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Fundamental and Computational Sciences Directorate

Staff information

David Hoyt

Biosystms Dynamics & Simula
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352

PNNL Publications


  • Booker A.E., D.W. Hoyt, T. Meulia, E.K. Eder, C.D. Nicora, S.O. Purvine, and R. Daly, et al. 2019. "Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp." Applied and Environmental Microbiology 85, no. 12:e00018-19. PNNL-SA-144542. doi:10.1128/AEM.00018-19
  • Bowers G.M., H.T. Schaef, Q. Miller, E.D. Walter, S.D. Burton, D.W. Hoyt, and J.A. Horner, et al. 2019. "C-13 Nuclear Magnetic Resonance Spectroscopy of Methane and Carbon Dioxide in a Natural Shale." ACS Earth and Space Chemistry 3, no. 3:324-328. PNNL-SA-140683. doi:10.1021/acsearthspacechem.8b00214
  • Chamas A., L. Qi, H.S. Mehta, J.A. Sears, S.L. Scott, E.D. Walter, and D.W. Hoyt. 2019. "High Temperature/Pressure MAS-NMR for the Study of Dynamic Processes in Mixed Phase Systems." Magnetic Resonance Imaging 56. PNNL-SA-138048. doi:10.1016/j.mri.2018.09.026
  • Daly R., S. Roux, M. Borton, D.M. Morgan, M.D. Johnston, A.E. Booker, and D.W. Hoyt, et al. 2019. "Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing." Nature Microbiology 4, no. 2:352-361. PNNL-SA-134613. doi:10.1038/s41564-018-0312-6
  • Lynch L.M., M. Machmuller, C.M. Boot, T.P. Covino, C.D. Rithner, F. Cotrufo, and D.W. Hoyt, et al. 2019. "Dissolved organic matter chemistry and transport along an Arctic Tundra Hillslope." Global Biogeochemical Cycles 33, no. 1:47-62. PNNL-SA-136691. doi:10.1029/2018GB006030
  • Miller Q., D.A. Dixon, S.D. Burton, E.D. Walter, D.W. Hoyt, A.S. Mcneill, and J. Moon, et al. 2019. "Surface-Catalyzed Oxygen Exchange during Mineral Carbonation in Nanoscale Water Films." Journal of Physical Chemistry C 123, no. 20:12871-12885. PNNL-SA-141756. doi:10.1021/acs.jpcc.9b02215
  • Sharon G., N.J. Cruz, D. Kang, M. Gandal, B. Wang, Y. Kim, and E.M. Zink, et al. 2019. "Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice." Cell 177, no. 6:1600-1618. PNNL-SA-131563. doi:10.1016/j.cell.2019.05.004
  • Tfaily M., R.M. Wilson, H.M. Brewer, R.K. Chu, H.M. Heyman, D.W. Hoyt, and J.E. Kyle, et al. 2019. "Single-throughput complementary high-resolution analytical techniques for characterizing complex natural organic matter mixtures." Journal of Visualized Experiments. PNNL-SA-138197. doi:10.3791/59035


