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Jay Thomas

Jay Thomas

Jay Thomas

Associate Professor and Director of Undergraduate Studies: Petrology and Experimental Geochemistry


Earth and Environmental Sciences
011a Heroy Geology Laboratory
Office: 315.443.4707


  • PhD Virginia Tech 2003
  • MS Virginia Tech 1998
  • BA Guilford College 1995

Social/Academic Links

Courses Taught

  • Mineralogy
  • Earth Sciences
  • Electron Probe Microanalysis
Research and Teaching Interests

The majority of my research focuses on using laboratory-based experiments to reproduce conditions that exist on or in the Earth to make crystals, melts and rocks. Field-based studies form an important complementary research component that guides laboratory experiments and provides ‘ground truth’ information. The ultimate goal of my research is to determine what processes produced the geochemical variations that are observed in earth materials. Experiments are typically conducted over a range of P–T conditions applicable to the Earth’s crust and upper mantle. The experimental research can be broadly grouped into two themes: equilibrium investigations of rocks and minerals (chemical and microstructural) and diffusion in materials. Both research themes are used to characterize mass transport in planetary systems.


Research Scientist at Rensselaer Polytechnic Institute 2008-2014

Postdoctoral Scholar Rensselaer Polytechnic Institute 2003-2008

Current and Past Students/Postdoctoral Researchers

William Nachlas (Research Associate)

Ellie Was (MS),

Zach Osborne (PhD)

Glenn Thompson (PhD)

Carson Rufledt (PhD)

Benjamin Pummel (MS)


High pressure-temperature equipment: The Experimental Geochemistry Lab at Syracuse is equipped with three piston-cylinder devices (T up to 1800°C; P up to 50 kbar); one internally-heated pressure vessel (T up to 1200C; P up to 10 kbar); six cold-seal pressure vessels for hydrothermal experiments (T up to 1200C; P up to 2 kbar); three one-atmosphere furnaces with base-metal windings (suitable for sustained use up to ~1100°C); one one-atmosphere furnace with MoSi2 heating elements (for temperatures up to ~1550°C).

Heating/cooling microscope stages: Materials (fluid inclusions, glass, etc.) can be studied using a Linkam THMSG600 heating cooling stage (-196 to 600C°) and controller components that are attached to an Olympus BX53 microscope.

Supporting Facilities: The experimental lab is supported by complete facilities for preparing starting materials and high-pressure assemblies, and has equipment for sectioning and polishing specimens.

Fourier Transform Infrared Spectroscopy Microscope system: A Bruker Vertex 70 Fourier transform infrared spectrometer and Hyperion infrared microscope system will be installed in co-PI Thomas’ laboratory in March 2015. The FTIR system will have infrared ‘light’ sources and detectors capable of measuring vibrational frequencies of molecules in the mid- to near-infrared spectral regions of materials (solid, liquid, or gas). The IR beam can be transmitted or reflected on spots down to ~15 µm.

Selected Publications

Nachlas, W., Baldwin, S., Thomas, J., & Ackerson, M. (2020). Investigation of N in Ammonium-bearing Silicates with Electron Probe Microanalysis (EPMA). Microscopy and Microanalysis, 26(S2), 42-43. doi:10.1017/S1431927620013203

Joseph P. Gonzalez, Suzanne L. Baldwin, Jay B. Thomas, William O. Nachlas, Paul G. Fitzgerald, (2020) Evidence for ultrahigh-pressure metamorphism discovered in the Appalachian orogen. Geology doi:

Thomas, J.B., Nachlas, W.O. Discontinuous precipitation of rutilated quartz: grain-boundary migration induced by changes to the equilibrium solubility of Ti in quartz. Contrib Mineral Petrol 175, 38 (2020).

Andreas K. Kronenberg, Kyle T. Ashley, Matthew K. Francsis, Caleb W. Holyoke III, Lynna Jezek, Johannes A. Kronenberg, Richard D. Law, Jay B. Thomas; Water loss during dynamic recrystallization of Moine thrust quartzites, northwest Scotland. Geology ; 48 (6): 557–561. doi:

*Bonazzi M, Tumiati S, Thomas J, Angel RJ, Alvaro M (2019) Assessment of the reliability of elastic geobarometry with quartz inclusions. Lithos 105201.

