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Fundamental and Computational Sciences Directorate

Staff information


Timothy Scheibe

Earth & Biological Sciences
Earth Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-02
Richland, WA 99352


Dr. Scheibe is the Principal Investigator and Mechanistic Models Campaign lead for PNNL’s Scientific Focus Area (SFA) project sponsored by BER’s Subsurface Biogeochemistry Research (SBR) program. This project combines field observations, experiments, and multiscale numerical models to advance understanding of the biogeochemical impacts of hydrologic exchange flows (groundwater-surface water interactions) in river and watershed systems.

At EMSL, Dr. Scheibe is the Lead Scientist for multiscale modeling and high-performance computing. He develops the scientific vision for multiscale and computational science within EMSL, provides a national perspective on the future scientific and technological needs, and sets a strategy to integrate EMSL capabilities to address key scientific issues in environmental molecular science relevant to BER missions.

Research Interests

  • Groundwater-surface water interactions and controls on watershed biogeochemistry.
  • Characterization and modeling of natural subsurface heterogeneity and its impacts on contaminant transport in groundwater systems.
  • Subsurface biogeochemistry including microbial transport and bioremediation of metals and radionuclides.
  • Multiscale modeling of coupled biogeochemical processes in porous media.
  • Parameter estimation and conceptual model uncertainty characterization.

Education and Credentials

  • 1993 Ph.D., Civil Engineering, Stanford University
  • 1987 M.S., Civil Engineering, University of Washington
  • 1984 B.S., Geological Engineering, Washington State University

Affiliations and Professional Service

  • American Geophysical Union
  • National Ground Water Association
  • Member, Groundwater editorial board, 2001-present
  • Member, PeerJ editorial board, 2017-present
  • Member, Water editorial board, 2017-present
  • Associate Editor, Hydrogeology Journal, 2003-2007.

Awards and Recognitions

  • Henry Darcy Distinguished Lecturer, National Ground Water Association - international year-long lectureship, 2010
  • EMSL Wiley Research Fellow, 2013

PNNL Publications


  • Gonzalez-Duque D., J.D. Gomez-Velez, J.P. Zarnetske, X. Chen, and T.D. Scheibe. 2024. "Sinuosity-driven Hyporheic Exchange: Hydrodynamics and Biogeochemical Potentials." Water Resources Research 60, no. 4:Art. No. e2023WR036023. PNNL-SA-187573. doi:10.1029/2023WR036023
  • Zheng J., T.D. Scheibe, K.E. Boye, and H. Song. 2024. "Thermodynamic control on the decomposition of organic matter across different electron acceptors." Soil Biology and Biochemistry 193. PNNL-SA-191896. doi:10.1016/j.soilbio.2024.109364


  • Ahamed F., Y. You, A. Burgin, J.C. Stegen, T.D. Scheibe, and H. Song. 2023. "Exploring the determinants of organic matter bioavailability through substrate-explicit thermodynamic modeling." Frontiers in Water 5. PNNL-SA-184205. doi:10.3389/frwa.2023.1169701
  • Perez Mesa G., J.D. Gomez Velez, X. Chen, and T.D. Scheibe. 2023. "The Directional Unit Hydrograph Method: Connecting Streamflow Response to Storm Dynamics." Journal of Hydrology 627, no. Part A:130422. PNNL-SA-178480. doi:10.1016/j.jhydrol.2023.130422


  • Bao J., Y. Chen, Y. Fang, X. Song, W.A. Perkins, Z. Duan, and P. Shuai, et al. 2022. "Modeling framework for evaluating the impacts of hydrodynamic pressure on hydrologic exchange fluxes and residence time for a large-scale river section over a long-term period." Environmental Modelling & Software 148. PNNL-SA-152147. doi:10.1016/j.envsoft.2021.105277
  • Chen Y., J. Bao, Y. Fang, W.A. Perkins, H. Ren, X. Song, and Z. Duan, et al. 2022. "Modeling of streamflow in a 30 km long reach spanning 5 years using OpenFOAM 5.x." Geoscientific Model Development 15, no. 7:2917-2947. PNNL-SA-151719. doi:10.5194/gmd-15-2917-2022
  • Dwivedi D., C.I. Steefel, B. Arora, J.F. Banfield, J.R. Bargar, J.R. Bargar, and M.I. Boyanov, et al. 2022. "From Legacy Contamination to Watershed Systems Science: A Review of Scientific Insights and Technologies Developed through DOE-Supported Research in Water and Energy Security." Environmental Research Letters 17, no. 4:Art. No. 043004. PNNL-SA-161347. doi:10.1088/1748-9326/ac59a9
  • Karra S., S.V. Apte, X. He, and T.D. Scheibe. 2022. "PARTICLE RESOLVED DNS STUDY OF TURBULENCE EFFECTS ON HYPORHEIC MIXING IN RANDOMLY PACKED SEDIMENT BEDS." In 12th International Symposium on Turbulence and Shear Flow Phenomena (TSFP 2022), July 19-22, 2022, Osaka, Japan, Virtual. Danbury, Connecticut:Begell House, Inc. PNNL-SA-173463.
  • Perez L., R. Parashar, A.E. Plymale, and T.D. Scheibe. 2022. "Contributions of biofilm-induced flow heterogeneities to solute retention and anomalous transport features in porous media." Water Research 209. PNNL-SA-164581. doi:10.1016/j.watres.2021.117896


