Skip to Main Content U.S. Department of Energy

Yilin Fang

Yilin Fang

Pacific Northwest National Laboratory
PO Box 999
Richland, WA 99352

PNNL Publications


  • Fang Y, LY Leung, Z Duan, MS Wigmosta, RM Maxwell, JQ Chambers, and J Tomasella. 2017. "Influence of landscape heterogeneity on water availability to tropical forests in an Amazonian catchment and implications for modeling drought response." Journal of Geophysical Research: Atmospheres 122(16):8410-8426.  doi:10.1002/2017JD027066


  • Danczak RE, SB Yabusaki, KH Williams, Y Fang, C Hobson, and MJ Wilkins. 2016. "Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer." Frontiers in Earth Science 4:57.  doi:10.3389/feart.2016.00057
  • Freedman VL, DH Bacon, and Y Fang. 2016. Integrated Disposal Facility FY 2016: ILAW Verification and Validation of the eSTOMP SimulatorPNNL-25185; RPT-IGTP-010 Rev. 0, Pacific Northwest National Laboratory, Richland, WA. 


  • Fang Y, C Liu, and LYR Leung. 2015. "Accelerating the spin-up of the coupled carbon and nitrogen cycle model in CLM4." Geoscientific Model Development 8(3):781-789.  doi:10.5194/gmd-8-781-2015
  • Bao J, Z Hou, Y Fang, H Ren, and G Lin. 2015. "Uncertainty quantification for evaluating the impacts of fracture zone on pressure build-up and ground surface uplift during geological CO2 sequestration." Greenhouse Gases: science and technology 5(3):254-267.  doi:10.1002/ghg.1456
  • Bao J, Z Xu, and Y Fang. 2015. "A coupled discrete element and finite element model for multiscale simulation of geological carbon sequestration." Greenhouse Gases: science and technology 5(4):474-486.  doi:10.1002/ghg.1491
  • Bao J, Z Xu, and Y Fang. 2015. "Uncertainty Quantification for the Reliability of the Analytical Analysis for the Simplified Model of CO2 Geological Sequestration." Greenhouse Gases: science and technology 5(1002):141-151.  doi:10.1002/ghg.1436
  • Bonneville A, E Heggy, CE Strickland, J Normand, JA Dermond, Y Fang, and EC Sullivan. 2015. "Geophysical Monitoring of Ground Surface Deformation Associated with a Confined Aquifer Storage and Recovery Operation." Water Resources Management 29(13):4667-4682.  doi:10.1007/s11269-015-1083-y
  • Long PE, KH Williams, JA Davis, PM Fox, MJ Wilkins, SB Yabusaki, Y Fang, SR Waichler, ES Berman, M Gupta, DP Chandler, CJ Murray, AD Peacock, L Giloteaux, KM Handley, DR Lovley, and JF Banfield. 2015. "Bicarbonate Impact on U(VI) Bioreduction in a Shallow Alluvial Aquifer." Geochimica et Cosmochimica Acta 150:106-124.  doi:10.1016/j.gca.2014.11.013
  • Yabusaki SB, S Sengor, and Y Fang. 2015. "A Uranium Bioremediation Reactive Transport Benchmark." Computational Geosciences 19(3):551-567.  doi:10.1007/s10596-015-9474-y
  • Yang X, C Liu, Y Fang, R Hinkle, H Li, VL Bailey, and B Bond-Lamberty. 2015. "Simulations of Ecosystem Hydrological Processes Using a Unified Multi-Scale Model." Ecological Modelling 296:93-101.  doi:10.1016/j.ecolmodel.2014.10.032


  • Fang Y, C Liu, M Huang, H Li, and LYR Leung. 2014. "Steady state estimation of soil organic carbon using satellite-derived canopy leaf area index." Journal of Advances in Modeling Earth Systems 6(4):1049-1064.  doi:10.1002/2014MS000331
  • Bao J, Y Chu, Z Xu, AM Tartakovsky, and Y Fang. 2014. "Uncertainty quantification for the impact of injection rate fluctuation on the geomechanical response of geological carbon sequestration." International Journal of Greenhouse Gas Control 20:160-167.  doi:10.1016/j.ijggc.2013.10.023
  • Bao J, Z Xu, and Y Fang. 2014. "A Finite-Element Model for Simulation of Carbon Dioxide Sequestration." Environmental Geotechnics 1(3):152-160.  doi:10.1680/envgeo.13.00024
  • Fang Z, Z Hou, G Lin, DW Engel, Y Fang, and PW Eslinger. 2014. "Exploring the effects of data quality, data worth, and redundancy of CO2 gas pressure and saturation data on reservoir characterization through PEST Inversion." Environmental Earth Sciences 71(7):3025-3037.  doi:10.1007/s12665-013-2680-9
  • Hou Z, DH Bacon, DW Engel, G Lin, Y Fang, H Ren, and Z Fang. 2014. "Uncertainty analyses of CO2 plume expansion subsequent to wellbore CO2 leakage into aquifers." International Journal of Greenhouse Gas Control 27:69-80.  doi:10.1016/j.ijggc.2014.05.004
  • Yang X, C Liu, J Shang, Y Fang, and VL Bailey. 2014. "A Unified Multi-Scale Model for Pore-Scale Flow Simulations in Soils." Soil Science Society of America Journal 78(1):108-118.  doi:10.2136/sssaj2013.05.0190


