Jirka Simunek - Publications

Peer-Reviewed Journal Articles:

Last updated in June 2020

1. Kacimov, A. R., A. Al-Maktoumi, and J. Šimůnek, Water table rise in urban shallow aquifer with vertically-heterogeneous soils: Girinskii’s potential revisited, Hydrological Sciences Journal, (in press).
2. Liu, K., G. Huang, Z. Jiang, X. Xu, Y. Xiong, Q. Huang, and J. Šimůnek, A Gaussian process-based Iterative Ensemble Kalman Filter for parameter estimation of unsaturated flow, Journal of Hydrology, doi: 10.1016/j.jhydrol.2020.125210 (in press).
3. Tu, K., Q. Wu, J. Šimůnek, C. Chen, K. Zhu, Y. Zeng, S. Xu, and Y. Wang, An analytical solution of the seepage field for single-well circulation ground water heat pump systems, Water Resources Research, doi: 10.1029/2020WR027529 (in press).
4. Glass, J., J. Šimůnek, and C. Stefan, Scaling factors in HYDRUS to simulate a reduction in hydraulic conductivity during infiltration from recharge wells and infiltration basins,  Vadose Zone Journal, 19, e20027, 19 p., doi: 10.1002/vzj2.20027, 2020.
5. Kanzari S., I. Daghari, J. Šimůnek, A. Younes, R. Ilahy, S. B. Mariem, M. Rezig, B. B. Nouna, H. Bahrouni, and M. A. B. Abdallah, Simulation of water and salts dynamics in the soil profile with a tomato crop in the semi-arid region of Tunisia – Evaluation of the irrigation strategy, Water, 12, 1594, 16 p., doi: 10.3390/w12061594, 2020.
6. Al-Mayahi, A., S. Al-Ismaily, A. Al-Maktoumi, H. Al-Busaidi, A. Kacimov, R. Janke, J. Bouma, and J. Šimůnek, A smart capillary barrier-wick irrigation system for home gardens in arid zones, Irrigation Science, 38, 235-250, doi: 10.1007/s00271-020-00666-3, 2020.
7. Peddinti, S. R., B. V. N. P. Kambhammettu, R. Lad, J. Šimůnek, R. M. Gade, and J. Adinarayana, A macroscopic soil-water transport model to simulate root water uptake in the presence of water and disease stress, Journal of Hydrology, 587, 124940, 13 p., doi: 10.1016/j.jhydrol.2020.124940, 2020.
8. Turunen, M., G. Gurarslan, J. Šimůnek, M. Myllys, and H. Koivusalo, What is the worth of drain discharge and surface runoff data in hydrological simulations?, Journal of Hydrology, 587, 125030, 9 p., doi: 10.1016/j.jhydrol.2020.125030, 2020.
9. Filipović, V., K. L. Bristow, L. Filipović, Y. Wang, H. Y. Sintim, M. Flury, and J. Šimůnek, Sprayable biodegradable polymer membrane technology for cropping systems: Challenges and opportunities, Viewpoint paper, Environmental Science & Technology, 54(8), 4709-4711, 3 p., doi: 10.1021/acs.est.0c00909, 2020.
10. Phogat, V., T. Pitt, R. M. Stevens, J. W. Cox, J. Šimůnek, and P. R. Petrie, Assessing the role of rainfall redirection techniques for arresting land degradation under drip irrigated grapevines, Journal of Hydrology, 587, 125000, 12 p., doi: 10.1016/j.jhydrol.2020.125000, 2020.
11. Zheng, C., Y. Lu, X. Liu, J. Šimůnek, Y. Zeng, C. Shi, and H. Li, In-situ monitoring and characteristic analysis of freezing-thawing cycles in a deep vadose zone, Water, 12(5), 1261, 18 p., doi: 10.3390/w12051261, 2020.
12. Phogat, V., D. Mallants, J. W. Cox, J. Šimůnek, D. P. Oliver, T. Pitt, and P. Petrie, Impact of long-term recycled water irrigation on crop yield and soil chemical properties, Agricultural Water Management, 237, 106167, 14 p., doi: 10.1016/j.agwat.2020.106167, 2020.