  • Borton M., D.W. Hoyt, S. Roux, R. Daly, S. Welch, C.D. Nicora, and S.O. Purvine, et al. 2018. "Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales." Proceedings of the National Academy of Sciences of the United States of America 115, no. 28:E6585-E6594. PNNL-SA-134972. doi:10.1073/pnas.1800155115
  • Borton M., R. Daly, B. O'Banion, D.W. Hoyt, D.N. Marcus, S. Welch, and S.S. Hastings, et al. 2018. "Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale." Environmental Microbiology 20, no. 12:4596-4611. PNNL-SA-138432. doi:10.1111/1462-2920.14467
  • Bowers G.M., J.S. Loring, H.T. Schaef, E.D. Walter, S.D. Burton, D.W. Hoyt, and S.S. Cunniff, et al. 2018. "Interaction of Hydrocarbons with Clays under Reservoir Conditions: In Situ Infrared and Nuclear Magnetic Resonance Spectroscopy and X-ray Diffraction for Expandable Clays with Variably Wet Supercritical Methane." ACS Earth and Space Chemistry 2, no. 7:640-652. PNNL-SA-136218. doi:10.1021/acsearthspacechem.8b00039
  • Kang D., Z.E. Ilhan, N.G. Isern, D.W. Hoyt, D.P. Howsmon, M. Shaffer, and C. Lozupone, et al. 2018. "Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders." Anaerobe 49. PNNL-SA-127135. doi:10.1016/j.anaerobe.2017.12.007
  • Kothandaraman J., R.A. Dagle, V. Dagle, S.D. Davidson, E.D. Walter, S.D. Burton, and D.W. Hoyt, et al. 2018. "Condensed-Phase Low Temperature Heterogeneous Hydrogenation of CO2 to Methanol." Catalysis Science & Technology 8, no. 19:5098-5103. PNNL-SA-133245. doi:10.1039/C8CY00997J
  • Roy Chowdhury T., L.M. Bramer, D.W. Hoyt, Y. Kim, T.O. Metz, L. McCue, and H.L. Diefenderfer, et al. 2018. "Temporal dynamics of CO2 and CH4 loss potentials in response to rapid hydrological shifts in tidal freshwater wetland soils." Ecological Engineering 114. PNNL-SA-123359. doi:10.1016/j.ecoleng.2017.06.041


  • Angle J., T.A. Morin, L. Solden, A.B. Narrowe, G.J. Smith, M. Borton, and C. Rey-Sanchez, et al. 2017. "Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions." Nature Communications 8. PNNL-SA-125731. doi:10.1038/s41467-017-01753-4
  • Booker A.E., M. Borton, R. Daly, S. Welch, C.D. Nicora, D.W. Hoyt, and T. Wilson, et al. 2017. "Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales." mSphere 2. PNNL-SA-128950. doi:10.1128/mSphereDirect.00257-17
  • Bowers G.M., H.T. Schaef, J.S. Loring, D.W. Hoyt, S.D. Burton, E.D. Walter, and R.J. Kirkpatrick. 2017. "Role of Cations in CO2 Adsorption, Dynamics, and Hydration in Smectite Clays Under in situ Supercritical CO2 Conditions." Journal of Physical Chemistry C 121, no. 1:577-592. PNNL-SA-122523. doi:10.1021/acs.jpcc.6b11542
  • Dalcin Martins P., D.W. Hoyt, S. Bansal, C. Mills, M.M. Tfaily, B.A. Tangen, and R.G. Fincchiaro, et al. 2017. "Abundant carbon substrates drive extremely high sulfate reduction rates and methane fluxes in Prairie Pothole Wetlands." Global Change Biology 23, no. 8:3107-3120. PNNL-SA-120033. doi:10.1111/gcb.13633
  • Ilhan Z.E., J.K. DiBaise, N.G. Isern, D.W. Hoyt, A.K. Marcus, D. Kang, and M. Crowell, et al. 2017. "Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding." The ISME Journal 11, no. 9:2047-2058. PNNL-SA-119449. doi:10.1038/ismej.2017.71
  • Ok S., D.W. Hoyt, A. Andersen, J. Sheets, S. Welch, D.R. Cole, and K.T. Mueller, et al. 2017. "Surface Interactions and Confinement of Methane: A High Pressure Magic Angle Spinning NMR and Computational Chemistry Study." Langmuir 33, no. 6:1359-1367. PNNL-SA-123185. doi:10.1021/acs.langmuir.6b03590
  • Qi L., R. Alamillo, W.A. Elliott, A. Andersen, D.W. Hoyt, E.D. Walter, and K. Han, et al. 2017. "Operando solid-state NMR observations of solvent-mediated adsorption-reaction of carbohydrates in zeolites." ACS Catalysis 7, no. 5:3489-3500. PNNL-SA-119548. doi:10.1021/acscatal.7b01045
  • Schaef H.T., N. Loganathan, G.M. Bowers, R.J. Kirkpatrick, A.O. Yazaydin, S.D. Burton, and D.W. Hoyt, et al. 2017. "Tipping Point for Expansion of Layered Aluminosilicates in Weakly Polar Solvents: Supercritical CO2." ACS Applied Materials & Interfaces 9, no. 42:36783-36791. PNNL-SA-127664. doi:10.1021/acsami.7b10590
  • Solden L., D.W. Hoyt, W.B. Collins, J.E. Plank, R. Daly, E. Hildebrand, and T.J. Beavers, et al. 2017. "New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11." The ISME Journal 11, no. 3:691-703. PNNL-SA-115562. doi:10.1038/ismej.2016.150
  • White R.A., A. Rivas-Ubach, M.I. Borkum, M. Koberl, A. Bilbao Pena, S.M. Colby, and D.W. Hoyt, et al. 2017. "The state of rhizospheric science in the era of multi-omics: A practical guide to omics technologies." Rhizosphere 3, no. 2:212-221. PNNL-SA-124859. doi:10.1016/j.rhisph.2017.05.003