  • Chen X., R.M. Lee, D. Dwivedi, K. Son, Y. Fang, X. Zhang, and E.B. Graham, et al. "Integrating Field Observations and Reactive Transport Modeling to Predict Watershed Water Quality under Environmental Perturbations."
  • Chen X., R.M. Lee, D. Dwivedi, K. Son, Y. Fang, X. Zhang, and E.B. Graham, et al. 2021. "Integrating Field Observations and Process-based Modeling to Predict Watershed Water Quality under Environmental Perturbations." Journal of Hydrology 602. PNNL-SA-148272. doi:10.1016/j.jhydrol.2020.125762
  • Dwivedi D., S.E. Godsey, and T.D. Scheibe. 2021. "Editorial: Linking hydrological and biogeochemical processes in riparian corridors." Frontiers in Water 3. PNNL-SA-161453. doi:10.3389/frwa.2021.693763
  • Hou Z., H. Ren, C.J. Murray, X. Song, Y. Fang, E.V. Arntzen, and X. Chen, et al. 2021. "A Novel Construct for Scaling Groundwater-River Interactions Based on Machine-Guided Hydromorphic Classification." Environmental Research Letters 16, no. 10:104016. PNNL-SA-151112. doi:10.1088/1748-9326/ac24ce
  • Ren H., X. Song, Y. Fang, Z. Hou, and T.D. Scheibe. 2021. "Machine Learning Analysis of Hydrologic Exchange Flows and Transit Time Distributions in a Large Regulated River." Frontiers in Artificial Intelligence 4. PNNL-SA-158855. doi:10.3389/frai.2021.648071
  • Song H., J.C. Stegen, E.B. Graham, and T.D. Scheibe. 2021. "Historical Contingency in Microbial Resilience to Hydrologic Perturbations." Frontiers in Water 3. PNNL-SA-156061. doi:10.3389/frwa.2021.590378
  • Song X., Y. Fang, J. Bao, H. Ren, Z. Duan, W.A. Perkins, and H. Zhou, et al. 2021. "Scale-dependent spatial variabilities of hydrological exchange flows and transit time in a large regulated river." Journal of Hydrology 598. PNNL-SA-152146. doi:10.1016/j.jhydrol.2021.126283


  • Fang Y., X. Song, H. Ren, W.A. Perkins, P. Shuai, M.C. Richmond, and Z. Hou, et al. 2020. "High-performance simulation of dynamic hydrologic exchange and implications for surrogate flow and reactive transport modeling in a large river corridor." Frontiers in Water 2. PNNL-SA-153319. doi:10.3389/frwa.2020.564211
  • Lin X., H. Ren, A.E. Goldman, J.C. Stegen, and T.D. Scheibe. 2020. "WHONDRS-GUI: A Web Application for Global Survey of Surface Water Metabolites." PeerJ 8. PNNL-SA-142949. doi:10.7717/peerj.9277
  • Ren H., Z. Hou, Z. Duan, X. Song, W.A. Perkins, M.C. Richmond, and E.V. Arntzen, et al. 2020. "Spatial Mapping of Riverbed Grain-size Distribution Using Machine Learning." Frontiers in Water 2. PNNL-SA-151819. doi:10.3389/frwa.2020.551627
  • Song H., J.C. Stegen, E.B. Graham, J. Lee, V.A. Garayburu-Caruso, W.C. Nelson, and X. Chen, et al. 2020. "Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling." Frontiers in Microbiology 11. PNNL-SA-151734. doi:10.3389/fmicb.2020.531756


  • Fang Y., S.B. Yabusaki, A. Ahkami, X. Chen, and T.D. Scheibe. 2019. "An efficient three-dimensional rhizosphere modeling capability to study the effect of root system architecture on soil water and reactive transport." Plant and Soil 441, no. 1-2:33-48. PNNL-SA-138450. doi:10.1007/s11104-019-04068-z
  • Graham E.B., J.C. Stegen, M. Huang, X. Chen, and T.D. Scheibe. 2019. "Subsurface biogeochemistry is a missing link between ecology and hydrology in dam-impacted river corridors." Science of the Total Environment 657. PNNL-SA-132468. doi:10.1016/j.scitotenv.2018.11.414
  • Hou Z., T.D. Scheibe, C.J. Murray, W.A. Perkins, E.V. Arntzen, H. Ren, and R.D. Mackley, et al. 2019. "Identification and mapping of riverbed sediment facies in the Columbia River through integration of field observations and numerical simulations." Hydrological Processes 33, no. 8:1245-1259. PNNL-SA-123667. doi:10.1002/hyp.13396
  • Meile C., and T.D. Scheibe. 2019. "Reactive transport modeling of microbial dynamics." Elements 15, no. 2:111-116. PNNL-SA-141688. doi:10.2138/gselements.15.2.111
  • Yang X., R. Parashar, N. Sund, A.E. Plymale, T.D. Scheibe, D. Hu, and R.T. Kelly. 2019. "On Modeling Ensemble Transport of Metal Reducing Motile Bacteria." Scientific Reports 9. PNNL-SA-134947. doi:10.1038/s41598-019-51271-0