13. Beegum, S., J. Vanderborght, J. Šimůnek, M. Herbst, K. P. Sudheer, and I. M. Nambi, Investigating the atrazine contamination in the Zwischenscholle aquifer using MODFLOW with the HYDRUS-1D package and MT3DMS, Water, 12(4), 1019, 24 p., doi: 10.3390/w12041019, 2020.
14. Zhou, T., P. Xin, L. Li, D. A. Barry, J. Šimůnek, Effects of large macropores on soil evaporation in salt marshes, Journal of Hydrology, 585, 124754, 10 p., doi: 10.1016/j.jhydrol.2020.124754, 2020.
15. Brunetti, G., J. Šimůnek, D. Glöckler, and C. Stumpp, Handling model complexity with parsimony: Numerical analysis of the nitrogen turnover in a controlled aquiter model setup, Journal of Hydrology, 584, 124681, 18 p., doi: 10.1016/j.jhydrol.2020.124681, 2020.
16. Chen, N., X. Li, J. Šimůnek, H. Shi, Q. Hu, and Y. Zhang, Evaluating soil nitrate dynamics in an intercropping dripped ecosystem using HYDRUS-2D, Science of Total Environment, 718, 137314, 13 p., doi: 10.1016/j.jhydrol.2020.124681, 2020.
17. Bristow, K. L., J. Šimůnek, S. A. Helalia, and A. A. Siyal, Numerical simulations of the effects furrow surface conditions and fertilizer locations have on plant nitrogen and water use in furrow irrigated systems, Agricultural Water Management, 232, 106044, 11 p., doi: 10.1016/j.agwat.2020.106044, 2020.
18. Ali, A., A. J. W. Biggs, J. Šimůnek, and J. McL. Bennett, A pH based pedotransfer function for scaling saturated hydraulic conductivity reduction: Improved estimation of hydraulic dynamics in HYDRUS, Vadose Zone Journal, 18(1), 190072,  doi: 10.2136/vzj2019.07.0072, 2020.
19. Sasidharan, S., S. A. Bradford, J. Šimůnek, and S. R. Kraemer, Groundwater recharge from drywells under constant head conditions, Journal of Hydrology, 583, 124569, 14 p., doi: 10.1016/j.jhydrol.2020.124569, 2020.
20. Chen, N., X. Li, J. Šimůnek, H. Shi, J. Shi, Z. Ding, and Y. Zhang, The effects of biodegradable and plastic film mulching on nitrogen uptake, leaching in a drip-irrigated sandy field, Agriculture, Ecosystems and Environment, 292, 106817, 13 p., doi: 10.1016/j.agee.2020.106817, 2020.
21. Liang, Y., J. Zhou, Y. Dong, E. Klumpp, J. Šimůnek, and S. A. Bradford, Evidence for the critical role of nanoscale surface roughness on the retention and release of silver nanoparticles in porous media, Environmental Pollution, 258, 113803, 9 p., doi: 10.1016/j.envpol.2019.113803, 2020.
22. Phogat, V., D. Mallants, J. W. Cox, J. Šimůnek, D. P. Oliver, and J. Awad, Management of soil chemical changes associated with irrigation of protected crops, Agricultural Water Management, 227, 105845, doi: 10.1016/j.agwat.2019.105845, 2020.
23. Kacimov, A. R., N. D. Yakimov, and J. Šimůnek, Phreatic seepage flow through an earth dam with an impeding strip, Computational Geosciences, 24, 17-35, doi: 10.1007/s10596-019-09879-8, 2020.
24. Brunetti, G., R. Kodešová, and J. Šimůnek, Modeling the translocation and transformation of chemicals in the soil-plant continuum: A Dynamic Plant Uptake module for the HYDRUS model, Water Resources Research, 55, 8967–8989, doi: 10.1029/2019WR025432, 2019.
