is to run them in the order of the list below. (Demos that are displayed on the CHNOSZ website (http://chnosz.net/demos) are indicated with an asterisk.)

sources Cross-check the reference list with the thermodynamic database
protein.equil Chemical activities of two proteins in metastable equilibrium (Dick and Shock, 2011)
affinity Affinities of metabolic reactions and amino acid synthesis (Amend and Shock, 1998, 2001)
NaCl * Equilibrium constant for aqueous NaCl dissociation (Shock et al., 1992)
density * Density of \H2O, inverted from IAPWS-95 equations (rho.IAPWS95)
ORP * Temperature dependence of oxidation-reduction potential for redox standards
revisit Coefficient of variation of metastable equilibrium activities of proteins
findit Minimize the standard deviation of logarithms of activities of sulfur species
ionize ionize.aa(): contour plots of net charge and ionization properties of LYSC_CHICK
buffer * Minerals and aqueous species as buffers of hydrogen fugacity (Schulte and Shock, 1995)
protbuff Chemical activities buffered by thiol peroxidases or sigma factors
yeastgfp * Subcellular locations: \logfO2 - \logaH2O and \loga - \logfO2 diagrams (Dick, 2009)
mosaic * Eh-pH diagram with two sets of changing basis species (Garrels and Christ, 1965)
copper * Another example of mosaic: complexation of Cu with glycine (Aksu and Doyle, 2001)
solubility * Solubility of calcite (cf. Manning et al., 2013) or \CO2 (cf. Stumm and Morgan, 1996)
wjd * G minimization: prebiological atmospheres (Dayhoff et al., 1964) and cell periphery of yeast
dehydration * \logK of dehydration reactions; SVG file contains tooltips and links
bugstab * Formation potential of microbial proteins in colorectal cancer (Dick, 2016)
Shh * Affinities of transcription factors relative to Sonic hedgehog (Dick, 2015)
activity_ratios * Mineral stability plots with activity ratios on the axes
adenine * HKF regression of heat capacity and volume of aqueous adenine (Lowe et al., 2017)
DEW * Deep Earth Water (DEW) model for high pressures (Sverjensky et al., 2014a and 2014b)
lambda * Effects of lambda transition on thermodynamic properties of quartz (Berman, 1988)
TCA * Standard Gibbs energies of the tricarboxylic (citric) acid cycle (Canovas and Shock, 2016)
go-IU * Diagrams using thermodynamic data in the SUPCRTBL compilation (Zimmer et al., 2016)
carboxylase * Rank abundance distribution for RuBisCO and acetyl-CoA carboxylase

For either function, if save.png is TRUE, the plots are saved in png files whose names begin with the names of the help topics or demos.

Two of the demos have external dependencies and are not automatically run by demos. dehydration creates an interactive SVG file; this demo depends on RSVGTipsDevice, which is not available for Windows. carboxylase creates an animated GIF; this demo requires that the ImageMagick convert commmand be available on the system (tested on Linux and Windows).

carboxylase animates diagrams showing rankings of calculated chemical activities along a combined \T and \logaH2 gradient, or makes a single plot on the default device (without conversion to animated GIF) if a single temperature (T) is specified in the code. To run this demo, an empty directory named png must be present (as a subdirectory of the R working directory). The proteins in the calculation are 24 carboxylases from a variety of organisms. There are 12 ribulose phosphate carboxylase and 12 acetyl-coenzyme A carboxylase; 6 of each type are from nominally mesophilic organisms and 6 from nominally thermophilic organisms, shown as blue and red symbols on the diagrams. The activities of hydrogen at each temperature are calculated using logaH2 = -11 + 3/40 * T(degC); this equation comes from a model of relative stabilities of proteins in a hot-spring environment (Dick and Shock, 2011).

In the NaCl demo, the \logK lines calculated at \Psat and P=500 bar show discontinuities at 355 \degC. Although not realistic, this behavior is consistent with the output of SUPCRT92 (Johnson et al., 1992) at 500 bar. This is probably due to a transition between different regimes for the properties of water as coded in SUPCRT's H2O92D.F, which is used by CHNOSZ. (Note that SUPCRT does not output thermodynamic properties above 350 \degC at \Psat; see Warning in subcrt.)

