Earth Scientist
Earth Scientist


Xingyuan Chen is an Earth scientist with extensive research experience in modeling groundwater surface water interactions, stochastic inverse modeling, data assimilation, uncertainty quantification, and sensitivity analyses. Since joining PNNL in 2010, she has developed and applied various sensitivity analyses and inverse modeling techniques to understand the sources of uncertainty in predictive models and reduce such uncertainty through data-model integration. In her research, Chen has leveraged open-source parallel simulation codes and high-performance computing resources to enable ensemble simulations of coupled hydrologic and biogeochemical processes in complex systems.


  • PhD in Civil and Environmental Engineering, University of California, Berkeley, 2009
  • MA in Statistics, University of California, Berkeley, 2007
  • M Phil in Civil Engineering, Hong Kong University of Science and Technology, 2002
  • BE in Hydraulic Engineering, Tsinghua University, 2000

Affiliations and Professional Service

  • American Geophysical Union
  • AGU Uncertainty Quantification Technical Committee Deputy Chair 
  • Environmental System Sciences Cyberinfrastructure Working Groups Executive Committee Member  



  • Yao J, H Liu, J Huang, Z Gao, G Wang, D Li, H Yu X Chen. (2020). “Accelerated dryland expansion regulates future variability in dryland gross primary production.” Nature Communications, 11(1):1665. DOI:10.1038/s41467-020-15515-2.
  • Zachara J, X Chen, X Song, P Shuai, C Murray, CT Resch. (2020). “Kilometer-scale Hydrologic Exchange Flows in a Gravel-bed River Corridor and Their Implications to Solute Migration.” Water Resources Research, 56. DOI: 10.1029/2019WR025258.
  • Li B, X Liu, M Kaufman, A Turetcaia, X Chen, and MB Cardenas. (2020). “Flexible and modular simultaneous modeling of flow and reactive transport in rivers and hyporheic zones.” Water Resources Research, 56, e2019WR026528.
  • Villa JA, GJ Smith, Y Ju, L Renteria, JC Angle, E Arntzen, SF Harding, H Ren, X Chen, AH Sawyer, EB Graham, JC Stegen, KC Wrighton, and G & Bohrer. (2020). “Methane and nitrous oxide porewater concentrations and surface fluxes of a regulated river.” Science of the Total Environment, 715, 136920. doi:


  • Song X, X Chen, M Ye, Z Dai, GE Hammond, and JM Zachara. (2019). “Delineating facies spatial distribution by integrating ensemble data assimilation and indicator geostatistics with level‐set transformation.” Water Resources Research, 55. doi: 10.1029/2018WR023262.
  • Dai H, X Chen, M Ye, X Song, GE Hammond, B Hu, and JM Zachara (2019). “Using Bayesian networks for sensitivity analysis of complex biogeochemical models.” Water Resources Research, 55. doi: 10.1029/2018WR023589.
  • Shuai P, X Chen, X Song, GE Hammond, J Zachara, P Royer, et al. (2019). “Dam operations and subsurface hydrogeology control dynamics of hydrologic exchange flows in a regulated river reach.” Water Resources Research, 55. doi: 10.1029/2018WR024193.
  • Yang Q, X Zhang, JE Almendinger, M Huang, X Chen, G Leng, Y Zhou, K Zhao, GR Asrar, X Li. (2019). Climate change will pose challenges to water quality management in the St. Croix River basin.” Environmental Pollution. doi:10.1016/j.envpol.2019.04.129.
  • Gao Z, H Liu, J Missik, J Yao, M Huang, X Chen, E Arntzen, and D Mcfarland. (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, 044016; doi:10.1088/1748-9326/ab082d. 
  • Fang Y, SB Yabusaki, AH Ahkami, X Chen, and TD 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: 33-48. doi: 10.1007/s11104-019-04068-z.
  • Missik J, H Liu, Z Gao, M Huang, X Chen, E Arntzen, D Mcfarland, H Ren, PS Titzler, JN Thomle, and A Goldman. (2019). “Groundwater-river water exchange enhances growing season evapotranspiration and carbon uptake in a semiarid riparian ecosystem.” Journal of Geophysical Research-Biogeosciences, 124, 99-114. doi: 10.1029/2018jg004666
  • Graham EB, JC Stegen, M Huang, X Chen, and TD 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. doi: 10.1016/J.SCITOTENV.2018.11.414.