  • Daly R., M.A. Borton, M.J. Wilkins, D.W. Hoyt, D.J. Kountz, R. Wolfe, and S. Welch, et al. 2016. "Microbial metabolisms in a new 2.5 km deep ecosystem created by hydraulic fracturing in shales." Nature Microbiology 1, no. 10:Article No. 16146. PNNL-SA-115522. doi:10.1038/nmicrobiol.2016.146
  • Walker L.R., D.W. Hoyt, S. Walker, J.K. Ward, C.D. Nicora, and A.K. Bingol. 2016. "Unambiguous Metabolite Identification in High-throughput Metabolomics by Hybrid 1D 1H NMR/ESI MS1 Approach." Magnetic Resonance in Chemistry 54, no. 12:998-1003. PNNL-SA-117020. doi:10.1002/mrc.4503


  • Jung H., K. Carroll, S. Kabilan, D.J. Heldebrant, D.W. Hoyt, L. Zhong, and T. Varga, et al. 2015. "Stimuli-Responsive/Rheoreversible Hydraulic Fracturing Fluids as a Greener Alternative to Support Geothermal and Fossil Energy Production." Green Chemistry 17, no. 5:2799-2812. PNNL-SA-106027. doi:10.1039/c4gc01917b


  • Bowers G.M., D.W. Hoyt, S.D. Burton, B.O. Ferguson, T. Varga, and R.J. Kirkpatrick. 2014. "In Situ 13C and 23Na Magic Angle Spinning NMR Investigation of Supercritical CO2 Incorporation in Smectite-Natural Organic Matter Composites." Journal of Physical Chemistry C 118, no. 7:3564-3573. PNNL-SA-99489. doi:10.1021/jp410535d
  • Wilkins M.J., D.W. Hoyt, M.J. Marshall, P.A. Alderson, A.E. Plymale, L.M. Markillie, and A.E. Tucker, et al. 2014. "CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough." Frontiers in Microbiology 5. PNNL-SA-103791. doi:10.3389/fmicb.2014.00507


  • Feng J., J.Z. Hu, S.D. Burton, and D.W. Hoyt. 2013. "High Resolution Magic Angle Spinning 1H-NMR Metabolic Profiling of Nanoliter Biological Tissues at High Magnetic Field." Chinese Journal of Magnetic Resonance 30, no. 1:1-11. PNNL-SA-89007.
  • Loring J.S., H.T. Schaef, C.J. Thompson, R.V. Turcu, Q.R. Miller, J. Chen, and J.Z. Hu, et al. 2013. "Clay hydration/dehydration in dry to water-saturated supercritical CO2: Implications for caprock integrity." Energy Procedia 37. PNNL-SA-91508. doi:10.1016/j.egypro.2013.06.463
  • Miller Q., C.J. Thompson, J.S. Loring, C.F. Windisch, M.E. Bowden, D.W. Hoyt, and J.Z. Hu, et al. 2013. "Insights into Silicate Carbonation Processes in Water-Bearing Supercritical CO2 Fluids." International Journal of Greenhouse Gas Control 15. PNNL-SA-89916. doi:10.1016/j.ijggc.2013.02.005
  • Turcu R.V., D.W. Hoyt, K.M. Rosso, J.A. Sears, J.S. Loring, A.R. Felmy, and J.Z. Hu. 2013. "Rotor Design for High Pressure Magic Angle Spinning Nuclear Magnetic Resonance." Journal of Magnetic Resonance 226. PNNL-SA-88703. doi:10.1016/j.jmr.2012.08.009


