Lab Fellow, Earth Scientist
Environmental Dynamics & Simulations
Lab Fellow, Earth Scientist
Environmental Dynamics & Simulations


Dr. Tim Scheibe is a laboratory fellow working with the Environmental Transformations and Interactions group in PNNL’s Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. Scheibe is EMSL’s lead scientist for multiscale modeling and high-performance computing and the principal investigator for PNNL’s River Corridor Scientific Focus Area project, sponsored by the U.S. Department of Energy, Office of Science’s Biological and Environmental Research (BER) program’s Environmental System Science program. This work 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. 

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 critical scientific issues in environmental molecular science relevant to BER missions. He has been with PNNL since 1992. 

Research Interest

  • 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.


  • PhD in Civil Engineering, Stanford University, 1993
  • MS in Civil Engineering, University of Washington, 1987
  • BS in Geological Engineering, Washington State University, 1984

Affiliations and Professional Service

  • Member, American Geophysical Union 

  • Member, National Ground Water Association 

  • Member, Editorial Board, Groundwater, 2001 – 2019 

  • Member, Editorial Board, PeerJ, 2017 – Present 

  • Member, Editorial Board, Water, 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 



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.


Fang, Y., S. B. Yabusaki, A. H. 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 (1-2): 33-48.

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: 435-445.

Hou, Z., T. D. Scheibe, C. J. Murray, W. A. Perkins, E. V. Arntzen, H. Ren, R. D. Mackley, and M. C. Richmond. 2019. “Identification and Mapping of Riverbed Sediment Facies in the Columbia River through Integration of Field Observations and Numerical Simulations.” Hydrological Processes 33 (8): 1245-1259.

Meile, C., and T. D. Scheibe. 2019. “Reactive Transport Modeling of Microbial Dynamics.” Elements 15 (2): 111-116.

Yang, X., R. Parashar, N. L. 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 (1).


Korneev, S. V., 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 (4): 2871-2890.

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 (Switzerland) 10 (12).

Meile, C., and T. D. Scheibe. 2018. “Reactive Transport Modeling and Biogeochemical Cycling.” In Reactive Transport Modeling: Applications in Subsurface Energy and Environmental Problems, 485-510.


Hou, Z., W. C. Nelson, J. C. Stegen, C. J. Murray, E. Arntzen, A. R. Crump, D. W. Kennedy, M. C. Perkins, T. D. Scheibe, J. K. Fredrickson, and J. M. Zachara. 2017. “Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies.” Scientific Reports 7 (1).

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: 259-262.


Yang, X., Y. Mehmani, W. A. Perkins, A. Pasquali, M. Schönherr, K. Kim, M. Perego, M. L. Parks, N. Trask, M. T. Balhoff, M. C. Richmond, M. Geier, M. Krafczyk, L. S. Luo, A. M. Tartakovsky, and T. D. Scheibe. 2016. “Intercomparison of 3D Pore-Scale Flow and Solute Transport Simulation Methods.” Advances in Water Resources 95: 176-189.


Scheibe, T. D., E. M. Murphy, X. Chen, A. K. Rice, K. C. Carroll, B. J. Palmer, A. M. Tartakovsky, I. Battiato, and B. D. Wood. 2015. “An Analysis Platform for Multiscale Hydrogeologic Modeling with Emphasis on Hybrid Multiscale Methods.” Groundwater 53 (1): 38-56.

Scheibe, T. D., W. A. Perkins, M. C. Richmond, M. I. McKinley, P. D. J. Romero-Gomez, M. Oostrom, T. W. Wietsma, J. A. Serkowski, and J. M. Zachara. 2015. “Pore-Scale and Multiscale Numerical Simulation of Flow and Transport in a Laboratory-Scale Column.” Water Resources Research 51 (2): 1023-1035.

Scheibe, T. D., K. Schuchardt, K. Agarwal, J. Chase, X. Yang, B. J. Palmer, A. M. Tartakovsky, T. Elsethagen, and G. Redden. 2015. “Hybrid Multiscale Simulation of a Mixing-Controlled Reaction.” Advances in Water Resources 83: 228-239.

Scheibe, T. D., X. Yang, X. Chen, and G. Hammond. 2015. “A Hybrid Multiscale Framework for Subsurface Flow and Transport Simulations.”


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 (2): 295-314.


Fang, Y., B. N. Nguyen, K. 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: 138-147.

Freshley, M., P. Dixon, P. Black, B. Robinson, T. Stockton, J. David Moulton, T. Scheibe, R. Seitz, K. Gerdes, and J. Marble. 2013. “Advanced Simulation Capability for Environmental Management - Current Status and Future Applications.”