*Osborne, Z.R., Thomas, J.B., Nachlas, W.O., Baldwin, S.L., Holycross, M.E., Spear, F.S., and Watson E.B., 2019, An experimentally calibrated thermobarometric solubility model for titanium in coesite (TitaniC), Contributions to Mineralogy and Petrology,174:34,

*Gonzalez JP, Baldwin SL, Thomas JB, Nachlas WO, Fitzgerald P (2019) Discovery of coesite in the Appalachian orogen: First evidence for subduction to mantle depths during the Taconic orogeny. Geology (in review)

*Gonzalez JP, Thomas JB, Baldwin SL (2019) Quartz inclusion thermobarometry: methodology and first application to a quartzofeldspathic gneiss from the (ultra)high-pressure terrane in eastern Papua New Guinea. Journal of Metamorphic Geology DOI: 10.1111/jmg.12508

*del Real I, Smieska L, Thompson JFH, Martinez C, Thomas J, Layton-Matthews D (2019) Using multiple micro-analytical techniques for evaluating quantitative synchrotron-XRF elemental mapping of hydrothermal pyrite. Journal of Analytical Atomic Spectrometry 34:1724. DOI: 10.1039/c9ja00083f

Gabitov R, Borrelli C., Buettner J, Thirumalai KG, Roobanvenkatesh BG, Testa, M, Kirkland B, Skarake A, Thomas JB, Weremeichik J (2018) Characterization of carbonate crust from a recently discovered methane seep on the North Atlantic continental margin of the US. Minerals 9:138. DOI: 10.3390/min9030138

*Guerette M, *Ackerson MR, Thomas JB, Watson EB, Walker D, Huang L (2018) Thermally induced polyamorphic transition in hot-compressed silica glass. Physical Review B 148: 194501

Nachlas WO, Thomas JB, Hirth G (2018) TitaniQ deformed: Experimental deformation of out-of-equilibrium quartz porphyroclasts. Journal of Structural Geology 116: 207-222

Thomas JB, Spear FS (2018) Experimental study of quartz inclusions in garnet at pressures up to 3.0 GPa: evaluation of the quartz-in-garnet inclusion elastic thermobarometer. Contributions to Mineralogy and Petrology 173: 42

Kronenberg AK, Hasnan HFB, Holyoke C, Law RD, Liu Z, Thomas JB (2017) Synchrotron FTIR imaging of OH in quartz mylonites. Solid Earth 8: 1025–1045

Zeitler PK, Enkelmann E, Thomas JB, Watson EB, Ancuta LD, Idleman BD (2017) Solubility and trapping of helium in apatite. Geochimica et Cosmochimica Acta 209:1–8

Watson EB, Cherniak DJ, Thomas JB, Hanchar JM, Wirth R (2016) Crystal surface integrity and diffusion measurements on Earth and planetary materials. Earth and Planetary Science Lett 450: 346–354.

Cherniak DJ, Watson EB, Trappisch R, Thomas JB, Chaussende D (2016) Diffusion of helium in SiC and implications for retention of cosmogenic He. Geochimica et Cosmochemica Acta

Thomas JB (2016) Titanium. In: White WM (ed) Encyclopedia of Geochemistry: A Comprehensive Reference Source on the Chemistry of the Earth. Springer International Publishing, Cham, pp 1–7.

Trail D, Tailby ND, Lanzirotti A, Newville M, Thomas JB, Watson EB (2015) Redox evolution of silicic magmas: Insights from XANES measurements of Ce valence in Bishop Tuff zircons. Chemical Geology 402, 77–88. DOI: 10.1016/j.chemgeo.2015.02.033

Guerette M, Ackerson MR, Thomas JB, Yuan F, Watson, EB, Walker, D, Huang L (2015) Structure and Properties of Silica Glass Densified in Cold Compression and Hot Compression. Scientific Reports 5, 15343. DOI: 10.1038/srep15343

Thomas JB, Watson EB, Spear FS, Wark DA (2015) TitaniQ recrystallized: experimental confirmation of the original Ti-in-quartz calibrations. Contributions to Mineralogy and Petrology 169:27

Thomas JB, Watson EB (2014) An experimental study of Mg diffusion in grain boundaries of quartzites. Contributions to Mineralogy and Petrology 168:1068

Spear FS, Hallet BW, Thomas JB (2014) Overstepping the garnet isograd: A comparison of Quig barometry and thermodynamic modeling. Contributions to Mineralogy and Petrology 168:1059

Lanzillo NA, Thomas JB, Nayak S, Watson EB (2014) Pressure induced phonon engineering in metals. Proceedings of the National Academy of Science 111:8712–8716

Cherniak DJ, Thomas JB, Watson EB (2014) Neon diffusion in olivine and quartz. Chemical Geology 371, 68-82

Lanzillo NA, Watson EB, Thomas JB, Nayak S, Curioni A (2014) Near-surface controls on the composition of growing crystals: Car-Parrinello molecular dynamics (CPMD) simulations of Ti4+ energetics and diffusion in alpha quartz. Geochimica et Cosmochimica Acta 131, 33-46.

