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2011 Publications

  1. Armstrong, R., Ajo-Franklin, J. "Investigating Biomineralization using Synchrotron based X-Ray Computed Microtomography.” Geophysical Research Letters, 38, L08406, 4 PP., 2011. (article)
  2. Barkouki, T.H., Martinez, B.C., Mortensen, B.M., Weathers, T.S., De Jong, J.D., Ginn, T.R., Spycher, N.F., Smith,R.W., Fuijita, Y., Forward and inverse bio-geochemical modeling of microbially induced calcite precipitation in half-meter column experiments, Springer, Vol. 90, Number 1, 23-39, 2011. (article)
  3. Berryman, J., “Bounds and self-consistent estimates for elastic constants of granular polycrystals composed of orthorhombics or crystals with higher symmetries.  Physical Review E, 83, 046130, 2011. (article)
  4. Boutchko, R., Rayz, V., Vandehey, N., O’Neil, J., Budinger, T., Nico, P., Druhan, J., Saloner, D., Gullberg, G., Moses, W., Imaging and modeling of flow in porous media using clinical nuclear emission tomography systems and computational fluid dynamics, Journal of Applied Geophysics, Vol 76, PP 74-81, 2011. (article)
  5. Brodie, E. L., D. C. Joyner, B. Faybishenko, M. E. Conrad, C. Rios-Velazquez, B. Mork, R. Kelley, A. Willet, S. Koenigsberg, D. Herman, M. K. Firestone, and T. C. Hazen,  Evaluation of sustained release polylactate electron donors for removal of hexavalent chromium from contaminated groundwater.  Chemosphere, 85:660-665, 2011. (article)
  6. Chhabra, S. R., G. Butland, D. Elias, J-M. Chandonia, O-Y Fok, T. Juba, A. Gorur, S. Allen, C.M. Leung, K. Keller, S. Reveco, G. Zane, E. Semkiw, R. Prathapam, B. Gold, M. Singer, M. Ouellet, D. Sazakal, D. Jorgens, M.N. Price, E. Witkowska, H. R. Beller, A.P. Arkin, T.C. Hazen, M.D. Biggin, M. Auer, J.D. Wall, and J. D. Keasling,  Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome.  Appl. Environ. Microbiol. 77:7595-7604, 2011. (article)
  7. Chakraborty, R., T. C. Hazen, D. C. Joyner, K. Küsel, M. E. Singer, J. Sitte, and T. Torok,  Use of immunomagnetic separation for the detection of Desulfovibrio vulgaris from environmental samples.  J. Microbiol. Methods, 86-204-209, 2011. (article)
  8. Commer, M.,  Newman, G. A., Williams, K. H., and Hubbard, S. S.  “Three-dimensional  induced polarization data inversion for complex resistivity.” Geophysics, Vol. 76, No. 3, P. F157-171, 2011. (article)
  9. DeAngelis, K. M., C. H. Wu, H. R. Beller et al., PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip.  Appl. Environ. Microbiol. 77: 6313 – 6322, 2011. (article)
  10. Dohnalkova, A. C., M. J. Marshall, B. W. Arey, K. H. Williams, E. C. Buck, and J. K. Fredrickson, Imaging hydrated microbial extracellular polymers: Comparative analysis by electron microscopy. Applied & Environmental Microbiology, 77(4), 1254‐1262, doi:10.1128/AEM.02001‐10, 2011. (article)
  11. Finsterle, S., and Kowalsky, M.B., A truncated Levenberg-Marquardt algorithm for the calibration of highly parameterized nonlinear models, Computers and Geosciences, 37(6), 731-738, 2011. (article)
  12. Flores Orozco, A., K.H. Williams, P.E. Long, S.S. Hubbard and A. Kemna, Using spectral induced polarization (SIP) to infer biogeochemical processes associated with bioremediation of a uranium-contaminated aquifer, JGR-Biogeosciences, 116, G03001, 2011. (article)
  13. Kerkhof, L., Williams, K. H., Long, P.E., and McGuinness, L., Phase preference by acetate‐utilizing bacteria during DNA replication at the Rifle, CO Integrated Field Research Challenge Site, Environmental Science & Technology, 45(4), 1250–1256, doi: 0.1021/es102893r, 2011.