  • Fang Y, BN Nguyen, KC Carroll, Z Xu, SB Yabusaki, TD 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.  doi:10.1016/j.ijrmms.2013.05.002
  • Fang Y, M Huang, C Liu, H Li, and LYR Leung. 2013. "A Generic Biogeochemical Module for Earth System Models: Next Generation BioGeoChemical Module (NGBGC), Version 1.0." Geoscientific Model Development 6(6):1977-1988.  doi:10.5194/gmd-6-1977-2013
  • Bao J, Z Hou, Y Fang, H Ren, and G Lin. 2013. "Uncertainty quantification for evaluating impacts of caprock and reservoir properties on pressure buildup and ground surface displacement during geological CO2 sequestration." Greenhouse Gases: science and technology 3(5):338-358. 
  • Bao J, Z Hou, Y Fang, H Ren, and G Lin. 2013. "Uncertainty quantification for evaluating impacts of caprock and reservoir properties on pressure buildup and ground surface displacement during geological CO2 sequestration." Greenhouse Gases: science and technology 3(5):338-358.  doi:10.1002/ghg.1362
  • Bao J, Z Xu, and Y Fang. 2013. "A Finite Element Model for Simulation of Carbon Dioxide Sequestration." Environmental Geotechnics 1(3):152-160.  doi:10.1680/envgeo.13.00024
  • Bao J, Z Xu, G Lin, and Y Fang. 2013. "Evaluating the impact of aquifer layer properties on geomechanical response during CO2 geological sequestration." Computers & Geosciences 54:28-37.  doi:10.1016/j.cageo.2013.01.015
  • Hou Z, DW Engel, G Lin, Y Fang, and Z Fang. 2013. "An Uncertainty Quantification Framework for Studying the Effect of Spatial Heterogeneity in Reservoir Permeability on CO2 Sequestration." Mathematical Geosciences 45(7):799-817.  doi:10.1007/s11004-013-9459-0
  • Tartakovsky GD, AM Tartakovsky, TD Scheibe, Y Fang, R Mahadevan, and DR 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.  doi:10.1016/j.advwatres.2013.05.007
  • Yeh GT, JPJ Gwo, MD Siegel, MH Li, Y Fang, F Zhang, W Luo, and SB Yabusaki. 2013. "Innovative mathematical modeling in environmental remediation." Journal of Environmental Radioactivity 119:26-38.  doi:10.1016/j.jenvrad.2011.06.010


  • Fang Y, MJ Wilkins, SB Yabusaki, MS Lipton, and PE Long. 2012. "Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens Using Proteomic Data from a Field Biostimulation Experiment." Applied and Environmental Microbiology 78(24):8735 - 8742.  doi:10.1128/AEM.01795-12
  • Liu C, and Y Fang. 2012. "Kinetic Modeling of Microbiological Processes." Journal of Petroleum & Environmental Biotechnology 3(6):Article No. e109. 
  • White MD, and Y Fang. 2012. "STOMP-ECKEChem: An Engineering Perspective on Reactive Transport in Geologic Media." In Groundwater Reactive Transport Models, ed. F Zhang, GT Yeh and JC Parker, pp. 112--140.  Bentham Science Publishers, Oak Park, IL. 
  • Xu Z, Y Fang, TD Scheibe, and A Bonneville. 2012. "A fluid pressure and deformation analysis for geological sequestration of carbon dioxide." Computers & Geosciences 46:31-37. 
  • Xu Z, Y Fang, TD Scheibe, and A Bonneville. 2012. "A Hydro-mechanical Model and Analytical Solutions for Geomechanical Modeling of Carbon Dioxide Geological Sequestration." Chapter 7 in Energy Technology 2012: Carbon Dioxide Management and Other Technologies, ed. MD Salazar-Villalpando, et al.  John Wiley & Sons, Inc., Hoboken, NJ. 