Ashley KT, Webb LE, Spear FS, Thomas JB (2013) P-T-D histories from quartz: A case study of the application of the TitaniQ thermobarometer to progressive fabric development in metapelites, Geochemistry, Geophysics, Geosystems, doi: 10.1002/ggge.20237.

Spear FS, Ashley KT, Webb LE, Thomas JB (2012) Ti diffusion in quartz inclusions: implications for metamorphic timescales. Contributions to Mineralogy and Petrology 164, 977–986.

Thomas JB, Watson EB (2012) Application of the Ti-in-quartz thermobarometer to rutile-free systems. Reply to: A comment on: 'TitaniQ under pressure: the effect of pressure and temperature on the solubility of Ti in quartz' by Thomas et al. Contributions to Mineralogy and Petrology 164, 369–374.

Leeman WP, MacRae CM, Wilson NC, Torpy A, Lee C-T A, Student JJ, Thomas JB, Vicenzi EP (2012) A Study of Cathodoluminescence and Trace Element Compositional Zoning in Natural Quartz from Volcanic Rocks: Mapping Titanium Content in Quartz. Microscopy and Microanalysis 18, 1322–1341.

Behr WM, Thomas JB, Hervig RL (2011) Calibrating Ti concentrations in quartz on the SIMS using NIST silicate glasses with applications to the TitaniQ geothermobarometer. American Mineralogist 96, 1100–1106.

Trail D, Thomas JB, Watson EB (2010) The incorporation of OH into zircon. American Mineralogist 96, 60–67.

Thomas JB, Watson EB, Spear FS, Shemella PT, Nayak SK, Lanzirotti A (2010) TitaniQ under pressure: the effect of pressure and temperature on the solubility of Ti in quartz. Contributions to Mineralogy and Petrology 160: 743–759.

Clay PL, Baxter EF, Cherniak DJ, Kelley SP, Thomas JB, Watson EB (2010) Two diffusion pathways in quartz: A combined UV-laser and RBS study. Geochimica et Cosmochimica Acta 74, 5906–5925.

Cherniak DJ, Watson EB, Thomas JB (2009) Diffusion of helium in zircon and apatite. Chemical Geology 268, 155–166.

Thomas JB, Watson EB, Cherniak DJ (2008) Lattice diffusion and solubility of argon in forsterite, enstatite, quartz and corundum. Chemical Geology, 253, 1–22.

Watson EB, Thomas JB, Cherniak DJ (2007) 40Ar retention in the terrestrial planets. Nature 449, 299–304.

Severs MJ, Azbej T, Thomas JB, Mandeville CW, Bodnar RJ (2007) Experimental determination of H2O loss from melt inclusions during laboratory heating: Evidence from Raman spectroscopy. Chemical Geology 237, 358–371.

Watson EB, Wark DA, Thomas JB (2006) Crystallization thermometers for zircon and rutile. Contributions to Mineralogy and Petrology 151, 413–433.

Thomas JB, Bodnar RJ, Shimizu N, Chesner C (2003) Melt inclusions in zircon. In: Reviews in Mineralogy and Geochemistry, 2003, 53, pp.63–87. Society of America and Geochemical Society: Washington, DC, United States.

Thomas JB, Bodnar RJ (2002) A technique for mounting and polishing melt inclusions in small (<1 mm) crystals, American Mineralogist 1505–1508.

Thomas JB, Bodnar RJ, Shimizu N, Sinha AK (2002) Determination of zircon/melt trace element partition coefficients from SIMS analysis of melt inclusions in zircon, Geochimica et Cosmochimica Acta 2887–2901.

Thomas JB, Sinha AK (1999) Field, petrographic, geochemical, and isotopic characterization of the Quottoon Igneous Complex, S. E. Alaska and N. W. British Columbia, Canadian Journal of Earth Sciences 36, 819–831.

Thomas JB (1994) Mangrove vegetation detection using remote sensing and image processing techniques, Proceedings of the Eighth National Conference on Undergraduate Research 699–703