  • Korneev S., X. Yang, J.M. Zachara, T.D. Scheibe, and I. Battiato. 2018. "Downscaling-based segmentation for unresolved images of highly heterogeneous granular porous samples." Water Resources Research 54, no. 4:2871-2890. PNNL-SA-125744. doi:10.1002/2018WR022886
  • Mays D.C., and T.D. Scheibe. 2018. "Groundwater Contamination, Subsurface Processes, and Remediation Methods: Overview of the Special Issue of Water on Groundwater Contamination and Remediation." Water 10, no. 12:Article No. 1708. PNNL-SA-139166. doi:10.3390/w10121708


  • Graham E.B., J.C. Stegen, A.R. Crump, C.T. Resch, S.J. Fansler, E.V. Arntzen, and D.W. Kennedy, et al. 2017. "Organic carbon thermodynamics elucidate spatiotemporal mechanisms governing hyporheic zone biogeochemical cycling." In Proceedings of the Subsurface Biogeochemical Research and Terrestrial Ecosystem Science Joint Meeting April 25-26, 2017, Potomac, Maryland. Washington, District Of Columbia:US Department of Energy, Office of Biological and Environmental Research. PNNL-SA-125130.
  • Hou Z., W.C. Nelson, J.C. Stegen, C.J. Murray, E.V. Arntzen, A.R. Crump, and D.W. Kennedy, et al. 2017. "Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies." Scientific Reports 7. PNNL-SA-121286. doi:10.1038/s41598-017-12275-w
  • Song H., D.G. Thomas, J.C. Stegen, M. Li, C. Liu, X. Song, and X. Chen, et al. 2017. "Regulation-structured dynamic metabolic model provides a potential mechanism for delayed enzyme response in denitrification process." Frontiers in Microbiology 8. PNNL-SA-129317. doi:10.3389/fmicb.2017.01866
  • Yang X., T. Varga, C. Liu, and T.D. Scheibe. 2017. "What Can We Learn from In-Soil Imaging of A Live Plant: X-ray Computed Tomography and 3D Numerical Simulation of Root-Soil System." Rhizosphere 3, no. 2:259-262. PNNL-SA-124115. doi:10.1016/j.rhisph.2017.04.017


  • Yang X., Y. Mehmani, W.A. Perkins, A. Pasquali, M. Schoenherr, K. Kim, and M. Perego, et al. 2016. "Intercomparison of 3D Pore-scale Flow and Solute Transport Simulation Methods." Advances in Water Resources 95. PNNL-SA-109346. doi:10.1016/j.advwatres.2015.09.015


  • Scheibe T.D., E.M. Murphy, X. Chen, A.K. Rice, K.C. Carroll, B.J. Palmer, and A.M. Tartakovsky, et al. 2015. "An Analysis Platform for Multiscale Hydrogeologic Modeling with Emphasis on Hybrid Multiscale Methods." Groundwater 53, no. 1:38-56. PNNL-SA-93006. doi:10.1111/gwat.12179
  • Scheibe T.D., K.L. Schuchardt, K. Agarwal, J.M. Chase, X. Yang, B.J. Palmer, and A.M. Tartakovsky, et al. 2015. "Hybrid multiscale simulation of a mixing-controlled reaction." Advances in Water Resources 83. PNNL-SA-105960. doi:10.1016/j.advwatres.2015.06.006
  • Scheibe T.D., W.A. Perkins, M.C. Richmond, M.I. McKinley, P. Romero Gomez, M. Oostrom, and T.W. Wietsma, et al. 2015. "Pore-Scale and Multiscale Numerical Simulation of Flow and Transport in a Laboratory-Scale Column." Water Resources Research 51, no. 2:1023-1035. PNNL-SA-103382. doi:10.1002/2014WR015959
  • Scheibe T.D., X. Yang, X. Chen, and G.E. Hammond. 2015. "A Hybrid Multiscale Framework for Subsurface Flow and Transport Simulations." Procedia Computer Science 51. PNNL-SA-107927. doi:10.1016/j.procs.2015.05.276


  • Scheibe T.D., X. Yang, K.L. Schuchardt, K. Agarwal, J.M. Chase, B.J. Palmer, and A.M. Tartakovsky. 2014. "A Many-Task Parallel Approach for Multiscale Simulations of Subsurface Flow and Reactive Transport." In 7th Workshop on Many-Task Computing on Clouds, Grids, and Supercomputers (MTAGS 2014), November 16, 2014, New Orleans, Louisiana. New York, New York:ACM. PNNL-SA-105263.
  • Yang X., M.C. Richmond, T.D. Scheibe, W.A. Perkins, and H. Resat. 2014. "Flow Partitioning in Fully Saturated Soil Aggregates." Transport in Porous Media 103, no. 2:295-314. PNNL-SA-92858. doi:10.1007/s11242-014-0302-y


