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Brunetti, G., J. Šimůnek, and P. Piro, A comprehensive analysis of the variably-saturated hydraulic behavior of a green roof in Mediterranean climate, Vadose Zone Journal, 15(9), pp. 15, doi: 10.2136/vzj2016.04.0032, 2016.

Brunetti, G., J. Šimůnek, and P. Piro, A comprehensive numerical analysis of the hydraulic behavior of a permeable pavement, Journal of Hydrology, 540, 1146-1161, doi: 10.1016/j.jhydrol.2016.07.030, 2016.

Brunetti, G., J. Šimůnek, M. Turco, and P. Piro, On the use of surrogate-based modeling for the numerical analysis of Low Impact Development techniques, Journal of Hydrology, 548, 263-277, doi: 10.1016/j.jhydrol.2017.03.013, 2017.

Brunetti, G., J. Šimůnek, and E. Bautista, A hybrid finite volume-finite element model for the numerical analysis of furrow irrigation and fertigation, Computers and Electronics in Agriculture, 150, 312-327, doi: 10.1016/j.compag.2018.05.013, 2018.

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Hartmann, A., J. Šimůnek, M. K. Aidoo, S. J. Seidel, and N. Lazarovitch, Modeling root growth as a function of different environmental stresses using HYDRUS, Vadose Zone Journal, pp. 16, doi: 10.2136/vzj2017.02.0040, 2017.

Hopmans, J. W., J. Šimůnek, N. Romano, and W. Durner, Inverse Modeling of Transient Water Flow, In: Methods of Soil Analysis, Part 1, Physical Methods, Chapter 3.6.2, Eds. J. H. Dane and G. C. Topp, Third edition, SSSA, Madison, WI, 963-1008, 2002.

Jacques, D., and J. Šimůnek, User Manual of the Multicomponent Variably-Saturated Flow and Transport Model HP1, Description, Verification and Examples, Version 1.0, SCK•CEN-BLG-998, Waste and Disposal, SCK•CEN, Mol, Belgium, 79 pp., 2005.

Jacques, D., J. Šimůnek, D. Mallants, and M. Th. van Genuchten, Operator-splitting errors in coupled reactive transport codes for transient variably saturated flow and contaminant transport in layered soil profiles, J. Contam. Hydrology, 88, 197-218, 2006.

Jacques, D., J. Šimůnek, D. Mallants, and M. Th. van Genuchten, Modeling coupled hydrological and chemical processes: Long-term uranium transport following mineral phosphorus fertilization, Vadose Zone Journal, 7(2), 698-711, 2008.

Jacques, D., and J. Šimůnek, Notes on HP1 – a software package for simulating variably-saturated water flow, heat transport, solute transport and biogeochemistry in porous media, HP1 Version 2.2, SCK•CEN-BLG-1068, Waste and Disposal, SCK•CEN, Mol, Belgium, 113 pp., 2010.

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Langergraber, G. and J. Šimůnek, Modeling variably-saturated water flow and multi-component reactive transport in constructed wetlands, Vadose Zone Journal, 4, 924-938, 2005.

Langergraber, G., and J. Šimůnek, The Multi-component Reactive Transport Module CW2D for Constructed Wetlands for the HYDRUS Software Package, Manual – Version 1.0, HYDRUS Software Series 2, Department of Environmental Sciences, University of California Riverside, Riverside, CA, 72 pp., 2006.

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Langergraber, G., and J. Šimůnek, The HYDRUS Wetlands Module, Version 2, HYDRUS Software Series 4, Department of Environmental Sciences, University of California Riverside, Riverside, CA, 56 pp., 2011.

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Šimůnek, J., D. Jacques, J. W. Hopmans, M. Inoue, M. Flury, and M. Th. van Genuchten, Solute Transport During Variably-Saturated Flow - Inverse Methods, In: Methods of Soil Analysis, Part 1, Physical Methods, Chapter 6.6, Eds. J. H. Dane and G. C. Topp, Third edition, SSSA, Madison, WI, 1435-1449, 2002.

Šimůnek, J., N. J. Jarvis, M. Th. van Genuchten, and A. Gärdenäs, Review and comparison of models for describing non-equilibrium and preferential flow and transport in the vadose zone, Journal of Hydrology, 272, 14-35, 2003.

Šimůnek, J., M. Šejna, H. Saito, M. Sakai, and M. Th. van Genuchten, The HYDRUS-1D Software Package for Simulating the Movement of Water, Heat, and Multiple Solutes in Variably Saturated Porous Media, Version 4.0, HYDRUS Software Series 3, Department of Environmental Sciences, University of California Riverside, Riverside, California, USA, pp. 315, 2008.

Šimůnek, J., M. Th. van Genuchten, and M. Šejna, Development and applications of the HYDRUS and STANMOD software packages, and related codes, Vadose Zone Journal, doi:10.2136/VZJ2007.0077, Special Issue “Vadose Zone Modeling”, 7(2), 587-600, 2008.

Šimůnek, J. and J. W. Hopmans, Modeling compensated root water and nutrient uptake, Ecological Modeling, doi:10.1016/j.ecolmodel.2008.11.004, 220(4), 505-521, 2009.

Šimůnek, J., D. Jacques, M. Šejna, and M. Th. van Genuchten, The HP2 Program for HYDRUS (2D/3D): A Coupled Code for Simulating Two-Dimensional Variably-Saturated Water Flow, Heat Transport, and Biogeochemistry in Porous Media, Version 1.0, PC Progress, Prague, Czech Republic, 71 pp., 2012a.

Šimůnek, J., M. Šejna, S. A. Bradford, and M. Th. van Genuchten, The C-Ride Module for HYDRUS (2D/3D) Simulating Two-Dimensional Colloid-Facilitated Solute Transport in Variably-Saturated Media, Version 1.0, PC Progress, Prague, Czech Republic, 43 pp., 2012b.

Šimůnek, J., M. Šejna, and M. Th. van Genuchten, The UNSATCHEM Module for HYDRUS (2D/3D) Simulating Two-Dimensional Movement of and Reactions Between Major Ions in Soils, Version 1.0, PC Progress, Prague, Czech Republic, 52 pp., 2012c.

Šimůnek, J., M. Th. van Genuchten, and M. Šejna, The HYDRUS Software Package for Simulating Two- and Three Dimensional Movement of Water, Heat, and Multiple Solutes in Variably-Saturated Porous Media, Version 2.0, Technical Manual, PC Progress, Prague, Czech Republic, 258 pp., 2012d.

Šimůnek, J., M. Šejna, and M. Th. van Genuchten, The DualPerm Module for HYDRUS (2D/3D) Simulating Two-Dimensional Water Movement and Solute Transport in Dual-Permeability Porous Media, Version 1.0, PC Progress, Prague, Czech Republic, 32 pp., 2012e.

Šimůnek, J., M. Th. van Genuchten, and M. Šejna, Recent developments and applications of the HYDRUS computer software packages, Vadose Zone Journal, 15(7), pp. 25, doi: 10.2136/vzj2016.04.0033, 2016.

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