25. Chen, N., X. Li, J. Šimůnek, H. Shi, Z. Ding, and Z. Peng, Evaluating the effects of biodegradable film mulching on soil water dynamics in a drip-irrigated field, Agricultural Water Management, 226, 105788, 12 p., doi: 10.1016/j.agwat.2019.105788, 2019.
26. Adrian, Y. F., U. Schneidewind, S. A. Bradford, J. Šimůnek, E. Klumpp, and R. Azzam, Transport and retention of engineered silver nanoparticles in carbonate-rich sediments in the presence and absence of soil organic matter, 255(1), 113124, 11 p., doi: 10.1016/j.envpol.2019.113124, 2019.
27. Torkzaban, S., M. Hocking, S. A. Bradford, S. S. Tazehkand, S. Sasidharan, and J. Šimůnek, Stochasting modeling of virus transport and removal during aquifer storage and recovery, Journal of Hydrology, 578, 124082, 11 p., doi: 10.1016/j.jhydrol.2019.124082, 2019.
28. Xie, M., J. Šimůnek, Z. Zhang, P. Zhang, J. Xu, and Q. Lin, Nitrate subsurface transport and losses in response to its initial distributions in sloped soils: An experimental and modeling study, Hydrological Processes, 15 p., doi: 10.1002/hyp.13556, 2019.
29. Yang, T., J. Šimůnek, M. Mo, B. Mcculloug-Sanden, H. Shahrokhnia, S. Cherchian, and L. Wu, Assessing salinity leaching efficiency in three soils by the HYDRUS-1D and -2D simulations, Soil & Tillage Research, 194, 104342, 10 p., doi: 10.1016/j.still.2019.104342, 2019.
30. Jia, M., D. Jacques, F. Gérard, D. Su, K. U. Mayer, and J. Šimůnek, A benchmark for soil organic matter degradation under variably-saturated flow conditions, Computational Geosciences, 19 p., doi: 10.1007/s10596-019-09862-3, (in press).
31. Hansson, L., J. Šimůnek, E. Ring, K. Bishop, and A. I. Gärdenäs, Soil compaction effects on root-zone hydrology and vegetation in boreal forest clearcuts, Soil Science Society of America Journal, 83(Suppl. 1), S105-S115, doi: 10.2136/sssaj2018.08.0302, 2019.
32. Mokari, E., M. Shukla, J. Šimůnek, and J. Fernandez, Numerical modeling of nitrate in a flood-irrigated pecan orchard, Soil Science Society of America Journal, 83(3), 555-564, doi: 10.2136/sssaj2018.08.0302, 2019.
33. Vereecken, H., L. Weihermüller, S. Assouline, J. Šimůnek, A. Verhoef, M. Herbst, N. Archer, B. Mohanty, C. Montzka, J. Vanderborght, G. Balsamo, M. Bechtold, A. Boone, S. Chadburn, M. Cuntz, B. Decharme, A. Ducharne, M. Ek, S. Garrigues, K. Görgen, J. Ingewersen, S. Kollet, D. M. Lawrence, Q. Li, D. Or, S. Swenson, P. de Vrese, R. Walko, Y. Wu, and Y. Xue, Infiltration from the pedon to global grid scales: An overview and outlook for land surface modelling, Vadose Zone Journal, 18(1), 18019, 53 p., doi: 10.2136/vzj2018.10.0191, 2019.
34. Kacimov, A. R., Y. V. Obnosov, and J. Šimůnek, Minimal evaporation by optimal layering of topsoil: Revisiting Ovsinsky’s smart mulching-tillage technology via Gardner-Warrick’s unsaturated analytical model and HYDRUS, Water Resources Research, 55, 3606-3618, doi: 10.1029/2018WR024025, 2019.
35. Beegum, S., J. Šimůnek, A. Szymkiewicz, K. P. Sudheer, and I. M. Nambi, Implementation of solute transport in the vadose zone into the 'HYDRUS package for MODFLOW', Groundwater, 57(3), 392-408, doi: 10.1111/gwat.12815, 2019.