  •  Gao M, H Li, D Liu, J Tang, X Chen, Xi Chen, G Blöschl, and R Leung. (2018). “Identifying the dominant controls on macropore flow velocity in soils: A meta-analysis.” Journal of Hydrology, 567, 590-604, doi: 10.1016/j.jhydrol.2018.10.044.  
  • Dai H, M Ye, B Hu, AW Niedoroda, X Zhang, X Chen, X Song, J Niu. (2018). “Hierarchical sensitivity analysis for simulating barrier island geomorphologic responses to future storms and sea-level rise.” Theoretical and Applied Climatology, doi: 10.1007/s00704-018-2700-5.
  • Song X, X Chen, JC Stegen, GE Hammond, H Dai, EB Graham, JM Zachara, and HS Song. (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, 7361–7382. doi:10.1029/2018WR022586.
  • Yang Q, JE Almendinger, X Zhang, M Huang, X Chen, G Leng, Y Zhou, K Zhao, GR Asrar, R Srinivasan, and X Li.  (2018). “Enhancing SWAT simulation of forest ecosystems for water resource assessment: A case study in the St. Croix River basin.” Ecological Engineering, 120, 422-431. doi: 10.1016/j.ecoleng.2018.06.020.
  • Zhou T, J Bao, M Huang, Z Hou, EV Arntzen, SF Harding, PS Titzler, CJ Murray, WA Perkins, X Chen, JC Stegen, G Hammond, PD Thorne, and JM Zachara. (2018). “Riverbed hyporheic exchange dynamics in a large regulated river reach.” Water Resources Research, 54(4), 2715-2730.


  • Bisht G, M Huang, T Zhou, X Chen, H Dai, G Hammond, W Riley, JL Downs, Y Liu, and JM Zachara.  (2017). “Coupling a Three-Dimensional Subsurface Flow Model with a Land Surface Model to Simulate Stream-Aquifer-Land interactions.” Geoscientific Model Development, 12(10). 4539-4562. doi:10.5194/gmd-10-4539-2017.
  • Song H-S, DG Thomas, JC Stegen, M Li, C Liu, X Song, X Chen, JK Fredrickson, JM Zachara and TD Scheibe (2017). “Regulation-structured dynamic metabolic model provides a potential mechanism for delayed enzyme response in denitrification process.” Front. Microbiol., 8:1866. doi: 10.3389/fmicb.2017.01866.
  • Stegen JC, CG Anderson, B Bond-Lamberty, AR Crump, X Chen, and N Hess (2017). “Soil respiration across a permafrost transition zone: spatial structure and environmental correlates.” Biogeosciences, 14, 4341-4354. doi:10.5194/bg-14-4341-2017.
  • Gao Z, ES Russell, JEC Missik, M Huang, X Chen, CE Strickland, R Clayton, E Arntzen, Y Ma, and H Liu (2017). “A novel approach to evaluate soil heat flux calculation: An analytical review of nine methods.” Journal of Geophysical Research. D. (Atmospheres), 122(13):6934-3649. doi: 10.1002/2017JD027160.
  • Song H-S, TG Dennis, JC Stegen, M Li, C Liu, X Song, X Chen, JK Fredrickson, JM Zachara, and TD Scheibe. (2017). “Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process.” Frontiers in Microbiology, 8:1866. doi: 10.3389/fmicb.2017.01866.
  • Dai H, M Ye, AP 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, 3476–3490. doi:10.1002/2016WR019715.
  • Dai H, X Chen, M Ye, X Song, and JM Zachara. (2017). “A geostatistics-informed hierarchical sensitivity analysis method for complex groundwater flow and transport modelling.” Water Resources Research, 53(5):4327–4343. doi: 10.1002/2016WR019756.
  • Johnson TC, GE Hammond, X and Chen. (2017) “PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data.” Computers & Geosciences, 99, 72–80; DOI: 10.1016/j.cageo.2016.09.006. 
  • Wan H, K Zhang, PJ 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).” Geosci. Model Dev., 10, 537-552. doi:10.5194/gmd-10-537-2017.


