List of Publications

Si3D has been widely used within the scientific community, and the following are studies in which a version of the source code Si3D has been used to understand and adress lake hydrodynamics and water quality implications

Rueda, Francisco J. 2001. “A Three-Dimensional Hydrodynamic and Transport Model for Lake Environments.” University of California Davis.
Rueda, F. J., & Schladow, S. G. (2002). Quantitative Comparison of Models for Barotropic Response of Homogeneous Basins. Journal of Hydraulic Engineering, 128(2), 201–213. doi.org/10.1061/(ASCE)0733-9429(2002)128:2(201).
Rueda, F. J., & Schladow, S. G. (2002). Surface seiches in lakes of complex geometry. Limnology and Oceanography, 47(3), 906–910. doi.org/10.4319/lo.2002.47.3.0906.
Rueda, F. J., Schladow, S. G., Monismith, S. G., & Stacey, M. T. (2003). Dynamics of large polymictic lake. I: Field observations. Journal of Hydraulic Engineering, 129(2), 82–91. doi.org/10.1061/(ASCE)0733-9429(2003)129:2(82).
Rueda, F. J., Schladow, S. G., & Pálmarsson, S. Ó. (2003). Basin-scale internal wave dynamics during a winter cooling period in a large lake. Journal of Geophysical Research C: Oceans, 108(3), 42–1. doi.org/10.1029/2001jc000942.
Rueda, F. J., Schladow, S. G., Monismith, S. G., & Stacey, M. T. (2005). On the effects of topography on wind and the generation of currents in a large multi-basin lake. Hydrobiologia, 532(1), 139–151. doi.org/10.1007/s10750-004-9522-4.
Rueda, F. J., & Cowen, E. A. (2005). Residence time of a freshwater embayment connected to a large lake. Limnology and Oceanography, 50(5), 1638–1653. doi.org/10.4319/lo.2005.50.5.1638.
Smith, Peter. 2006. “A Semi-Implicit, Three-Dimensional Model for Estuarine Circulation.” USGS Report 176.
Schladow, S. G., Rueda, F. J., Fleenor, E., & Chung, E. G. (2006). Predicting the effects of configuration changes on Salton Sea stratification using a three-dimensional hydrodynamic model. TERC Rep. 06-007, Report to CH2M HILL and California Department of Water Resources.
Rueda, F. J., Fleenor, W. E., & de Vicente, I. (2007). Pathways of river nutrients towards the euphotic zone in a deep-reservoir of small size: Uncertainty analysis. Ecological Modelling, 202(3–4), 345–361. doi.org/10.1016/j.ecolmodel.2006.11.006.
Rueda, Francisco J., S. Geoffrey Schladow, and Jordan F. Clark. 2008. “Mechanisms of Contaminant Transport in a Multi-Basin Lake.” Ecological Applications: A Publication of the Ecological Society of America 18(8 Suppl):A72-88.doi: 10.1890/06-1617.1.
Rueda, F. J., & MacIntyre, S. (2009). Flow paths and spatial heterogeneity of stream inflows in a small multibasin lake. Limnology and Oceanography, 54(6), 2041–2057. doi.org/10.4319/lo.2009.54.6.2041.
Rueda, F. J., Vidal, J., & Schladow, G. (2009). Modeling the effect of size reduction on the stratification of a large wind-driven lake using an uncertainty-based approach. Water Resources Research, 45(3), 1–15. doi.org/10.1029/2008WR006988.
Llebot, Clara. 2010. “Interactions between Physical Forcing, Water Circulation and Phytoplankton Dynamics in a Microtidal Estuary.” 212.
Doyle, L. 2010. “A Three-Dimensional Water Quality Model for Estuary Environments.” 213.
Rueda, F. J., & MacIntyre, S. (2010). Modelling the fate and transport of negatively buoyant storm-river water in small multi-basin lakes. Environmental Modelling and Software, 25(1), 146–157. doi.org/10.1016/j.envsoft.2009.07.002.
Ramón, Cintia L., Joan. Armengol, Josep. Dolz, Jordi. Prats, and Francisco J. Rueda. 2014. “Mixing Dynamics at the Confluence of Two Large Rivers Undergoing Weak Density Variations.” Journal of Geophysical Research: Oceans 119(4):2386–2402.doi: 10.1002/2013JC009488.
Hoyer, Andrea B., Marion E. Wittmann, Sudeep Chandra, S. Geoffrey Schladow, and Francisco J. Rueda. 2014. “A 3D Individual-Based Aquatic Transport Model for the Assessment of the Potential Dispersal of Planktonic Larvae of an Invasive Bivalve.” Journal of Environmental Management 145:330–40.doi: 10.1016/j.jenvman.2014.05.011.
Acosta, M., Anguita, M., Fernández-Baldomero, F. J., Ramón, C. L., Schladow, S. G., & Rueda, F. J. (2015). Evaluation of a nested-grid implementation for 3D finite-difference semi-implicit hydrodynamic models. Environmental Modelling & Software, 64, 241–262.doi.org/10.1016/j.envsoft.2014.10.015.
Ramón, C. L., A. Cortés, and Francisco J. Rueda. 2015. “Inflow–Outflow Boundary Conditions along Arbitrary Directions in Cartesian Lake Models.” Computers & Geosciences 74:87–96. doi: 10.1016/j.cageo.2014.10.002.
Hoyer, A. B., Schladow, S. G., & Rueda, F. J. (2015). A hydrodynamics-based approach to evaluating the risk of waterborne pathogens entering drinking water intakes in a large, stratified lake. Water Research, 83, 227–236. doi.org/10.1016/j.watres.2015.06.014.
Hoyer, A. B., Schladow, S. G., & Rueda, F. J. (2015). Local dispersion of nonmotile invasive bivalve species by wind-driven lake currents. Limnology and Oceanography, 60(2), 446–462. doi.org/10.1002/lno.10046.
Ramón, Cintia L., Jordi Prats, and Francisco J. Rueda. 2016. “The Influence of Flow Inertia, Buoyancy, Wind, and Flow Unsteadiness on Mixing at the Asymmetrical Confluence of Two Large Rivers.” Journal of Hydrology 539:11–26.doi: 10.1016/j.jhydrol.2016.05.008.
Chen, Shengyang, Chengwang Lei, Cayelan C. Carey, Paul A. Gantzer, and John C. Little. 2017. “A Coupled Three-Dimensional Hydrodynamic Model for Predicting Hypolimnetic Oxygenation and Epilimnetic Mixing in a Shallow Eutrophic Reservoir.” Water Resources Research 53(1):470–84.doi: 10.1002/2016WR019279.
Chen, Shengyang, John C. Little, Cayelan C. Carey, Ryan P. McClure, Mary E. Lofton, and Chengwang Lei. 2018. “Three‐Dimensional Effects of Artificial Mixing in a Shallow Drinking‐Water Reservoir.” Water Resources Research 54(1):425–41.doi: 10.1002/2017WR021127.
Valbuena, S. A., Bombardelli, F. A., Cortés, A., Largier, J. L., Roberts, D. C., Forrest, A. L., & Schladow, S. G. (2022). 3D Flow Structures During Upwelling Events in Lakes of Moderate Size. Water Resources Research, 58(3), 1–35.

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