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Kemanian, A. R., Y. Shi, C. M. White, F. Montes, C. O. Stöckle, D. R. Huggins, M. L. Cangiano, G. Stefani-Faé, and R. K. N. Rozum, 2022: The Cycles agroecosystem model: Fundamentals, testing, and applications. Agricultural and Forest Meteorology.
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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.
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.
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.
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 sensitivities of a coupled land surface hydrologic model at a critical zone observatory. Journal of Hydrometeorology, 15, 279–299. doi:10.1175/JHM-D-12-0177.1.
Duffy, C., Y. Shi, K. Davis, R. Slingerland, L. Li, P. L. Sullivan, Y. Goddéris, 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.
Yu, X., C. Duffy, J. Kaye, W. Crow, G. Bhatt, and Y. Shi, 2014: Watershed reanalysis of water and carbon cycle models at a Critical Zone Observatory. Remote Sensing of the Terrestrial Water Cycle, in Remote Sensing of the Terrestrial Water Cycle (eds. Lakshmi, V. et al.), John Wiley & Sons, Inc., Hoboken, New Jersey. doi:10.1002/9781118872086.ch31.
Shi, Y., K. J. Davis, F. Zhang, 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.
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 watershed using a land surface hydrologic model. Hydrological Processes, 29, 4624–4637. doi:10.1002/hyp.10593.
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.
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.
Yu, X., C. 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, 1055779. doi:10.1061/(ASCE)HE.1943-5584.0001431.
Bao, C., L. Li, Y. Shi, and C. Duffy, 2017: 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, 2017: Understanding watershed hydrogeochemistry: 2. Synchronized hydrological and geochemical processes drive stream chemostatic behavior. Water Resources Research, 53, 2346–2367. doi:10.1002/2016WR018935.
Shi, Y., D. M. Eissenstat, Y. He, and K. J. Davis, 2018: 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, 380, 8–21. doi:10.1016/j.ecolmodel.2018.04.007.
Brantley, S. L., T. White, N. West, J. Z. Williams, B. Forsythe, D. Shapich, J. Kaye, H. Lin, Y. Shi, M. Kaye, E. Herndon, K. J. Davis, Y. He, D. Eissenstat, J. Weitzman, R. DiBiase, L. Li, W. Reed, K. Brubaker, and X. Gu, 2018: Susquehanna Shale Hills Critical Zone Observatory: Shale Hills in the context of Shaver's Creek watershed. Vadose Zone Journal, 17, 180092. doi:10.2136/vzj2018.04.0092.
Crow, W. T., S. Milak, M. Moghaddam, A. Tabatabaeenejad, S.Jaruwatanadilok, X. Yu, Y. Shi, R. H. Reichle, Y. Hagimoto, and R. H. Cuenca, 2018: Spatial and temporal variability of root-zone soil moisture acquired from hydrologic modeling and AirMOSS P-band radar. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 11, 4578–4590. doi:10.1109/JSTARS.2018.2865251.
Pravia, M., A. R. Kemanian, J. A. Terra, Y. Shi, I. Macedo, and S. Goslee, 2019: Soil carbon saturation, productivity, and carbon and nitrogen cycling in crop-pasture rotations. Agricultural Systems, 171, 13–22. doi:10.1016/j.agsy.2018.11.001.
Sullivan, P. L., Y. Godderis, Y. Shi, X. Gu, J. Schott, E. A. Hasenmueller, J. Kaye, C. Duffy, L. Jin, and S. L. Brantley, 2019: Exploring the effect of aspect to inform future earthcasts of climate-driven changes in weathering of shale. Journal of Geophysical Research: Earth Surface, 124, 974–993. doi:10.1029/2017JF004556.
Xiao, D., Y. Shi, S. Brantley, B. Forsythe, R. DiBiase, K. Davis, and L. Li, 2019: Streamflow generation from catchments of contrasting lithologies: The role of soil properties, topography, and catchment size. Water Resources Research, 55, 9234–9257. doi:10.1029/2018WR023736.
Kaye, J. P., S. L. Brantley, J. Z. Williams, and the SSHCZO team, 2019: Ideas and perspectives: Proposed best practices for collaboration at cross-disciplinary observatories. Biogeosciences, 16, 4661–4669. doi:10.5194/bg-16-4661-2019.
Da Silva, R. F., R. Mayani, Y. Shi, A. R. Kemanian, M. Rynge and E. Deelman, 2019: Empowering agroecosystem modeling with HTC scientific workflows: The Cycles model use case. 2019 IEEE International Conference on Big Data (Big Data), 4545–4552. doi:10.1109/BigData47090.2019.9006107.
He, Y., K. J. Davis, Y. Shi, D. M. Eissenstat, J. Kaye, and M. Kaye, 2020: Observing and simulating spatial variations of forest carbon stocks in complex terrain. Journal of Geophysical Research: Biogeosciences, 125, e2019JG005160. doi:10.1029/2019JG005160.