36. Pinheiro, E. A. R, Q. de Jong van Lier, and J. Šimůnek, The role of soil hydraulic properties in crop water use efficiency: A process-based analysis for some Brazilian scenarios, Agricultural Systems, 173, 364-377, doi: 10.1016/j.agsy.2019.03.019, 2019.
37. Ramos, T. B., H. Darouich, J. Šimůnek, M. C. Gonçalves, and J. C. Martins, Soil salinization in very high-density olive orchards grown in southern Portugal: current risks and possible trends, Agricultural Water Management, 217, 265-281, doi: 10.1016/j.agwat.2019.02.047, 2019.
38. Pinheiro, E. A. R, Q. de Jong van Lier, L. Inforsato, and J. Šimůnek, Measuring full-range soil hydraulic properties for the prediction of crop water availability using gamma-ray attenuation and inverse modeling, Agricultural Water Management, 216, 294-305, doi: 10.1016/j.agwat.2019.01.029, 2019.
39. Zhang, M., S. A. Bradford, J. Šimůnek, H. Vereecken, and E. Klumpp, Co-transport of multi-walled carbon nanotubes and sodium dodecylbenzenesulfonate in chemically heterogeneous porous media, Environmental Pollution, 247, 907-916, doi: 10.1016/j.envpol.2019.01.106, 2019.
40. Liang, J., W. Li, S. A. Bradford, and J. Šimůnek, Physics-informed data-driven models to predict surface runoff water quantity and quality in agricultural fields, Water, 11, 200, 21 p., doi: 10.3390/w11020200, 2019.
41. Brunetti, G., J. Šimůnek, H. Bogena, R. Baatz, J. A. Huisman, H. Dahlke, and H. Vereecken, On the information content of cosmic-ray neutrons in Bayesian optimization of soil hydraulic properties, Vadose Zone Journal, 18, 180123, 24 p., doi: 10.2136/vzj2018.06.0123, 2019.
42. Phogat, V., J. W. Cox, R. S. Kookana, J. Šimůnek, T. Pitt, and N. Fleming, Optimizing the riparian zone width near a stream for controlling lateral migration of irrigation water and solutes, Journal of Hydrology, 570, 37-646, 2019.
43. Sasidharan, S., S. A. Bradford, J. Šimůnek, and S. R. Kraemer, Drywell infiltration and hydraulic properties in heterogeneous soil profiles, Journal of Hydrology, 570, 598-561, doi: 10.1016/j.jhydrol.2018.12.073, 2019.
44. Karandish, F., and J. Šimůnek, A comparison of the HYDRUS (2D/3D) and SALTMED models to investigate the influence of various water-saving irrigation strategies on the maize water footprint, Agricultural Water Management, 213, 809-820, doi: 10.1016/j.agwat.2018.11.023, 2019.
45. Liu, K., G. Huang, X. Xu, Y. Xiong, Q. Huang, and J. Šimůnek, A coupled model for simulating water flow and solute transport in furrow irrigation, Agricultural Water Management, 213, 792-802, 2019.
46. Liang, Y., S, A. Bradford, J. Šimůnek, and E. Klumpp, Mechanism of graphene oxide aggregation, retention, and release in quartz sand, Science of the Total Environment, 656, 70-79, doi: 10.1016/j.scitotenv.2018.11.258, 2019.
47. Saefuddin, R., H. Saito, and J. Šimůnek, Experimental and numerical evaluation of a ring-shaped emitter for subsurface irrigation, Agricultural Water Management, 211, 111-122, doi: 10.1016/j.agwat.2018.09.039, 2019.
48. Phogat, V., J. W. Cox, J. Šimůnek, and P. Hayman, Modeling water and salinity risks to viticulture under prolonged sustained deficit and saline water irrigation, Journal of Water and Climate Change, 9, doi: 10.2166/wcc.2018.186, (in press). (https://doi.org/10.2166/wcc.2018.186)

1. Sasidharan, S., S. A. Bradford, J. Šimůnek, and S. Torkzaban, Minimizing virus transport in porous media by optimizing solid phase inactivation, Journal of Environmental Quality, 47(5), 1058-1067, doi: 10.2134/jeq2018.01.0027, 2018.