  • Zachara JM, X Chen, CJ Murray, and GE Hammond (2016). “River stage influences on uranium transport in a hydrologically dynamic groundwater-surface water transition zone.” Water Resources Research, 52(3):1568–1590. doi:10.1002/2015WR018009.
  • Johnson TC, GE Hammond, and X Chen (2016). “PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data.” Computers & Geosciences. doi:10.1016/j.cageo.2016.09.006.
  • Stegen JC, AH Hurlbert, B Bond-Lamberty, X Chen, CG Anderson, RK Chu, F Dini-Andreote, SJ Fansler, NJ Hess, and M Tfaily (2016). “Aligning the measurement of microbial diversity with macroecological theory.” Front. Microbiol, 7:1487. doi:10.3389/fmicb.2016.01487.


  • Scheibe TD, EM Murphy, X Chen, AK Rice, KC Carroll, BJ Palmer, AM Tartakovsky, I Battiato, and BD Wood (2015). “An analysis platform for multiscale hydrogeologic modeling with emphasis on hybrid multiscale methods.” Groundwater, 53(1), 38-56. doi: 10.1111/gwat.12179.
  • Johnson TC, RJ Versteeg, J Thomle, GE Hammond, X Chen, and JM 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(8), 6177-6196. doi: 10.1002/2014WR016129.
  • Scheibe TD, X Yang, X Chen, and G Hammond. (2015). “A Hybrid Multiscale Framework for Subsurface Flow and Transport Simulations.” Procedia Computer Science, 51:1098-1107. doi:10.1016/j.procs.2015.05.276.


  • Freedman VL, X Chen, SA Finsterle, MD Freshley, I Gorton, LJ Gosink, E Keating, C Lansing, WAM Moeglein, CJ Murray, GSH Pau, EA Porter, S Purohit, ML Rockhold, KL Schuchardt, C Sivaramakrishnan, VV Vesselinov, and SR Waichler (2014). “A high-performance workflow system for subsurface simulation.” Environmental Modeling & Software, 55:176-189. doi:10.1016/j.envsoft.2014.01.030.


  • Chen X, GE Hammond, CJ Murray, ML Rockhold, VR Vermeul, JM and Zachara. (2013). “Application of ensemble-based data assimilation techniques for aquifer characterization using tracer data at Hanford 300 area.” Water Resources Research, 49, 7064–7076; 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, 3257–3275, doi:10.1002/wrcr.20182.
  • Stegen J, X Lin, J Fredrickson, X Chen, D Kennedy, C Murray, M Rockhold, and A Konopka (2013). “Quantifying community assembly processes and identifying features that impose them.” ISME Journal, doi:10.1038/ismej.2013.93.


  • Chen X, GR Miller, Y Rubin, and DD 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, 1458–1470; DOI: 10.1093/treephys/tps100.
  • Chen X, H Murakami, MS Hahn, GE Hammond, ML Rockhold, JM Zachara, and Y Rubin. (2012). “Three-dimensional Bayesian geostatistical aquifer characterization at the Hanford 300 Area using tracer test data.” Water Resources Research, 48, W06501; DOI: 10.1029/2011WR010675.


  • Miller G, X Chen, Y Rubin, S Ma, and D Baldocchi. (2010). “Groundwater uptake by woody vegetation in a semiarid oak savanna.” Water Resources Research, 46, W10503, doi:10.1029/2009WR008902.
  • Murakami H, X Chen, M Hahn, Y Liu, M Rockhold, V Vermeul, J Zachara, and Y Rubin. (2010). “Bayesian Approach for Three-dimensional Aquifer Characterization at the Hanford 300 Area.” Hydrology and Earth System Sciences, 14, 1989-2001, doi:10.5194/hess-14-1989-2010.
  • Rubin Y, X Chen, H Murakami, and M Hahn. (2010). „A Bayesian approach for data assimilation and conditional simulation of spatial random fields.” Water Resources Research, 46, W10523, doi:10.1029/2009WR008799.


  • Chen X, Y Rubin, S Ma, and D Baldocchi. (2008). “Observations and stochastic modeling of soil moisture control on evapotranspiration in a Californian oak savanna.” Water Resources Research, 44, W08409; DOI: 10.1029/2007WR006646.


  • Chen X, and Y-K Tung (2003). “Investigation of polynomial normal transformation.” Journal of Structural Safety, 25(4), 423-445.​​​​​​​