Wlostowski A. N., N. Molotch, S. P. Anderson, S. L. Brantley, J. Chorover, D. Dralle, P. Kumar, L. Li, K. A. Lohse, J. M. Mallard, J. C. McIntosh, S. F. Murphy, E. Parrish, M. Safeeq, M. Seyfried, Y. Shi, and C. Harman, 2021: Signatures of hydrologic function across the critical zone observatory network. Water Resources Research, 57, e2019WR026635. doi:10.1029/2019WR026635.
Gil, Y., D. Garijo, D. Khider, C. A. Knoblock, V. Ratnakar, M. Osorio, H. Vargas, M. Pham, J. Pujara, B. Shbita, B. Vu, Y.-Y. Chiang, D. Feldman, Y. Lin, H. Song, V. Kumar, A. Khandelwal, M. Steinbach, K. Tayal, S. Xu, S. A. Pierce, L. Pearson, D. Hardesty-Lewis, E. Deelman, R. F. Da Silva, R. Mayani, A. R. Kemanian, Y. Shi, L. Leonard, S. Peckham, M. Stoica, K. Cobourn, Z. Zhang, C. Duffy, and L. Shu, 2021: Artificial intelligence for modeling complex systems: Taming the complexity of expert models to improve decision making. ACM Transactions on Interactive Intelligent Systems, 11, 1–49. doi:10.1145/3453172.
Zhi, W., Y. Shi, H. Wen, L. Saberi, G.-H. C. Ng, K. Sadayappan, D. Kerins, B. Stewart, and L. Li, 2022: BioRT-Flux-PIHM v1.0: a biogeochemical reactive transport model at the watershed scale. Geoscientific Model Development, 15, 315–333. doi:10.5194/gmd-15-315-2022.
Novick, K. A., D. L. Ficklin, D. Baldocchi, K. J. Davis, T. A. Ghezzehei, A. G. Konings, N. MacBean, N. Raoult, R. L. Scott, Y. Shi, B. N. Sulman, and J. D. Wood, 2022: Confronting the water potential information gap. Nature Geoscience, 15, 158–164. doi:10.1038/s41561-022-00909-2.
Kopp, M., J. Kaye, Y. H. Smeglin, T. Adams, E. J. Primka IV, B. Bradley, Y. Shi, and D. Eissenstat, 2022: Topography mediates the response of soil CO2 efflux to precipitation over days, seasons, and years. Ecosystems, . doi:10.1007/s10021-022-00786-1.
McConnell, C. A., R. K. N. Rozum, Y. Shi, and A. R. Kemanian, 2023: Tradeoffs when interseeding cover crops into corn across the Chesapeake Bay watershed. Agricultural Systems, 209, 103684. doi:10.1016/j.agsy.2023.103684.
Shi, Y., F. Montes, and A. R. Kemanian, 2023: Cycles-L: A coupled, 3-D, land surface, hydrologic, and agroecosystem landscape model. Water Resources Research, e2022WR033453. doi:10.1029/2022WR033453.
Weng, W., K. M. Cobourn, A. R. Kemanian, K. J. Boyle, Y. Shi, J. Stachelek, and C. White, 2023: Quantifying co-benefits of water quality policies: an integrated assessment model of land and nitrogen management. American Journal of Agricultural Economics, 1–26. doi:10.1111/ajae.12423.
Kodero, J., B. Felzer, and Y. Shi, 2024: Future transition from forests to shrublands and grasslands in the western United States is expected to reduce carbon storage. Communications Earth & Environment, accepted. doi:.
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Co-authors: K. J. Davis, F. Zhang, and C. J. Duffy.
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Co-authors: K. J. Davis, F. Zhang, and C. J. Duffy.
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Co-authors: S. L. Brantley and Penn State CZO Team.
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Co-authors: K. J. Davis, F. Zhang, C. J. Duffy, and X. Yu. More information here.
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Co-authors: K. J. Davis, F. Zhang, C. J. Duffy, and X. Yu. More information here.
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Co-authors: D. M. Eissenstat, A. Kemanian, and K. J. Davis. More information here.
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Co-authors: K. J. Davis, F. Zhang, C. J. Duffy, and X. Yu. More information here.
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Co-authors: D. M. Eissenstat, K. J. Davis, and Y. He. More information here.
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Co-authors: L. Li, D. Xiao, F. Zhang, and K. J. Davis. Watch the recorded presentation here.
Undergraduate course, Penn State University METEO 300 Survey of Atmospheric Science, 2007
Grade homework and hold office hours.
Undergraduate course, Penn State University METEO 431 Atmospheric Thermodynamics, 2008
Grade homework and hold office hours.
Undergraduate course, Penn State University METEO 436 Radiation and Climate, 2008
Grade homework, hold office hours, and lead review sessions.
REU, NSF CZO REU Program, 2014
Lead field experiment and lecture on watershed water balance.
Workshop, The Penn State Integrated Hydrologic Model Workshop, 2016
Organize and present at the PIHM Workshop.
Workshop, The Penn State Integrated Hydrologic Model Developer Workshop, 2016
Organize and present at the PIHM Developer Workshop. More information here.
Graduate course, Penn State University METEO 597A The Atmospheric Boundary Layer, 2017
Guest lecture on land surface modeling.
Graduate course, Lehigh University EES 440 Earth System Modeling, 2017
Guest lecture on numerical model uncertainties.