  • Fang Y., B.N. Nguyen, K.C. Carroll, Z. Xu, S.B. Yabusaki, T.D. Scheibe, and A. Bonneville. 2013. "Development of a coupled thermo-hydro-mechanical model in discontinuous media for carbon sequestration." International Journal of Rock Mechanics and Mining Sciences 62. PNNL-SA-88739. doi:10.1016/j.ijrmms.2013.05.002
  • Keyes D., L.C. McInnes, C. Woodward, W. Gropp, E. Myra, M. Pernice, and J. Bell, et al. 2013. "Multiphysics Simulations: Challenges and Opportunities." International Journal of High Performance Computing Applications 27, no. 1:4-83. PNNL-SA-93581. doi:10.1177/1094342012468181
  • Landkamer L.L., R.W. Harvey, T.D. Scheibe, and J.N. Ryan. 2013. "Colloid Transport in Saturated Porous Media: Elimination of Attachment Efficiency in a New Colloid Transport Model." Water Resources Research 49, no. 5:2952-2965. PNNL-SA-61490. doi:10.1002/wrcr.20195
  • Richmond M.C., W.A. Perkins, T.D. Scheibe, A. Lambert, and B.D. Wood. 2013. "Flow and axial dispersion in a sinusoidal-walled tube: Effects of inertial and unsteady flows." Advances in Water Resources 62, no. Part B:215-226. PNNL-SA-91772. doi:10.1016/j.advwatres.2013.06.014
  • Scheibe T.D., M.D. White, S.K. White, C. Sivaramakrishnan, S. Purohit, G.D. Black, and R. Podgorney, et al. 2013. "Simulation of Enhanced Geothermal Systems: A Benchmarking and Code Intercomparison Study." In MODFLOW and More 2013: Translating Science into Practice, June 2-5, Golden, Colorado. Golden, Colorado:Integrated Ground Water Modeling Center. PNNL-SA-94774.
  • Scheibe T.D., Z. Hou, B.J. Palmer, and A.M. Tartakovsky. 2013. "Pore-Scale Simulation of Intragranular Diffusion: Effects of Incomplete Mixing on Macroscopic Manifestations." Water Resources Research 49, no. 7:4277-4294. PNNL-SA-91962. doi:10.1002/wrcr.20333
  • Tartakovsky G.D., A.M. Tartakovsky, T.D. Scheibe, Y. Fang, R. Mahadevan, and D.R. Lovley. 2013. "Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport." Advances in Water Resources 59. PNNL-SA-90155. doi:10.1016/j.advwatres.2013.05.007
  • Yang X., T.D. Scheibe, M.C. Richmond, W.A. Perkins, S.J. Vogt, S.L. Codd, and J.D. Seymour, et al. 2013. "Direct Numerical Simulation of Pore-Scale Flow in a Bead Pack: Comparison with Magnetic Resonance Imaging Observations." Advances in Water Resources 54. PNNL-SA-90263. doi:10.1016/j.advwatres.2013.01.009


  • Xu Z., Y. Fang, T.D. Scheibe, and A. Bonneville. 2012. "A fluid pressure and deformation analysis for geological sequestration of carbon dioxide." Computers & Geosciences 46. PNNL-SA-82750.
  • Xu Z., Y. Fang, T.D. Scheibe, and A. Bonneville. 2012. "A Hydro-mechanical Model and Analytical Solutions for Geomechanical Modeling of Carbon Dioxide Geological Sequestration." In Energy Technology 2012: Carbon Dioxide Management and Other Technologies, edited by MD Salazar-Villalpando, et al. Hoboken, New Jersey:John Wiley & Sons, Inc. PNNL-SA-85371.