  14. Li, L., Gawande, N., Kowalsky, M.B., Steefel, C., Hubbard, S., Physicochemical heterogeneity controls on uranium bioreduction rates at the field scale. Environmental Science and Technology, 45 (23): 9959-9966 2011. (article)
  15. Mohanty, S. R., B. Kollah, E. L. Brodie, T. C. Hazen, and E. E. Roden.  2011.  16S rRNA Gene Microarray Analysis of Microbial Communities in Ethanol-Stimulated Subsurface Sediment.  Microbes and Environments doi:10.1264/jsme.ME11111.
  16. Scheibe, T., S. Hubbard, T.C. Onstott and M.F. DeFlaun, Lessons Learned from Bacterial Transport Research at the South Oyster Field Research Site, Ground water,  Vol. 49, Issue 5, pages 745-763, 2011. (article)
  17. Van Nostrand, J. D., L. Wu, W.M. Wu, A. Huang, T. J. Gentry, Y. Deng, J. Carley, S. Carrol, Z. He, B. Gu, J. Luo, C. S. Criddle, D. B. Watson, P. M. Jardine, T. L. Marsh, J. M. Tiedje, T. C. Hazen, and J. Zhou,   Dynamics of microbial community composition and function during in-situ bioremediation of a uranium-contaminated aquifer. Appl. Environ. Microbiol. 77:3860-3869, 2011. (article)
  18. Wan, J., Dong, W. and Tokunaga, T., “Method to Attenuate U(VI) Mobility in Acidic Waste Plumes Using Humic Acids,” Environmental Science & Technology, 2011. composition: Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI). Microbial Biotechnology, 4 (1), 55–63, 2011.
  19. Wilkins, M.J., S.J. Callister, M. Miletto, K.H. Williams, C.D. Nicora, D.R. Lovley, P.E. Long, and M.S. Lipton: Development of a biomarker for Geobacter activity and strain composition: Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI). Microbial Biotechnology, 2011. (article)
  20. Williams, K. H., P. E. Long, J. A. Davis, C. I. Steefel, M. J. Wilkins, A. L. N’Guessan, L. Yang, D. Newcomer, F. A. Spane, L. J. Kerkhof, L. McGuinness, R. Dayvault, and D. R. Lovely, Acetate availability and its influence on sustainable bioremediation of uranium-contaminated groundwater. Geomicrobiology Journal, 28(5-6 SP ISS) 519-539, 2011. (article)
  21. Wu, Yuxin, Ajo-Franklin, J., Spycher, N., Hubbard, S., Zhang, G., Williams, K., Taylor, J., Fujita, Y., Smith, R., Geophysical monitoring and reactive transport modeling of ureolytically-driven calcium carbonate precipitation. Geochemical Transactions-Chemistry Central, doi:10.1186/1467-4866-12-7, 2011. (article)
  22. Zhou, J., Q. He, C. L. Hemme, A. Mukhopadhyay, K. Hillesland, A. Zhou, Z. He, J. D. van Nostrand, T. C. Hazen, D. A. Stahl, J. D. Wall, and A. P. Arkin. How sulphate-reducing microorganisms cope with stress: lessons from systems biology.  Nature Reviews in Microbiology 9:452-466, 2011. (article)
  23. Yabusaki, S. B., Fan, Y., Williams, K. H., Murray, C. J., Ward, A. L., Dayvault, R. D., Waichler, S., Newcomer, D. R., Spane, F. A., and Long, P. E., Variably saturated flow and multicomponent biogeochemical reactive transport modeling of a uranium bioremediation field experiment, Journal of Contaminant Hydrology., 126(3), 271-290, doi:10.1016/j.conhyd.2011.09.002, 2011. (article)