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Fundamental and Computational Sciences Directorate

Staff information


Xingyuan Chen

Earth System Measuremts & Data
Earth Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K9-24
Richland, WA 99352


Dr. Xingyuan Chen is an earth scientist with extensive research experience in groundwater flow and transport modeling, stochastic inverse modeling, data assimilation, geostatistics, and ecohydrology. Since joining PNNL in 2010, Dr. Chen has applied various Bayesian data assimilation techniques to characterize the heterogeneous aquifer properties of the Hanford 300 Area by integrating multi-scale and multi-type lab and field experimental data available at the site. In her research, Dr. Chen has leveraged high performance computing resources, e.g., community flow and transport code PFLOTRAN and the supercomputers at the National Energy Research Scientific Computing Center (NERSC) and Oak Ridge Leadership Computing Facility (OLCF), to enable increasingly mechanistic non-linear forward simulations for a complex system within the stochastic data assimilation framework.

Research Interests

  • Uncertainty quantification and data assimilation
  • Subsurface flow and transport modeling
  • Watershed hydrologic and biogeochemical modeling
  • Spatial-temporal data analysis using machine learning
  • Ecohydrology

Education and Credentials

  • Ph.D., Civil and Environmental Engineering, University of California at Berkeley, 2009
  • M.A., Statistics, University of California at Berkeley, 2007
  • M.Phil., Civil Engineering, Hong Kong University of Science and Technology, 2002
  • B.E., Hydraulic Engineering, Tsinghua University, Beijing, 2000

Affiliations and Professional Service

  • Member of American Geophysical Union (AGU)

PNNL Publications


  • Fang Y., X. Chen, J.D. Gomez Velez, X. Zhang, Z. Duan, G. Hammond, and A.E. Goldman, et al. 2020. "A multirate mass transfer model to represent the interaction of multicomponent biogeochemical processes between surface water and hyporheic zones (SWAT-MRMT-R 1.0)." Geoscientific Model Development 13, no. 8:3553-3569. PNNL-SA-148784. doi:10.5194/gmd-13-3553-2020
  • Gao Z., H. Liu, E.V. Arntzen, D.P. McFarland, X. Chen, and M. Huang. 2020. "Uncertainties in turbulent statistics and fluxes of CO2 associated with density effect corrections." Geophysical Research Letters 47, no. 15:Article No. e2020GL088859. PNNL-SA-153577. doi:10.1029/2020GL088859
  • Rizzo C., X. Song, F. De Barros, and X. Chen. 2020. "Temporal flow variations interact with spatial physical heterogeneity to impact solute transport in managed river corridors." Journal of Contaminant Hydrology 235. PNNL-SA-153233. doi:10.1016/j.jconhyd.2020.103713
  • 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
  • Song X., X. Chen, J.M. Zachara, J. Gomez-Velez, P. Shuai, H. Ren, and G.E. Hammond. 2020. "River Dynamics Control Transit Time Distributions and Biogeochemical Reactions in a Dam-Regulated River Corridor." Water Resources Research 56, no. 9:Article No. e2019WR026470. PNNL-SA-146640. doi:10.1029/2019WR026470
  • Tso C., T.C. Johnson, X. Song, X. Chen, O. Kuras, P. Wilkinson, and S. Uhlemann, et al. 2020. "Integrated hydrogeophysical modelling and data assimilation for geoelectrical leak detection." Journal of Contaminant Hydrology 234. PNNL-SA-152552. doi:10.1016/j.jconhyd.2020.103679
  • Yabusaki S.B., A.N. Myers-Pigg, N.D. Ward, S.R. Waichler, A. Sengupta, Z. Hou, and X. Chen, et al. 2020. "Floodplain inundation and salinization from a recently restored first-order tidal stream." Water Resources Research 56, no. 7:Article No. e2019WR026850. PNNL-SA-149723. doi:10.1029/2019WR026850
  • Yao J., H. Liu, J. Huang, Z. Gao, G. Wang, D. Li, and H. Yu, et al. 2020. "Accelerated dryland expansion regulates future variability in dryland gross primary production." Nature Communications 11, no. 1:1665. PNNL-SA-151970. doi:10.1038/s41467-020-15515-2
  • Zachara J.M., X. Chen, X. Song, P. Shuai, C.J. Murray, and C.T. Resch. 2020. "Kilometer-scale hydrologic exchange flows in a gravel bed river corridor and their implications to solute migration." Water Resources Research 56, no. 2:Article NO. e2019WR025258. PNNL-SA-137616. doi:10.1029/2019WR025258
  • Zhu B., M. Huang, Y. Cheng, X. Xie, Y. Liu, X. Zhang, and G. Bisht, et al. 2020. "Effects of irrigation on water, carbon, and nitrogen budgets in a semi-arid watershed in the Pacific Northwest: A modelling study." Journal of Advances in Modeling Earth Systems 12, no. 9:Article No. e2019MS001953. PNNL-SA-149346. doi:10.1029/2019MS001953