  • Agarwal K., J.M. Chase, K.L. Schuchardt, T.D. Scheibe, B.J. Palmer, and T.O. Elsethagen. 2011. "Design and Implementation of “Many Parallel Task” Hybrid Subsurface Model." In MTAGS '11: Proceedings of the 2011 ACM International Workshop on Many Task Computing on Grids and Supercomputers, November 12-18, 2011, Seattle, Washington, 25-32. New York, New York:Association for Computing Machinery. PNNL-SA-83048. doi:10.1145/2132876.2132884
  • Battiato I., D.M. Tartakovsky, A.M. Tartakovsky, and T.D. Scheibe. 2011. "Hybrid Models of Reactive Transport in Porous and Fractured Media." Advances in Water Resources 37, no. 9:1140-1150. PNNL-SA-74317. doi:10.1016/j.advwatres.2011.01.012
  • Fang Y., T.D. Scheibe, R. Mahadevan, S. Garg, P.E. Long, and D.R. Lovley. 2011. "Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model." Journal of Contaminant Hydrology 122, no. 1-4:96-103. PNNL-SA-75520. doi:10.1016/j.jconhyd.2010.11.007
  • Scheibe T.D., A.M. Tartakovsky, U.C. Bandara, B.J. Palmer, M. Oostrom, C. Zhang, and A. Bonneville. 2011. "Physical and Numerical Models of Pore-Scale Trapping of CO2." In Les Rencontres Scientifiques d’IFP Energies Nouvelles: International Conference on Flows and Mechanics in Natural Porous Media from Pore to Field Scale - Pore2Field, November 16-18, 2011, Rueil-Malmaison, France. Paris:IFP Energies Nouvelles. PNNL-SA-83932.
  • Scheibe T.D., S.S. Hubbard, T.C. Onstott, and M.F. Deflaun. 2011. "Lessons Learned from Bacterial Transport Experiments at the South Oyster Site." Groundwater 49, no. 5:745-763. PNNL-SA-76534. doi:10.1111/j.1745-6584.2011.00831.x
  • Tartakovsky A.M., and T.D. Scheibe. 2011. "Dimension reduction method for SPH equations." In Proceedings of the 6th international SPHERIC Workshop, June 8-10, 2011, Hamburg, Germany, edited by T Rund and C Ulrich, 22-29. Hamburg:Schriftenreihe Schiffbau. PNNL-SA-80227.
  • Tartakovsky A.M., and T.D. Scheibe. 2011. "DIMENSION REDUCTION NUMERICAL CLOSURE METHOD FOR ADVECTION-DIFFUSION-REACTION SYSTEMS." Advances in Water Resources 34, no. 12:1616-1626. PNNL-SA-79493. doi:10.1016/j.advwatres.2011.07.011
  • Xu Z., P. Meakin, A.M. Tartakovsky, and T.D. Scheibe. 2011. "Dissipative-particle-dynamics model of biofilm growth." Physical Review E 83, no. 6:Article No. 066702. PNNL-SA-75521. doi:10.1103/PhysRevE.83.066702
  • Zhao J., J. Zhao, T.D. Scheibe, and R. Mahadevan. 2011. "Model-Based Analysis of the Role of Biological, Hydrological and Geochemical Factors Affecting Uranium Bioremediation." Biotechnology and Bioengineering 108, no. 7:1537-1548. PNNL-SA-78433.


  • Guin A., R. Ramanathan, R.W. Ritzi, D.F. Dominic, I.A. Lunt, T.D. Scheibe, and V.L. Freedman. 2010. "Simulating the Heterogeneity in Braided Channel Belt Deposits: 2. Examples of Results and Comparison to Natural Deposits." Water Resources Research 46. PNNL-SA-69315.
  • Gurumoorthi V., A.M. Tartakovsky, T.D. Scheibe, and B.J. Palmer. 2010. "A Component-Based Framework for Smoothed Particle Hydrodynamics Simulations of Reactive Fluid Flow in Porous Media." International Journal of High Performance Computing Applications 24, no. 2:228-239. PNNL-SA-65869. doi:10.1177/1094342009358415
  • Ramanathan R., A. Guin, R.W. Ritzi, D.F. Dominic, V.L. Freedman, T.D. Scheibe, and I.A. Lunt. 2010. "Simulating the Heterogeneity in Braided Channel Belt Deposits: Part 1. A Geometric-Based Methodology and Code." Water Resources Research 46. PNNL-SA-69314.
  • Scheibe T.D., B.J. Palmer, K.L. Schuchardt, Y. Fang, and A.M. Tartakovsky. 2010. "Simulations of Subsurface Flow and Transport at the Pore and Continuum Scales." In SciDAC 2010 Scientific Discovery Through Advanced Computing, July 11-15, 2010, Chattanooga, Tennessee. Washington Dc:US Department of Energy, Office of Science. PNNL-SA-74118.
  • Schuchardt K.L., K. Agarwal, J.M. Chase, M.L. Rockhold, V.L. Freedman, T.O. Elsethagen, and T.D. Scheibe, et al. 2010. "Task parallel sensitivity analysis and parameter estimation of groundwater simulations through the SALSSA framework." In Proceedings of the 2010 Scientific Discovery through Advanced Computing (SciDAC) Conference, July 11-15, 2010, Cattanooga, Tennessee, 233-237. Oak Ridge, Tennessee:Oak Ridge National Laboratory. PNNL-SA-73770.
  • Zhao J., J. Zhao, Y. Fang, T.D. Scheibe, D.R. Lovley, and R. Mahadevan. 2010. "Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments." Journal of Contaminant Hydrology 112, no. 1-4:30-44. PNNL-SA-64401. doi:10.1016/j.jconhyd.2009.10.002