  • Fang Y, TD Scheibe, R Mahadevan, S Garg, PE Long, and DR 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.  doi:10.1016/j.jconhyd.2010.11.007
  • Yabusaki SB, Y Fang, KH Williams, CJ Murray, AL Ward, R Dayvault, SR Waichler, DR Newcomer, FA Spane, and PE Long. 2011. "Variably Saturated Flow and Multicomponent Biogeochemical Reactive Transport Modeling of a Uranium Bioremediation Field Experiment." Journal of Contaminant Hydrology 126(3-4):271-290.  doi:10.1016/j.jconhyd.2011.09.002


  • Scheibe TD, BJ Palmer, KL Schuchardt, Y Fang, and AM 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.  US Department of Energy, Office of Science, Washington DC. 
  • Yeh GT, Y Fang, F Zhang, J Sun, Y Li, MH Li, and MD Siegel. 2010. "Numerical modeling of coupled fluid flow and thermal and reactive biogeochemical transport in porous and fractured media ." Computational Geosciences 14(1):149-170. 
  • Zhao J, Y Fang, TD Scheibe, DR 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.  doi:10.1016/j.jconhyd.2009.10.002


  • Fang Y, SB Yabusaki, SJ Morrison, JE Amonette, and PE Long. 2009. "Multicomponent reactive transport modeling of uranium bioremediation field experiments." Geochimica et Cosmochimica Acta 73(20):6029-6051. 
  • Gurumoorthi V, MK Krishnan, Y Fang, BJ Palmer, and D Chavarría-Miranda. 2009. "Multiple Component Multiple Data Programming in Subsurface Simulations: The CCA Approach." In Proceedings of the Workshop on Component-Based High Performance Computing (CBHPC 2009).  ACM Press, New York, NY. 
  • Palmer BJ, Y Fang, V Gurumoorthi, GE Hammond, JA Fort, and TD Scheibe. 2009. "Developing a Component-Based Framework for Subsurface Simulation using the Common Component Architecture." In SciDAC 2009: Journal of Physics: Conference Series , vol. 180, no. 1, p. Paper No. 012064.  IOP Publishing, London, United Kingdom.  doi:10.1088/1742-6596/180/1/012064
  • Scheibe TD, R Mahadevan, Y Fang, S Garg, PE Long, and DR Lovley. 2009. "Coupling a Genome-Scale Metabolic Model with a Reactive Transport Model to Describe In Situ Uranium Bioremediation." Microbial Biotechnology 2(2):274-286.  doi:10.1111/j.1751-7915.2009.00087.x


  • Yabusaki SB, Y Fang, and SR Waichler. 2008. "Building Conceptual Models of Field-Scale Uranium Reactive Transport in a Dynamic Vadose Zone-Aquifer-River System." Water Resources Research 44:W12403.  doi:10.1029/2007WR006617


  • Palmer BJ, Y Fang, GE Hammond, and V Gurumoorthi. 2007. "Component-Based Framework for Subsurface Simulations." In SciDAC 2007. Published in Journal of Physics: Conference Series, vol. 78, p. 012056 (5 pages).  IOP Publishing, Bristol, United Kingdom.  doi:10.1088/1742-6596/78/1/012056
  • Yabusaki SB, Y Fang, PE Long, CT Resch, AD Peacock, J Komlos, Jr., PR Jaffe, SJ Morrison, R Dayvault, DC White, and RT Anderson. 2007. "Uranium Removal from Groundwater via In Situ Biostimulation: Field-Scale Modeling of Transport and Biological Processes." Journal of Contaminant Hydrology 93(2007):216-235.  doi:10.1016/j.jconhyd.2007.02.005


  • Fang Y, SB Yabusaki, and G Yeh. 2006. "A General Simulator for Reaction-Based Biogeochemical Processes." Computers & Geosciences 32(1):64-72.  doi:10.1016/j.cageo.2005.05.003
  • Fang Y, TD Scheibe, EE Roden, W Kamolpornwijit, and SC 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, ed. PJ Binning, et al.  Technical University of Denmark, Kongens Lyngby, Denmark. 
  • Saripalli P, Y Fang, N Gupta, and JR Sminchak. 2006. "AN INTEGRATED NUMERICAL TRANSPORT MODELING APPROACH FOR RISK ASSESSMENT OF GEOLOGICAL SEQUESTRATION PROJECTS." In 8th International Conference on Greenhouse Gas Technologies (GHGT-8), June 1-22, 2006, Trondheim, Norway, vol. 2, pp. 962-967.  Elsevier Science, Oxford, United Kingdom. 
  • Scheibe TD, Y Fang, CJ Murray, EE Roden, J Chen, YJ Chien, SC Brooks, and SS Hubbard. 2006. "Transport and biogeochemical reaction of metals in a physically and chemically heterogeneous aquifer." Geosphere 2(4):220-235. 
  • Tartakovsky AM, TD 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, p. 8 pages.  Technical University of Denmark (DTU), Copenhagen, Denmark. 


  • Fang Y, SB Yabusaki, and GT Yeh. 2004. "A generic reaction-based biogeochemical simulator." In Proceedings of the 15th International Conference on Computational Methods in Water Resources (CMWR XV), June 13-17, 2004 Chapel Hill, NC, USA. Computational Methods in Water Resources, vol. 1, ed. C.T. Miller, M.W. Farthing, W.G. Gray, and G.F. Pinder, pp. 869-878.  Elsevier, Amsterdam, Netherlands. 


Additional Information