  • Hu J.Z., J.A. Sears, H.S. Mehta, J.J. Ford, J. Kwak, K. Zhu, and Y. Wang, et al. 2012. "A Large Sample Volume Magic Angle Spinning Nuclear Magnetic Resonance Probe for In-Situ Investigations with Constant Flow of Reactants." Physical Chemistry Chemical Physics. PCCP 14, no. 7:2137-2143. PNNL-SA-82533. doi:10.1039/c1cp22692d
  • Loring J.S., H.T. Schaef, R.V. Turcu, C.J. Thompson, Q. Miller, P.F. Martin, and J.Z. Hu, et al. 2012. "In Situ Molecular Spectroscopic Evidence for CO2 Intercalation into Montmorillonite in Supercritical Carbon Dioxide." Langmuir 28, no. 18:7125-7128. PNNL-SA-86500. doi:10.1021/la301136w


  • Ahring B.K., N.S. Baliga, J.R. Frederickson, S. Kaplan, H.B. Pakrasi, J.G. Pounds, and I. shah, et al. 2011. Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP). PNNL-20717. Richland, WA: Pacific Northwest National Laboratory. Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP)
  • Brown G.E., A. Chaka, D.K. Shuh, E.E. Roden, C.J. Werth, N.J. Hess, and A.R. Felmy, et al. 2011. EMSL Geochemistry, Biogeochemistry and Subsurface Science-Science Theme Advisory Panel Meeting. PNNL-20601. Richland, WA: Pacific Northwest National Laboratory. EMSL Geochemistry, Biogeochemistry and Subsurface Science-Science Theme Advisory Panel Meeting
  • Campbell C.T., A.K. Datye, G.A. Henkelman, R.F. Lobo, W.F. Schneider, L.D. Spicer, and W.T. Tysoe, et al. 2011. EMSL and Institute for Integrated Catalysis (IIC) Catalysis Workshop. PNNL-20426. Richland, WA: Pacific Northwest National Laboratory. EMSL and Institute for Integrated Catalysis (IIC) Catalysis Workshop
  • Hoyt D.W., R.V. Turcu, J.A. Sears, K.M. Rosso, S.D. Burton, A.R. Felmy, and J.Z. Hu. 2011. "High-pressure Magic Angle Spinning Nuclear Magnetic Resonance." Journal of Magnetic Resonance 212, no. 2:378-385. PNNL-SA-80681. doi:10.1016/j.jmr.2011.07.019
  • Hoyt D.W., R.V. Turcu, J.A. Sears, K.M. Rosso, S.D. Burton, J. Kwak, and A.R. Felmy, et al. 2011. "IN SITU MAGIC ANGLE SPINNING NMR FOR STUDYING GEOLOGICAL CO(2) SEQUESTRATION." In 241st National Meeting and Exposition of the American Chemical Society, March 27-31, 2011, Anaheim, California, 241, 245-Fuel. Washington Dc:American Chemical Society. PNNL-SA-77039.
  • Kwak J., J.Z. Hu, R.V. Turcu, K.M. Rosso, E.S. Ilton, C.M. Wang, and J.A. Sears, et al. 2011. "The Role of H2O in the Carbonation of Forsterite in Supercritical CO2." International Journal of Greenhouse Gas Control 5, no. 4:1081-1092. PNNL-SA-76665. doi:10.1016/j.ijggc.2011.05.013
  • Teklemichael S.T., W. Oo, M. Matthew, E.D. Walter, and D.W. Hoyt. 2011. "Acceptors in ZnO nanocrystals." Applied Physics Letters 98, no. 23:Article No. 232112. PNNL-SA-79839. doi:10.1063/1.3598411
  • White M.D., B.P. McGrail, H.T. Schaef, J.Z. Hu, D.W. Hoyt, A.R. Felmy, and K.M. Rosso, et al. 2011. "Multiphase Sequestration Geochemistry: Model for Mineral Carbonation." Energy Procedia 4. PNNL-SA-74658. doi:10.1016/j.egypro.2011.02.472


