extdata: Extra Data

Description Details References

Description

The files in the subdirectories of extdata provide additional thermodynamic data and other data to support the examples in the package documentation and vignettes. See thermo for a description of the files in extdata/OBIGT, which are used to generate the thermodynamic database.

Details

Files in Berman contain thermodynamic data for minerals using the Berman formulation:

Files in abundance contain protein abundance and microbial occurrence data:

Files in bison contain BLAST results and taxonomic information for an environmental metagenome from the Bison Pool hot spring in Yellowstone National Park:

Files in cpetc contain experimental and calculated thermodynamic and environmental data:

Files in fasta contain protein sequences:

Files in protein contain amino acid compositions for proteins.

Files in refseq contain code and results of processing NCBI Reference Sequences (RefSeq) for microbial proteins, using RefSeq release 61 of 2013-09-09:

Files in supcrt contain scripts for reading and comparing SUPCRT files (including slop98.dat and newer slop files from GEOPIG (http://geopig.asu.edu)) with the database in CHNOSZ:

Files in taxonomy contain taxonomic data files:

Files in adds contain additional thermodynamic data and group additivity definitions:

References

Akinfiev, N. N. and Diamond, L. W. (2003) Thermodynamic description of aqueous nonelectrolytes at infinite dilution over a wide range of state parameters. Geochim. Cosmochim. Acta 67, 613–629. https://doi.org/10.1016/S0016-7037(02)01141-9

Amend, J. P. and Helgeson, H. C. (1997) Calculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures. Part 1. L-\alpha-amino acids. J. Chem. Soc., Faraday Trans. 93, 1927–1941. https://doi.org/10.1039/A608126F

Bazarkina, E. F., Zotov, A. V. and Akinfiev, N. N. (2010) Pressure-dependent stability of cadmium chloride complexes: Potentiometric measurements at 1–1000 bar and 25°C. Geol. Ore Deposits 52, 167–178. https://doi.org/10.1134/S1075701510020054

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

Berman, R. G. and Aranovich, L. Ya. (1996) Optimized standard state and solution properties of minerals. I. Model calibration for olivine, orthopyroxene, cordierite, garnet, and ilmenite in the system FeO-MgO-CaO-Al\s2O\s3-TiO\s2-SiO\s2. Contrib. Mineral. Petrol. 126, 1-24. https://doi.org/10.1007/s004100050233

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

Dayhoff, M. O. and Lippincott, E. R., Eck, R. V. and Nagarajan (1967) Thermodynamic Equilibrium In Prebiological Atmospheres of C, H, O, N, P, S, and Cl. Report SP-3040, National Aeronautics and Space Administration.

Dick, J. M. (2014) Average oxidation state of carbon in proteins. J. R. Soc. Interface 11, 20131095. https://doi.org/10.1098/rsif.2013.1095

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

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. and Shock, E. L. (2013) A metastable equilibrium model for the relative abundance of microbial phyla in a hot spring. PLoS ONE 8, e72395. https://doi.org/10.1371/journal.pone.0072395

Gattiker, A., Michoud, K., Rivoire, C., Auchincloss, A. H., Coudert, E., Lima, T., Kersey, P., Pagni, M., Sigrist, C. J. A., Lachaize, C., Veuthey, A.-L., Gasteiger, E. and Bairoch, A. (2003) Automatic annotation of microbial proteomes in Swiss-Prot. Comput. Biol. Chem. 27, 49–58. https://doi.org/10.1016/S1476-9271(02)00094-4

Gaucher, E. A., Thomson, J. M., Burgan, M. F. and Benner, S. A (2003) Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425(6955), 285–288. https://doi.org/10.1038/nature01977

Ghaemmaghami, S., Huh, W., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K. and Weissman, J. S. (2003) Global analysis of protein expression in yeast. Nature 425(6959), 737–741. https://doi.org/10.1038/nature02046

Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S. and O'Shea, E. K. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959), 686–691. https://doi.org/10.1038/nature02026

Hnědkovský, L., Wood, R. H. and Majer, V. (1996) Volumes of aqueous solutions of \CH4, \CO2, \H2S, and \NH3 at temperatures from 298.15 K to 705 K and pressures to 35 MPa. J. Chem. Thermodyn. 28, 125–142. https://doi.org/10.1006/jcht.1996.0011

Hnědkovský, L. and Wood, R. H. (1997) Apparent molar heat capacities of aqueous solutions of \CH4, \CO2, \H2S, and \NH3 at temperatures from 304 K to 704 K at a pressure of 28 MPa. J. Chem. Thermodyn. 29, 731–747. https://doi.org/10.1006/jcht.1997.0192

Joint Genome Institute (2007) Bison Pool Environmental Genome. Protein sequence files downloaded from IMG/M (https://img.jgi.doe.gov/)

LaRowe, D. E. and Amend, J. P. (2019) The energetics of fermentation in natural settings. Geomicrobiol. J. 36, 492–505. https://doi.org/10.1080/01490451.2019.1573278

Merino, E. (1975) Diagenesis in teriary sandstones from Kettleman North Dome, California. II. Interstitial solutions: distribution of aqueous species at 100°C and chemical relation to diagenetic mineralogy. Geochim. Cosmochim. Acta 39, 1629–1645. https://doi.org/10.1016/0016-7037(75)90085-X

Privalov, P. L. and Makhatadze, G. I. (1990) Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: Protein unfolding effects. J. Mol. Biol. 213, 385–391. https://doi.org/10.1016/S0022-2836(05)80198-6

Richard, L. and Helgeson, H. C. (1998) Calculation of the thermodynamic properties at elevated temperatures and pressures of saturated and aromatic high molecular weight solid and liquid hydrocarbons in kerogen, bitumen, petroleum, and other organic matter of biogeochemical interest. Geochim. Cosmochim. Acta 62, 3591–3636. https://doi.org/10.1016/S0016-7037(97)00345-1

Robie, R. A. and Hemingway, B. S. (1995) Thermodynamic Properties of Minerals and Related Substances at 298.15 K and 1 Bar (10^5 Pascals) Pressure and at Higher Temperatures. U. S. Geol. Surv., Bull. 2131, 461 p. http://www.worldcat.org/oclc/32590140

Shock, E. and Canovas, P. (2010) The potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systems. Geofluids 10, 161–192. https://doi.org/10.1111/j.1468-8123.2010.00277.x

Shock, E. L. and Koretsky, C. M. (1995) Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures. Geochim. Cosmochim. Acta 59, 1497–1532. https://doi.org/10.1016/0016-7037(95)00058-8

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

Shock, E. L. and Schulte, M. D. (1998) Organic synthesis during fluid mixing in hydrothermal systems. J. Geophys. Res. 103, 28513–28527. https://doi.org/10.1029/98JE02142

Tutolo, B. M., Kong, X.-Z., Seyfried, W. E., Jr. and Saar, M. O. (2014) Internal consistency in aqueous geochemical data revisited: Applications to the aluminum system. Geochim. Cosmochim. Acta 133, 216–234. https://doi.org/10.1016/j.gca.2014.02.036


CHNOSZ documentation built on July 7, 2020, 3 p.m.