  • Battiato I., D.M. Tartakovsky, A.M. Tartakovsky, and T.D. Scheibe. 2009. "On breakdown of macroscopic models of mixing-controlled heterogeneous reactions in porous media." Advances in Water Resources 32, no. 11:1664-1673. PNNL-SA-64544.
  • Palmer B.J., Y. Fang, V. Gurumoorthi, G.E. Hammond, J.A. Fort, and T.D. Scheibe. 2009. "Developing a Component-Based Framework for Subsurface Simulation using the Common Component Architecture." In SciDAC 2009: Journal of Physics: Conference Series, 180, Paper No. 012064. London:IOP Publishing. PNNL-SA-66756. doi:10.1088/1742-6596/180/1/012064
  • Scheibe T.D., R. Mahadevan, Y. Fang, S. Garg, P.E. Long, and D.R. Lovley. 2009. "Coupling a Genome-Scale Metabolic Model with a Reactive Transport Model to Describe In Situ Uranium Bioremediation." Microbial Biotechnology 2, no. 2:274-286. PNNL-SA-61861. doi:10.1111/j.1751-7915.2009.00087.x
  • Schuchardt K.L., J.M. Chase, J.A. Daily, T.O. Elsethagen, B.J. Palmer, and T.D. Scheibe. 2009. "Application of SALSSA Framework to the Validation of Smoothed Particle Hydrodynamics Simulations of Low Reynolds Number Flows." Journal of Physics: Conference Series 180, no. 1:Article No. 012065. PNNL-SA-66754. doi:10.1088/1742-6596/180/1/012065
  • Tartakovsky A.M., G.D. Tartakovsky, and T.D. Scheibe. 2009. "EFFECTS OF INCOMPLETE MIXING ON MULTICOMPONENT REACTIVE TRANSPORT." Advances in Water Resources 32, no. 11:1674-1679. PNNL-SA-65914.
  • Tartakovsky A.M., T.D. Scheibe, and P. Meakin. 2009. "PORE-SCALE MODEL FOR REACTIVE TRANSPORT AND BIOMASS GROWTH." Journal of Porous Media 12, no. 5:417-434. PNNL-SA-57286.


  • Chase J.M., K.L. Schuchardt, G. Chin, J.A. Daily, and T.D. Scheibe. 2008. "Iterative Workflows for Numerical Simulations in Subsurface Sciences." In Proceedings of 2008 IEEE Congress on Services Part 1, 461-464. Los Alamitos, California:IEEE Computer Society. PNNL-SA-59717. doi:10.1109/SERVICES-1.2008.96
  • Ginn T.R., and T.D. Scheibe. 2008. "Introduction: Special Issue: Discussions on Metahydrogeology: Research Stocktaking or Identity Crisis? Essays on the Once and Future Merit of Research in Hydrogeology." Journal of Hydrologic Engineering 13, no. 1:1. PNNL-SA-59463.
  • Scheibe T.D., A.M. Tartakovsky, D.M. Tartakovsky, G.D. Redden, P. Meakin, B.J. Palmer, and K.L. Schuchardt. 2008. "Hybrid numerical methods for multiscale simulations of subsurface biogeochemical processes." Journal of Physics: Conference Series 125, no. 1:Article No. 012054. PNNL-SA-60981. doi:10.1088/1742-6596/125/1/012054
  • Scheibe T.D., P. Meakin, P.C. Lichtner, and D. Zachmann. 2008. "Science for Problems Under the Surface." SciDAC Review 2008, no. 7:32-41. PNNL-SA-57311.
  • Tartakovsky A.M., D.M. Tartakovsky, T.D. Scheibe, and P. Meakin. 2008. "Hybrid Simulations of Reaction-Diffusion Systems in Porous Media." SIAM Journal on Scientific Computing 30, no. 6:2799-2816. PNNL-SA-55164. doi:10.1137/070691097
  • Tartakovsky A.M., G.D. Redden, P.C. Lichtner, T.D. Scheibe, and P. Meakin. 2008. "Mixing-Induced Precipitation: Experimental Study and Multi-Scale Numerical Analysis." Water Resources Research 44, no. 6:Art. No. W06S04. PNNL-SA-52847. doi:10.1029/2006WR005725


