Research Interests

My research interest is applying numerical models to simulate land surface, hydrological, and ecosystem processes, to improve the understanding of the interaction among the atmosphere, ecosystem, and subsurface, and to incorporate this understanding into prediction frameworks that can be used for decision-making.


Ph.D. in Meteorology

The Pennsylvania State University, University Park, Pennsylvania

B.S. in Atmospheric Sciences

Peking University, Beijing, China


Research Experiences

Research Associate

2014 - Present
Department of Ecosystem Science and Management, The Pennsylvania State Unviversity

Postdoctoral Researcher

2012 - 2014
Earth and Environmental Systems Institute, The Pennsylvania State University

Research Assistant

2009 - 2012
Department of Meteorology, The Pennsylvania State University

Teaching Experiences

Guest Lecturer

Guest lecture on model uncertainty for Lehigh University EES 440: Earth System Modeling

Guest lecture on land surface modeling for Penn State METEO 597A: The Atmospheric Boundary Layer

Teaching Assistant

2007 - 2008
Department of Meteorology, The Pennsylvania State University

Grade homework, hold office hours, and lead review sessions for METEO 300, METEO431, and METEO 436.

Other Experiences

Journal Reviewer

Water Resources Research, Ecohydrology, Monthly Weather Review, Advances in Water Resources, Journal of Hydrology, Advances in Atmospheric Sciences, Geoscientific Model Development, Advances in Meteorology, Journal of the American Water Resources Association.

Proposal Reviewer

NSF Hydrology program.


Journal publications

Bao, C., L. Li., Y. Shi, and C. J. Duffy: Understanding watershed hydrogeochemistry: 1. Development of RT-Flux-PIHM. Water Resources Research, 53, 2328—2345, doi:10.1002/2016WR018934.

Li, L., C. Bao, P. L. Sullivan, S. Brantley, Y. Shi, and C. Duffy: Understanding watershed hydrogeochemistry: 2. Synchronized hydrological and geochemical processes drive stream chemostatic behavior. Water Resources Research, 53, 2346—2367, doi:10.1002/2016WR018935.

Yu, X., C. J. Duffy, Y. Zhang, G. Bhatt, and Y. Shi, 2016: Virtual experiments guide calibration strategies for a real-world watershed application of coupled surface-subsurface modeling. Journal of Hydrologic Engineering, 21, 04016043, doi:10.1061/(ASCE)HE.1943-5584.0001431.

Jepsen, S. M., T. C. Harmon, and Y. Shi, 2016: Watershed model calibration to the base flow recession curve with and without evapotranspiration effects. Water Resources Research, 52, 2919—2933, doi:10.1002/2015WR017827.

Brantley, S. L., R. A. DiBiase, T. A. Russo, Y. Shi, H. Lin, K. J. Davis, M. Kaye, L. Hill, J. Kaye, D. M. Eissenstat, B. Hoagland, A. L. Dere, A. L. Neal, K. M. Brubaker, and D. K. Arthur, 2016: Designing a suite of measurements to understand the critical zone. Earth Surface Dynamics, 4, 211—235, doi:10.5194/esurf-4-211-2016.

Shi, Y., D. C. Baldwin, K. J. Davis, X. Yu, C. J. Duffy, and H. Lin, 2015: Simulating high resolution soil moisture patterns in the Shale Hills catchment using a land surface hydrologic model. Hydrological Processes, 29, 4624—4637, doi:10.1002/hyp.10593.

Shi, Y., K. J. Davis, F. Zhang and C. J. Duffy, and X. Yu, 2015: Parameter estimation of a physically-based land surface hydrologic model using an ensemble Kalman filter: A multivariate real-data experiment. Advances in Water Resources, 83, 421—427, doi:10.1016/j.advwatres.2015.06.009.

Duffy, C. J., Y. Shi, K. Davis, R. Slingerland, L. Li, P. L. Sullivan, Y. Godderis, and S. L. Brantley, 2014: Designing a suite of models to explore Critical Zone function. Procedia Earth and Planetary Science, 10, 7—15, doi:10.1016/j.proeps.2014.08.003.

Shi, Y., K. J. Davis, F. Zhang, C. J. Duffy, and X. Yu, 2014: Parameter estimation of a physically-based land surface hydrologic model using the ensemble Kalman Filter: A synthetic experiment. Water Resources Research, 50, 706—724, doi:10.1002/2013WR014070.

Shi, Y., K. J. Davis, F. Zhang, and C. J. Duffy, 2014: Evaluation of the parameter sensitivity of a coupled land surface hydrologic model. Journal of Hydrometeorology, 15, 279—299, doi:10.1175/JHM-D-12-0177.1.

Shi, Y., K. J. Davis, C. J. Duffy, and X. Yu, 2013: Development of a coupled land surface hydrologic model and evaluation at a critical zone observatory. Journal of Hydrometeorology, 14, 1401—1420, doi:10.1175/JHM-D-12-0145.1.

Yu, X., G. Bhatt, C. Duffy, and Y. Shi, 2013: Parameterization for distributed watershed modeling using national data and evolutionary algorithm. Computers & Geosciences, 58, 80—90, doi:10.1016/j.cageo.2013.04.025.

Xu, Y., S. Liu, F. Hu, N. Ma, Y. Wang, Y. Shi, and H. Jia, 2009: Influence of Beijing urbanization on the characteristics of atmospheric boundary layer. Chinese Journal of Atmospheric Sciences (in Chinese), 33, 859—867, doi:10.3878/j.issn.1006-9895.2009.04.18.

Book Chapters

Yu, X., C. J. Duffy, J. Kaye, W. T. Crow, G. Bhatt, and Y. Shi, 2014: Watershed reanalysis of water and carbon cycle models at a Critical Zone Observatory, in Remote Sensing of the Terrestrial Water Cycle (eds. V. Lakshmi et al.), John Wiley & Sons, Inc, Hoboken, NJ. doi: 10.1002/9781118872086.ch31.

Manuscripts under Review

Shi, Y., D. M. Eissenstat, Y. He, and K. J. Davis: Using a spatially-distributed hydrologic biogeochemistry model with a nitrogen transport module to study the spatial variation of carbon processes in a Critical Zone Observatory. Ecological Modelling.

Sullivan, P. L., Y. Goddéris, Y. Shi, X. Gu, J. Schott, E. A. Hasenmueller, J. Kaye, C. Duffy, L. Jin, S. L. Brantley: Earthcasting reveals weathering fluxes increase with warming temperatures but decrease with nutrient cycling. Earth’s Future.

Pravia, J., A. R. Kemanian, J. A. Terra, Y. Shi, I. Macedo, and S. Goslee: Soil carbon saturation, productivity, and carbon and nitrogen cycling in crop-pasture rotations. Agricultural Systems.

Honors and Awards

Advances in Atmospheric Sciences Editor's Award
Penn State Earth and Environmental Systems Institute Scholar
2009 - 2010
Penn State Earth and Environmental Systems Institute Scholar
2008 - 2009
Beijing Excellent Graduates
Peking University Excellent Graduates
Peking University Excellent Student Award
Kwang-Hua Scholarship
Peking University Excellent Student Leader Award