  • Kwak J., J.Z. Hu, D.W. Hoyt, J.A. Sears, C.M. Wang, K.M. Rosso, and A.R. Felmy. 2010. "Metal Carbonation of Forsterite in Supercritical CO2 and H2O Using Solid State 29Si, 13C NMR Spectroscop." Journal of Physical Chemistry C 114, no. 9:4126 - 4134. PNNL-SA-68897. doi:10.1021/jp1001308


  • Chen B., X. Ren, T. Neville, W. Jerome, D.W. Hoyt, D.L. Sparks, and G. Ren, et al. 2009. "Apolipoprotein AI tertiary structures determine stability and phospholipid-binding activity of discoidal high-density lipoprotein particles of different sizes." Protein Science 18, no. 5:921-935. PNNL-SA-56783. doi:10.1002/pro.101
  • Hu J.Z., J.A. Sears, J. Kwak, D.W. Hoyt, Y. Wang, and C.H. Peden. 2009. "An Isotropic Chemical Shift-Chemical Shift Anisotropic Correlation Experiment Using Discrete Magic Angle Turning." Journal of Magnetic Resonance 198, no. 1:105-110. PNNL-SA-63634.


  • Briknarova K., X. Zhou, A.C. Satterthwait, D.W. Hoyt, K.R. Ely, S. Huang, and S. Huang. 2008. "Structural Studies of the SET Domain from RIZ1 Tumor Suppressor." Biochemical and Biophysical Research Communications 366, no. 3:807-813. PNNL-SA-56117. doi:10.1016/j.bbrc.2007.12.034


  • Ren X., Y. Yang, T. Neville, T. Neville, D.W. Hoyt, D.L. Sparks, and J. Wang. 2007. "A complete backbone spectral assignment of human apolipoprotein AI on a 38 kDa preßHDL (Lp1-AI) particle." Biomolecular NMR Assignments 1, no. 1:69-71. PNNL-SA-53926.
  • Smirnov S., N.G. Isern, Z.G. Jiang, D.W. Hoyt, and C.J. Mcknight. 2007. "The Isolated Sixth Gelsolin Repeat and Headpiece Domain of Villin Bundle F-Actin in the Presence of Calcium and Are Linked by a 40-Residue Unstructured Sequence." Biochemistry 46, no. 25:7488-7496. PNNL-SA-55624. doi:10.1021/bi700110v
  • Yang Y., D.W. Hoyt, and J. Wang. 2007. "A Complete NMR Spectral Assignment of the Lipid-free Mouse Apolipoprotein A-I (ApoAI) C-terminal Truncation Mutant, ApoAI(1-216)." Biomolecular NMR Assignments 1, no. 1:109-111. PNNL-SA-53927. doi:10.1007/s12104-007-9031-2


  • Brzovic P.S., A.V. Lissounov, D. Christensen, D.W. Hoyt, and R.E. Klevit. 2006. "A UbcH5/Ubiquitin Noncovalent Complex is Required for Processive BRCA1-Directed Ubiquitination." Molecular Cell 21, no. 6:873-880. PNNL-SA-48810.