  • Ginn T.R., F.J. Loge, and T.D. Scheibe. 2007. "Explaining "Noise" as Environmental Variations in Population Dynamics." Computing in Science & Engineering 9, no. 2:40-49. PNWD-SA-7477. doi:10.1109/MCSE.2007.30
  • Kamolpornwijit W., S.C. Brooks, Y. Kim, and T.D. Scheibe. 2007. "A Novel Approach to Estimate Iron Distribution Within Different Pore Domains of Structured Media." Applied Geochemistry 22. PNNL-SA-52606. doi:10.1016/j.apgeochem.2007.06.008
  • Meakin P., A.M. Tartakovsky, T.D. Scheibe, D.M. Tartakovsky, G. Redden, P.E. Long, and S.C. Brooks, et al. 2007. "Particle methods for simulation of subsurface multiphase fluid flow and biogeological processes." Journal of Physics: Conference Series 78, no. 1:Article No. 012047. PNNL-SA-55963. doi:10.1088/1742-6596/78/1/012047
  • Scheibe T.D., A.M. Tartakovsky, D.M. Tartakovsky, G.D. Redden, and P. Meakin. 2007. "Hybrid Numerical Methods for Multiscale Simulations of Subsurface Biogeochemical Processes." Journal of Physics: Conference Series 78, no. 1:Article No. 012063. PNNL-SA-55880. doi:10.1088/1742-6596/78/1/012063
  • Scheibe T.D., H. Dong, and Y. Xie. 2007. "Correlation Between Bacterial Attachment Rate Coefficients and Hydraulic Conductivity and its Effect on Field-Scale Bacterial Transport." Advances in Water Resources 30, no. 6-7:1571-1582. PNNL-SA-46481. doi:10.1016/j.advwatres.2006.05.021
  • Tartakovsky A.M., P. Meakin, and T.D. Scheibe. 2007. "Reactive transport and biomass growth in porous media." In Proceedings of the Second Workshop on Smoothed Particle Hydrodynamics European Research Interest Community (SPHERIC), May 23-25, 2007, Madrid, Spain, edited by AJC Crespo, et al, 139. San Ciprián De Viñas:Aica. PNNL-SA-55222.
  • Tartakovsky A.M., P. Meakin, T.D. Scheibe, and B.D. Wood. 2007. "A smoothed particle hydrodynamics model for reactive transport and mineral precipitation in porous and fractured porous media." Water Resources Research 43, no. 5:Art. No. W05437. PNNL-SA-47642. doi:10.1029/2005WR004770
  • Tartakovsky A.M., P. Meakin, T.D. Scheibe, and R.M. Eichler West. 2007. "Simulations of reactive transport and precipitation with smoothed particle hydrodynamics." Journal of Computational Physics 222, no. 2:654-672. PNNL-SA-46816.


  • Dong H., T.D. Scheibe, W.P. Johnson, C. Monkman, and M.E. Fuller. 2006. "Change of Collision Efficiency with Distance in Bacterial Transport Experiements." Ground Water 44, no. 3:415-429. PNNL-SA-37865. doi:10.1111/j.1745-6584.2005.00133.x
  • Fang Y., T.D. Scheibe, E.E. Roden, W. Kamolpornwijit, and S.C. Brooks. 2006. "3D Field-Scale Reactive Transport Modeling of In Situ Immobilization of Uranium in Structured Porous Media via Biostimulation." In Proceedings of teh XVI International Conference on Computational Methods in Water Resources (CMWR XVI), June 18-22, 2006, Copenhagen, Denmark, edited by PJ Binning, et al. Kongens Lyngby:Technical University of Denmark. PNNL-SA-49173.
  • Scheibe T.D., Y. Fang, C.J. Murray, E.E. Roden, J. Chen, Y. Chien, and S.C. Brooks, et al. 2006. "Transport and biogeochemical reaction of metals in a physically and chemically heterogeneous aquifer." Geosphere 2, no. 4:220-235. PNNL-SA-47423.
  • Tartakovsky A.M., T.D. Scheibe, G. Redden, P. Meakin, and Y. Fang. 2006. "Smoothed Particle Hydrodynamics Model for Reactive Transport and Mineral Precipitation." In CMWR XVI - International Conference on Computational Methods in Water Resources. Copenhagen, Denmark, June 18-22, 2006, 8 pages. Copenhagen:Technical University of Denmark (DTU). PNNL-SA-51850. Smoothed Particle Hydrodynamics Model for Reactive Transport and Mineral Precipitation


  • Ginn T.R., T. Camesano, T.D. Scheibe, K.B. Nelson, T.P. Clement, and B.D. Wood. 2005. "Microbial Transport in the Subsurface." In Encyclopedia of Hydrological Sciences. New York, New York:John Wiley & Sons, Ltd. PNNL-SA-40818.
  • Hall J.A., B.J. Mailloux, T.C. Onstott, T.D. Scheibe, M.E. Fuller, H. Dong, and M.F. Deflaun. 2005. "Physical versus chemical effects on bacterial and bromide transport as determined from on site sediment column pulse experiments." Journal of Contaminant Hydrology 76, no. 3-4:295-314. PNNL-SA-41974.
  • Roden E.E., and T.D. Scheibe. 2005. "Conceptual and numerical model of uranium(VI) reductive immobilization in fractured subsurface sediments." Chemosphere 59, no. 5:617-628. PNNL-SA-45141. doi:10.1016/j.chemosphere.2004.11.007


  • Engel D.W., A.M. Liebetrau, K.D. Jarman, T.A. Ferryman, T.D. Scheibe, and B.T. Didier. 2004. "An Iterative Uncertainty Assessment Technique for Environmental Modeling." In The joint proceedings of the sixth International Symposium on Spatial Accuracy Assessment in Natural Resources and Environmental Sciences and the fifteenth annual conference of TIES, the International Environmetrics Society Portland, Maine, USA, June 28-July 1, 2004, edited by H. Todd Mowrer, Ronald E. McRoberts, and Paul C. VanDeusen, 8 pages. Washington, District Of Columbia:USDA Forest Service. PNNL-SA-43990.
  • Li X., T.D. Scheibe, and W.P. Johnson. 2004. "Apparent Decreases in Colloid Deposition Rate Coefficients with Distance of Transport under Unfavorable Deposition Conditions: A General Phenomenon." Environmental Science & Technology 38, no. 21:5616-5625. PNNL-SA-38828.
  • Scheibe T.D. 2004. "Interactive models for ground water flow and solute transport." Ground Water 42, no. 1:8 - 11. PNNL-SA-41216.