Keyes, D. E., L. C. McInnes, C. Woodward, W. Gropp, E. Myra, M. Pernice, J. Bell, J. Brown, A. Clo, J. Connors, E. Constantinescu, D. Estep, K. Evans, C. Farhat, A. Hakim, G. Hammond, G. Hansen, J. Hill, T. Isaac, X. Jiao, K. Jordan, D. Kaushik, E. Kaxiras, A. Koniges, K. Lee, A. Lott, Q. Lu, J. Magerlein, R. Maxwell, M. McCourt, M. Mehl, R. Pawlowski, A. P. Randles, D. Reynolds, B. Rivière, U. Rüde, T. Scheibe, J. Shadid, B. Sheehan, M. Shephard, A. Siegel, B. Smith, X. Tang, C. Wilson, and B. Wohlmuth. 2013. “Multiphysics Simulations: Challenges and Opportunities.” International Journal of High Performance Computing Applications 27 (1): 4-83.

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 (5): 2952-2965.

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: 215-226.

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 (7): 4277-4294.

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: 256-270.

Yang, X., T. D. Scheibe, M. C. Richmond, W. A. Perkins, S. J. Vogt, S. L. Codd, J. D. Seymour, and M. I. McKinley. 2013. “Direct Numerical Simulation of Pore-Scale Flow in a Bead Pack: Comparison with Magnetic Resonance Imaging Observations.” Advances in Water Resources 54: 228-241.

Zhao, J., T. D. Scheibe, and R. Mahadevan. 2013. “Model-Based Analysis of Mixed Uranium(VI) Reduction by Biotic and Abiotic Pathways During in Situ Bioremediation.” Chemical Geology 357: 215-222.


Xu, Z., Y. Fang, T. D. Scheibe, and A. Bonneville. 2012. “A Fluid Pressure and Deformation Analysis for Geological Sequestration of Carbon Dioxide.” Computers and Geosciences 46: 31-37.

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, 47-53.


Agarwal, K., J. M. Chase, K. L. Schuchardt, T. D. Schiebe, B. J. Palmer, and T. O. Elsethagen. 2011. “Design and Implementation of "Many Parallel Task" Hybrid Subsurface Model.”

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 34 (9): 1140-1150.

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 (1-4): 96-103.

Scheibe, T. D., S. S. Hubbard, T. C. Onstott, and M. F. DeFlaun. 2011. “Lessons Learned from Bacterial Transport Research at the South Oyster Site.” Ground Water 49 (5): 745-763.

Tartakovsky, A. M., and T. D. Scheibe. 2011. “Dimension Reduction Numerical Closure Method for Advection-Diffusion-Reaction Systems.” Advances in Water Resources 34 (12): 1616-1626.

Xu, Z., P. Meakin, A. Tartakovsky, and T. D. Scheibe. 2011. “Dissipative-Particle-Dynamics Model of Biofilm Growth.” Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 83 (6).

Zhao, J., 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 (7): 1537-1548.


Guin, A., R. Ramanathan, R. W. Ritzi, Jr., 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 (4).

Palmer, B., V. Gurumoorthi, A. Tartakovsky, and T. Scheibe. 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 (2): 228-239.

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: A Geometric-Based Methodology and Code.” Water Resources Research 46 (4).

Zhao, J., 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 (1-4): 30-44.


Battiato, I., D. M. Tartakovsky, A. M. Tartakovsky, and T. Scheibe. 2009. “On Breakdown of Macroscopic Models of Mixing-Controlled Heterogeneous Reactions in Porous Media.” Advances in Water Resources 32 (11): 1664-1673.

Palmer, B., Y. Fang, V. Gurumoorthi, G. Hammond, J. Fort, and T. Scheibe. 2009. “Developing a Component-Based Framework for Subsurface Simulation Using the Common Component Architecture.” Journal of Physics: Conference Series.

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 (2 SPEC. ISS.): 274-286.

Schuchardt, K., J. Chase, J. Daily, T. Elsethagen, B. Palmer, and T. Scheibe. 2009. “Application of the SALSSA Framework to the Validation of Smoothed Particle Hydrodynamics Simulations of Low Reynolds Number Flows.” Journal of Physics: Conference Series.

Tartakovsky, A. M., T. D. Scheibe, and P. Meakin. 2009. “Pore-Scale Model for Reactive Transport and Biomass Growth.” Journal of Porous Media 12 (5): 417-434.

Tartakovsky, A. M., G. D. Tartakovsky, and T. D. Scheibe. 2009. “Effects of Incomplete Mixing on Multicomponent Reactive Transport.” Advances in Water Resources 32 (11): 1674-1679.


Ginn, T., and T. Scheibe. 2008. “Special Issue on Discussions on Metahydrogeology: Research Stocktaking or Identity Crisis? Essays on the Once and Future Merit of Research in Hydrogeology.” Journal of Hydrologic Engineering 13 (1): 1. 

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.

Tartakovsky, A. M., G. Redden, P. C. Lichtner, T. D. Scheibe, and P. Meakin. 2008. “Mixing-Induced Precipitation: Experimental Study and Multiscale Numerical Analysis.” Water Resources Research 44 (6).

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 (6): 2799-2816.


Ginn, T. R., F. J. Loge, and T. D. Scheibe. 2007. “Explaining "Noise" as Environmental Variations in Population Dynamics.” Computing in Science and Engineering 9 (2): 40-49.