  • Briknarova K., F. Nasertorabi, M.L. Havert, E. Eggleston, D.W. Hoyt, C. Li, and A.J. Olson, et al. 2005. "The Serine-rich Domain from Crk-associated Substrate (p130Cas) is a Four-helix Bundle." Journal of Biological Chemistry 280, no. 23:21908-21914. PNNL-SA-45324.
  • Xu C., A. Sivashanmugam, D.W. Hoyt, and J. Wang. 2005. "A Complete Backbone Assignment of the Apolipoprotein E LDL Receptor Binding Domain [Letter to the Editor]." Journal of Biomolecular NMR 32, no. 2:177. PNNL-SA-44749. doi:10.1007/s10858-005-6729-2


  • Hoyt D.W., S.D. Burton, M.R. Peterson, J.D. Myers, and G. Chin. 2004. "Expanding Your Laboratory by Accessing Collaboratory Resources." Analytical and Bioanalytical Chemistry 378, no. 6:1408-1410. PNNL-SA-39416.


  • Briknarova K., M. Akermann, D.W. Hoyt, E. Ruoslahti, and K.R. Ely. 2003. "Anastellin, an FN3 Fragment with Fibronectin Polymerization Activity, Resembles Amyloid Fibril Precursors." Journal of Molecular Biology 332, no. 1:205-215. PNNL-SA-38930.
  • Kreishman-Detrick M., C. Egile, D.W. Hoyt, J.J. Ford, R. Li, and M.K. Rosen. 2003. "NMR analysis of methyl groups at 100-500 kDa: model systems and Arp2/3 complex." Biochemistry 42, no. 28:8579-8586. PNNL-SA-39415.
  • Lowry D.F., D.W. Hoyt, F.A. Khazi, J.R. Bagu, A.G. Lindsey, and D.M. Wilson Iii. 2003. "Investigation of the role of the histidine-aspartate pair in the human exonuclease III-like abasic endonuclease, Ape1." Journal of Molecular Biology 329, no. 2:311-322. PNNL-SA-40864.
  • Lowry D.F., D.W. Hoyt, F.A. Khazi, J.R. Bagu, A.G. Lindsey, and D.M. Wilson. 2003. "Investigation of the Role of the Histidine-Aspartate Pair in the Human Exonuclease III-like Abasic Endonuclease, Ape1." Journal of Molecular Biology 329, no. 2:311-322. PNNL-SA-36499.


  • Briknarova K., S. Takayama, S. Homma, K. Baker, E. Cabezas, D.W. Hoyt, and Z. Li, et al. 2002. "BAG4/SODD Protein Contains a Short BAG Domain." Journal of Biological Chemistry 277, no. 34:31172-31178. PNNL-SA-36503.
  • Chin G., J.D. Myers, and D.W. Hoyt. 2002. "Social Networks in the Virtual Science Laboratory." Communications of the ACM 45, no. 8:87-92. PNNL-SA-35242.


  • Briknarova K., S. Takayama, L. Brive, M.L. Havert, D.A. Knee, J. Velasco, and S. Homma, et al. 2001. "Structural Analysis of BAG1 Cochaperone and Its Interactions With Hsc70 Heat Shock Protein." Nature Structural Biology 8, no. 4:349-352. PNNL-SA-33922.
  • Bryant P.L., C. Harwell, A.A. Mrse, E.F. Emery, Z. Gan, T. Caldwell, and A.P. Reyes, et al. 2001. "Structural Characterization of MAO and Related Aluminum Complexes. 1. Solid-State 27 Al NMR with Comparison to EFG Tensors from ab Initio Molecular Orbital Calculations." Journal of the American Chemical Society 123. PNNL-SA-33924.
  • Brzovic P.S., P. Rajagopal, D.W. Hoyt, M. King, and R.E. Klevit. 2001. "Structure of a BRCA1/BARD1 Complex: a Heterodimeric RING-RING Interaction." Nature Structural Biology 8, no. 10:833-837. PNNL-SA-34960.


  • Liu K., H.S. Cho, D.W. Hoyt, T.N. Nguyen, P. Olds, J.W. Kelly, and D. Wemmer. 2000. "Deuterium-proton Exchange on the Native Wild-type Transthyretin Tetramer Identifies the Stable Core of the Individual Subunits and Indicates Mobility at the Subunit Interface." Journal of Molecular Biology 303, no. 4:555-565. PNNL-SA-33925.

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