  • Savelieva-Trofimova E.A., M. Kanevski, v. timonin, A. Pozdnukhov, C.J. Murray, T.D. Scheibe, and Y. Xie, et al. 2003. "Aquifer Hydrogeologic Layer Zonation at the Hanford Site." In Proceedings IAMG 2003, 46+. Kingston, Ont:International Association for Mathematical Geosciences. PNNL-SA-38948.
  • Scheibe T.D., and B.D. Wood. 2003. "A particle-based model of size or anion exclusion with application to microbial transport in Porous Media." Water Resources Research 39, no. NO. 4:1080. PNNL-SA-33089. doi:10.1029/2001WR001223
  • Scheibe T.D., and Y. Chien. 2003. "An Evaluation of Conditioning Data for Solute Transport Prediction." Ground Water 41, no. 2:128-141. PNNL-SA-35841.
  • Scheibe T.D., C.J. Murray, Y. Xie, M.D. Williams, C.R. Cole, V.R. Vermeul, and M.P. Bergeron. 2003. "Temporal and Spatial Weighting of Head and Concentration Observations for a Large-Scale Transient Inverse Model." In Proceedings of Modflow and More 2003: Understanding through Modeling, 610-614. Golden, Colorado:Colorado School of Mines, International Ground Water Modeling Center. PNNL-SA-39048.


  • Dong H., T.C. Onstott, M.F. Deflaun, M.E. Fuller, T.D. Scheibe, S.H. Streger, and R.K. Rothmel, et al. 2002. "Relative Dominance of Physical versus Chemical Effects on the Transport of Adhesion-Deficient Bacteria in Intact Cores from South Oyster, Virginia." Environmental Science & Technology 36, no. 5:891-900. PNNL-SA-34868.
  • Ginn T.R., B.D. Wood, K.E. Nelson, T.D. Scheibe, E.M. Murphy, and T.P. Clement. 2002. "Processes in Microbial Transport in the Natural Subsurface." Advances in Water Resources 25, no. 8-12:1027 - 1042. PNNL-SA-35848.
  • Scheibe T.D. 2002. "Correlation Between Heterogeneous Bacterial Attachment Rate Coefficients and Hydraulic Conductivity and Impacts on Field-Scale Bacterial Transport." In Proceedings of the International Groundwater Symposium 2002; Bridging the Gap Between Measureemt and Modeling in Heterogeneous Media, edited by AN Findikakis. Madrid:International Association of Hydraulic Engineering and Research. PNNL-SA-35108.
  • Scheibe T.D., and M.C. Richmond. 2002. "Fish Individual-based Numerical Simulator (FINS): A particle-based model of juvenile salmonid movement and dissolved gas exposure history in the Columbia River Basin." Ecological Modelling 147, no. 3:233-252. PNNL-SA-33102.
  • Scheibe T.D., M.C. Richmond, and L.E. Fidler. 2002. "Impacts of individual fish movement patterns on estimates of mortality due to dissolved gas supersaturation in the Columbia River Basin." In HydroVision 2002: Issues Solutioins New Approaches, no. 155. Kansas City, Missouri:HCI Publications. PNNL-SA-35955.


  • Balkwill D., J. Chen, M. Deflaun, F. Dobbs, H. Dong, J.K. Fredrickson, and M. Fuller, et al. 2001. "Breakthroughs in field-scale bacterial transport." Eos 82, no. 38:417, 423-425. PNNL-SA-31732.
  • Johnson W.P., P. Zhang, M.E. Fuller, T.D. Scheibe, B.J. Mailloux, T.C. Onstott, and M.F. Deflaun, et al. 2001. "Ferrographic tracking of bacterial transport in the field at the Narrow Channel focus area, Oyster, VA." Environmental Science & Technology 35, no. 1:182-191. PNNL-SA-35083.
  • Scheibe T.D. 2001. "The Value of Conditioning Data for Prediction of Conservative Solute Transport at the Oyster Site, Virginia." In MODFLOW 2001 and Other Modeling Odysseys, 1, 276-282. Golden, Colorado:International Groundwater Modeling Center. PNNL-SA-34725.
  • Scheibe T.D., Y. Chien, and J. Radtke. 2001. "Use of quantitative models to design microbial transport experiments in a sandy aquifer." Ground Water 39, no. 2:210-222. PNNL-SA-33029.
  • Zhang P., W.P. Johnson, T.D. Scheibe, K. Choi, F.C. Dobbs, and B.J. Mailloux. 2001. "Extended tailing of bacteria following breakthrough at the Narrow Channel focus area, Oyster, Virginia." Water Resources Research 37, no. 11:2687-2698. PNNL-SA-34339.

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