  • Dai H., M. Ye, B.X. Hu, A.W. Niedoroda, X. Zhang, X. Chen, and X. Song, et al. 2019. "Hierarchical sensitivity analysis for simulating barrier island geomorphologic responses to future storms and sea-level rise." Theoretical and Applied Climatology 136, no. 3-4:1495-1511. PNNL-SA-142865. doi:10.1007/s00704-018-2700-5
  • Dai H., X. Chen, M. Ye, X. Song, G. Hammond, B.X. Hu, and J.M. Zachara. 2019. "Using Bayesian Networks for Sensitivity Analysis of Complex Biogeochemical Models." Water Resources Research 55, no. 4:3541-3555. PNNL-SA-141922. doi:10.1029/2018WR023589
  • 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
  • Gao Z., H. Liu, J.E. Missik, J. Yao, M. Huang, X. Chen, and E.V. Arntzen, et al. 2019. "Mechanistic links between underestimated CO2 fluxes and non-closure of the surface energy balance in a semi-arid sagebrush ecosystem." Environmental Research Letters 14, no. 4:Article Number 044016. PNNL-SA-142139. doi:10.1088/1748-9326/ab082d
  • 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
  • Missik J.E., H. Liu, Z. Gao, M. Huang, X. Chen, E.V. Arntzen, and D.P. McFarland, et al. 2019. "Groundwater-River Water Exchange Enhances Growing Season Evapotranspiration and Carbon Uptake in a Semiarid Riparian Ecosystem." Journal of Geophysical Research. Biogeosciences 124, no. 1:99-114. PNNL-SA-142097. doi:10.1029/2018JG004666
  • Shuai P., X. Chen, X. Song, G. Hammond, J.M. Zachara, P.D. Royer, and H. Ren, et al. 2019. "Dam Operations and Subsurface Hydrogeology Control Dynamics of Hydrologic Exchange Flows in a Regulated River Reach." Water Resources Research 55, no. 4:2593-2612. PNNL-SA-138598. doi:10.1029/2018WR024193
  • Song X., X. Chen, M. Ye, Z. Dai, G.E. Hammond, and J.M. Zachara. 2019. "Delineating Facies Spatial Distribution by Integrating Ensemble Data Assimilation and Indicator Geostatistics with Level-Set Transformation." Water Resources Research 55, no. 4:2652-2671. PNNL-SA-141921. doi:10.1029/2018WR023262
  • Yang Q., X. Zhang, J.E. Almendinger, M. Huang, X. Chen, G. Leng, and Y. Zhou, et al. 2019. "Climate change will pose challenges to water quality management in the St. Croix River basin." Environmental Pollution 251. PNNL-SA-143598. doi:10.1016/j.envpol.2019.04.129


  • Freedman V.L., P.D. Royer, X. Chen, S.A. Montgomery, and J.J. Garza. 2018. "ATLAS: Story Maps for Communicating Groundwater Cleanup Status - 18510." In Proceedings of the 44th Annual Waste Management Conference (WM2018): Nuclear and Industrial Robotics, Remote Systems and Other Emerging Technology, March 18-22, 2018, Phoenix, AZ, 8, 5530-5538. Tempe, Arizona:Waste Management Symposia, Inc. PNNL-SA-130420.
  • Gao M., H. Li, D. Liu, J. Tang, X. Chen, X. Chen, and G. Bloschl, et al. 2018. "Identifying the Dominant Controls on Macropore Flow Velocity in Soils: A Meta-analysis." Journal of Hydrology 567. PNNL-SA-139024. doi:10.1016/j.jhydrol.2018.10.044
  • Rockhold M.L., X. Song, J.D. Tagestad, P.D. Thorne, G.D. Tartakovsky, and X. Chen. 2018. Sensitivity Analysis of Contaminant Transport from Vadose Zone Sources to Groundwater. PNNL-28065. Richland, WA: Pacific Northwest National Laboratory. Sensitivity Analysis of Contaminant Transport from Vadose Zone Sources to Groundwater
  • Song X., X. Chen, J.C. Stegen, G. Hammond, H. Song, H. Dai, and E.B. Graham, et al. 2018. "Drought Conditions Maximize the Impact of High-Frequency Flow Variations on Thermal Regimes and Biogeochemical Function in the Hyporheic Zone." Water Resources Research 54, no. 10:7361-7382. PNNL-SA-123922. doi:10.1029/2018WR022586
  • Yang Q., J.E. Almendinger, X. Zhang, M. Huang, X. Chen, G. Leng, and Y. Zhou, et al. 2018. "Enhancing SWAT simulation of forest ecosystems for water resource assessment: A case study in the St. Croix River basin." Ecological Engineering 120. PNNL-SA-128496. doi:10.1016/j.ecoleng.2018.06.020
  • Zhou T., J. Bao, M. Huang, Z. Hou, E.V. Arntzen, X. Song, and S.F. Harding, et al. 2018. "Riverbed Hydrologic Exchange Dynamics in a Large Regulated River Reach." Water Resources Research 54, no. 4:2715-2730. PNNL-SA-123666. doi:10.1002/2017WR020508