Kamolpornwijit, W., S. C. Brooks, Y. J. Kim, and T. D. Scheibe. 2007. “A Novel Approach to Estimate Iron Distribution within Different Pore Domains of Structured Media.” Applied Geochemistry 22 (12): 2630-2636.

Meakin, P., A. Tartakovsky, T. Scheibe, D. Tartakovsky, G. Redden, P. E. Long, S. C. Brooks, and Z. Xu. 2007. “Particle Methods for Simulation of Subsurface Multiphase Fluid Flow and Biogeochemical Processes.” Journal of Physics: Conference Series 78 (1).

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 (6-7): 1571-1582.

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 (1).

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 (2): 654-672.

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 (5).


Dong, H., T. D. Scheibe, W. P. Johnson, C. M. Monkman, and M. E. Fuller. 2006. “Change of Collision Efficiency with Distance in Bacterial Transport Experiments.” Ground Water 44 (3): 415-429.

Scheibe, T. D., Y. Fang, C. J. Murray, E. E. Roden, J. Chen, Y. J. Chien, S. C. Brooks, and S. S. Hubbard. 2006. “Transport and Biogeochemical Reaction of Metals in a Physically and Chemically Heterogeneous Aquifer.” Geosphere 2 (4): 220-235.


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 (3-4): 295-314.

Roden, E. E., and T. D. Scheibe. 2005. “Conceptual and Numerical Model of Uranium(VI) Reductive Immobilization in Fractured Subsurface Sediments.” Chemosphere 59 (5): 617-628.


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 and Technology 38 (21): 5616-5625.

Scheibe, T. 2004. “Interactive Models for Ground Water Flow and Solute Transport.” Ground Water 42 (1): 8-11.


Scheibe, T. D., and Y. J. Chien. 2003. “An Evaluation of Conditioning Data for Solute Transport Prediction.” Ground Water 41 (2): 128-141.

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 (4): SBH31-SBH310.


Dong, H., T. C. Onstott, M. F. Deflaun, M. E. Fuller, T. D. Scheibe, S. H. Streger, R. K. Rothmel, and B. J. Mailloux. 2002. “Relative Dominance of Physical Versus Chemical Effects on the Transport of Adhesion-Deficient Bacteria in Intact Cores from South Oyster, Virginia.” Environmental Science and Technology 36 (5): 891-900.

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 (8-12): 1017-1042.

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 (3): 233-252.


Balkwill, D., J. Chen, M. DeFlaun, F. Dobbs, H. Dong, J. Fredrickson, M. Fuller, M. Green, T. Ginn, T. Griffin, W. Holben, S. Hubbard, W. Johnson, P. Long, B. Mailloux, E. Majer, M. McLnerney, C. Murray, T. Onstott, T. Phelps, T. Scheibe, D. Swift, D. White, and F. Wobber. 2001. “Breakthroughs in Field-Scale Bacterial Transport.” Eos 82 (38): 417+423-425.

Johnson, W. P., P. Zhang, M. E. Fuller, T. D. Scheibe, B. J. Mailloux, T. C. Onstott, M. F. Deflaun, S. S. Hubbard, J. Radtke, W. P. Kovacik, and W. Holben. 2001. “Ferrographic Tracking of Bacterial Transport in the Field at the Narrow Channel Focus Area, Oyster, Va.” Environmental Science and Technology 35 (1): 182-191.

Scheibe, T. D., Y. J. Chien, and J. S. Radtke. 2001. “Use of Quantitative Models to Design Microbial Transport Experiments in a Sandy Aquifer.” Ground Water 39 (2): 210-222.

Zhang, P., W. P. Johnson, T. D. Scheibe, K. H. 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 (11): 2687-2698.


Richmond, M. C., W. A. Perkins, and T. D. Scheibe. 1999. “Two-Dimensional Simulation of Hydrodynamics, Water Quality, and Fish Exposure in the Columbia/Snake River System.”


Scheibe, T., and S. Yabusaki. 1998. “Scaling of Flow and Transport Behavior in Heterogeneous Groundwater Systems.” Advances in Water Resources 22 (3): 223-238.


DeFlaun, M. F., C. J. Murray, W. Holben, T. Scheibe, A. Mills, T. Ginn, T. Griffin, E. Majer, and J. L. Wilson. 1997. “Preliminary Observations on Bacterial Transport in a Coastal Plain Aquifer.” FEMS Microbiology Reviews 20 (3-4): 473-487.


Scheibe, T. D., and D. L. Freyberg. 1995. “Use of Sedimentological Information for Geometric Simulation of Natural Porous Media Structure.” Water Resources Research 31 (12): 3259-3270.


Scheibe, T. D., and C. R. Cole. 1994. “Non‐Gaussian Particle Tracking: Application to Scaling of Transport Processes in Heterogeneous Porous Media.” Water Resources Research 30 (7): 2027-2039.


Scheibe, T. D., and D. P. Lettenmaier. 1989. “Risk‐Based Selection of Monitoring Wells for Assessing Agricultural Chemical Contamination of Ground Water.” Groundwater Monitoring & Remediation 9 (4): 98-108.