References

Aksu, S. and Doyle, F. M. (2001) Electrochemistry of copper in aqueous glycine solutions. J. Electrochem. Soc. 148, B51–B57. https://doi.org/10.1149/1.1344532

Amend, J. P. and Shock, E. L. (1998) Energetics of amino acid synthesis in hydrothermal ecosystems. Science 281, 1659–1662. https://doi.org/10.1126/science.281.5383.1659

Amend, J. P. and Shock, E. L. (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiol. Rev. 25, 175–243. https://doi.org/10.1016/S0168-6445(00)00062-0

Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na\s2O-K\s2O-CaO-MgO-FeO-Fe\s2O\s3-Al\s2O\s3-SiO\s2-TiO\s2-H\s2O-CO\s2. J. Petrol. 29, 445-522. https://doi.org/10.1093/petrology/29.2.445

Canovas, P. A., III and Shock, E. L. (2016) Geobiochemistry of metabolism: Standard state thermodynamic properties of the citric acid cycle. Geochim. Cosmochim. Acta 195, 293–322. https://doi.org/10.1016/j.gca.2016.08.028

Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V. (1964) Thermodynamic Equilibria In Prebiological Atmospheres. Science 146, 1461–1464. https://doi.org/10.1126/science.146.3650.1461

Dick, J. M. (2009) Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae. BMC Syst. Biol. 3:75. https://doi.org/10.1186/1752-0509-3-75

Dick, J. M. and Shock, E. L. (2011) Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. PLoS ONE 6, e22782. https://doi.org/10.1371/journal.pone.0022782

Dick, J. M. (2015) Chemical integration of proteins in signaling and development. bioRxiv. https://doi.org/10.1101/015826

Dick, J. M. (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. PeerJ 4:e2238. https://doi.org/10.7717/peerj.2238

Garrels, R. M. and Christ, C. L. (1965) Solutions, Minerals, and Equilibria, Harper & Row, New York, 450 p. http://www.worldcat.org/oclc/517586

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. Comp. Geosci. 18, 899–947. https://doi.org/10.1016/0098-3004(92)90029-Q

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 T = 278.15 K to 393.15 K. J. Chem. Thermodyn. 112, 129–145. https://doi.org/10.1016/j.jct.2017.04.005

Manning, C. E., Shock, E. L. and Sverjensky, D. A. (2013) The chemistry of carbon in aqueous fluids at crustal and upper-mantle conditions: Experimental and theoretical constraints. Rev. Mineral. Geochem. 75, 109–148. https://doi.org/10.2138/rmg.2013.75.5

Schulte, M. D. and Shock, E. L. (1995) Thermodynamics of Strecker synthesis in hydrothermal systems. Orig. Life Evol. Biosph. 25, 161–173. https://doi.org/10.1007/BF01581580

Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C. (1992) Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures: Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 \degC and 5 kbar. J. Chem. Soc. Faraday Trans. 88, 803–826. https://doi.org/10.1039/FT9928800803

Stumm, W. and Morgan, J. J. (1996) Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters, John Wiley & Sons, New York, 1040 p. http://www.worldcat.org/oclc/31754493

Sverjensky, D. A., Harrison, B. and Azzolini, D. (2014a) Water in the deep Earth: The dielectric constant and the solubilities of quartz and corundum to 60 kb and 1,200 \degC. Geochim. Cosmochim. Acta 129, 125–145. https://doi.org/10.1016/j.gca.2013.12.019

Sverjensky, D. A., Stagno, V. and Huang, F. (2014b) Important role for organic carbon in subduction-zone fluids in the deep carbon cycle. Nat. Geosci. 7, 909–913. https://doi.org/10.1038/ngeo2291

Zimmer, K., Zhang, Y., Lu, P., Chen, Y., Zhang, G., Dalkilic, M. and Zhu, C. (2016) SUPCRTBL: A revised and extended thermodynamic dataset and software package of SUPCRT92. Comp. Geosci. 90, 97–111. https://doi.org/10.1016/j.cageo.2016.02.013

Examples

1
demos(c("ORP", "NaCl"))

CHNOSZ documentation built on Nov. 17, 2017, 2:30 p.m.