  • Bisht G., M. Huang, T. Zhou, X. Chen, H. Dai, G. Hammond, and W. Riley, et al. 2017. "Coupling a Three-Dimensional Subsurface Flow and Transport Model with a Land Surface Model to Simulate Stream-Aquifer-Land Interactions (CP v1.0)." Geoscientific Model Development 10, no. 12:4539-4562. PNNL-SA-123895. doi:10.5194/gmd-10-4539-2017
  • Dai H., M. Ye, A.P. Walker, and X. Chen. 2017. "A new process sensitivity index to identify important system processes under process model and parametric uncertainty." Water Resources Research 53, no. 4:3476-3490. PNNL-SA-120642. doi:10.1002/2016WR019715
  • Gao Z., E. Russell, J.E. Missik, M. Huang, X. Chen, C.E. Strickland, and R.E. Clayton, et al. 2017. "A novel approach to evaluate soil heat flux calculation: An analytical review of nine methods." Journal of Geophysical Research. D. (Atmospheres) 122, no. 13:6934-3649. PNNL-SA-127368. doi:10.1002/2017JD027160
  • Johnson T.C., G. Hammond, and X. Chen. 2017. "PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data." Computers & Geosciences 99. PNNL-SA-113670. doi:10.1016/j.cageo.2016.09.006
  • Stegen J.C., C.G. Anderson, B. Bond-Lamberty, A.R. Crump, X. Chen, and N.J. Hess. 2017. "Soil respiration across a permafrost transition zone: spatial structure and environmental correlates." Biogeosciences 14, no. 18:4341-4354. PNNL-SA-122396. doi:10.5194/bg-14-4341-2017
  • Wan H., K. Zhang, P.J. Rasch, B. Singh, X. Chen, and J. Edwards. 2017. "A new and inexpensive non-bit-for-bit solution reproducibility test based on time step convergence (TSC1.0)." Geoscientific Model Development 10, no. 2:537-552. PNNL-SA-118076. doi:10.5194/gmd-10-537-2017


  • Stegen J.C., A.H. Hurlbert, B. Bond-Lamberty, X. Chen, C.G. Anderson, R.K. Chu, and F. Dini-Andreote, et al. 2016. "Aligning the Measurement of Microbial Diversity with Macroecological Theory." Frontiers in Microbiology 7. PNNL-SA-122085. doi:10.3389/fmicb.2016.01487
  • Zachara J.M., X. Chen, C.J. Murray, and G. Hammond. 2016. "River Stage Influences on Uranium Transport in a Hydrologically Dynamic Groundwater-Surface Water Transition Zone." Water Resources Research 52, no. 3:1568-1590. PNNL-SA-112480. doi:10.1002/2015WR018009


  • Johnson T.C., R. Versteeg, J.N. Thomle, G.E. Hammond, X. Chen, and J.M. Zachara. 2015. "Four-dimensional electrical conductivity monitoring of stage-driven river water intrusion: Accounting for water table effects using a transient mesh boundary and conditional inversion constraints." Water Resources Research 51, no. 8:6177-6196. PNNL-SA-103949. doi:10.1002/2014WR016129
  • 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." Ground Water 53, no. 1:38-56. PNNL-SA-93006. doi:10.1111/gwat.12179
  • 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


  • Freedman V.L., X. Chen, S.A. Finsterle, M.D. Freshley, I. Gorton, L.J. Gosink, and E. Keating, et al. 2014. "A high-performance workflow system for subsurface simulation." Environmental Modelling & Software 55. PNNL-SA-92680. doi:10.1016/j.envsoft.2014.01.030


  • Chen X., G.E. Hammond, C.J. Murray, M.L. Rockhold, V.R. Vermeul, and J.M. Zachara. 2013. "Applications of Ensemble-based Data Assimilation Techniques for Aquifer Characterization using Tracer Data at Hanford 300 Area." Water Resources Research 49. PNNL-SA-91954. doi:10.1002/2012WR013285
  • Over M., Y. Yang, X. Chen, and Y. Rubin. 2013. "A strategy for improved computational efficiency of the method of anchored distributions." Water Resources Research 49, no. 6:3257-3275. PNNL-SA-90988. doi:10.1002/wrcr.20182
  • Stegen J.C., X. Lin, J.K. Fredrickson, X. Chen, D.W. Kennedy, C.J. Murray, and M.L. Rockhold, et al. 2013. "Quantifying Community Assembly Processes and Identifying Features that Impose Them." The ISME Journal 7. PNNL-SA-86535. doi:10.1038/ismej.2013.93


  • Chen X., G.R. Miller, Y. Rubin, and D. Baldocchi. 2012. "A statistical method for estimating wood thermal diffusivity and probe geometry using in situ heat response curves from sap flow measurements." Tree Physiology 32, no. 12:1458-1470. PNNL-SA-78550. doi:10.1093/treephys/tps100
  • Chen X., H. Murakami, H. Murakami, M.S. Hahn, G.E. Hammond, M.L. Rockhold, and J.M. Zachara, et al. 2012. "Three-Dimensional Bayesian Geostatistical Aquifer Characterization at the Hanford 300 Area using Tracer Test Data." Water Resources Research 48. PNNL-SA-78432. doi:10.1029/2011WR010675

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