49. Beegum, S., J. Šimůnek, A. Szymkiewicz, K. P. Sudheer, and I. M. Nambi, Updating the coupling algorithm between HYDRUS and MODFLOW in the ‘HYDRUS Package for MODFLOW’, Technical Note, Vadose Zone Journal, 17(1), 180034, 8 p., doi: 10.2136/vzj2018.02.0034, 2018.
50. Wongkaew, A., H. Saito, H. Fujimaki, and J. Šimůnek, Numerical analysis of soil water dynamics in a soil column with an artificial capillary barrier growing leaf vegetables, Soil Use and Management, 34, 206-215, doi: 10.1111/sum.12423, 2018.
51. Karandish, F., and J. Šimůnek, An application of the Water Footprint concept to optimize the production of crops irrigated with saline water: Scenario assessment with HYDRUS, Agricultural Water Management, 208, 67-82, 2018.
52. 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.
53. Sasidharan, S. A. Bradford, J. Šimůnek, B. DeJong, and S. R. Kraemer, Evaluating drywells for stormwater management and enhanced aquifer recharge, Advances in Water Resources, 116, 167-177, doi: 10.1016/j.advwatres.2018.04.003, 2018.
54. Brunetti, G., J. Šimůnek, M. Turco, and P. Piro, On the use of global sensitivity analysis for the numerical analysis of permeable pavements, Urban Water Journal, 15(3), 269-275, doi: 10.1080/1573062X.2018.1439975, 2018.
55. Kacimov, A., Y. Obnosov, and J. Šimůnek, Steady flow from an array of subsurface emitters: Kornev’s irrigation technology and Kidder’s free boundary problems revisited, Transport in Porous Media, 121(3), 643-664, doi: 10.1007/s11242-017-0978-x, 2018.
56. Adrian, Y. F., U. Schneidewind, S. A. Bradford, J. Šimůnek, T. M. Fernandez-Steeger, and R. Azzam, Transport and retention of surfactant- and polymer-stabilized engineered silver nanoparticles in silicate-dominated aquifer material, Environmental Pollution, 236, 195-207, doi: 10.1016/j.envpol.2018.01.011, 2018.
57. Rahmatpour, S., M. R. Mosaddeghi, M. Shirvani, and J. Šimůnek, Transport of silver nanoparticles in intact columns of calcareous soils: The role of flow conditions and soil texture, Geoderma, 322, 89-100, doi: 10.1016/j.geoderma.2018.02.016, 2018.
58. Phogat, V., T. Pitt, J. W. Cox, J. Šimůnek, and M. A. Skewes, Soil water and salinity dynamics under sprinkler irrigated almond exposed to a varied salinity stress at different growth stages, Agricultural Water Management, 201, 70-82, doi: 10.1016/j.agwat.2018.01.018, 2018a.
59. Phogat, V., J. W. Cox, and J. Šimůnek, Identifying the future water and salinity risks to irrigated viticulture in the Murray-Darling Basin, South Australia, Agricultural Water Management, 201, 107-117, doi: 10.1016/j.agwat.2018.01.025, 2018b.
60. Šimůnek, J., M. Th. van Genuchten, and R. Kodešová, Thematic issue on HYDRUS applications to subsurface flow and contaminant transport problems, Journal of Hydrology and Hydromechanics, 66(2), 129-132, doi: 10.1515/johh-2017-0060, 2018.
61. Szymkiewicz, A., A. Gumuła-Kawęcka, J. Šimůnek, B. Leterme, S. Beegum, B. Jaworska-Szulc, M. Pruszkowska- Caceres, W. Gorczewska-Langner, R. Angulo-Jaramillo, and D. Jacques, Simulation of freshwater lens recharge and salt/freshwater interfaces using the Hydrus and SWI2 packages for Modflow, Journal of Hydrology and Hydromechanics, 66(2), 246-256, doi: 10.2478/johh-2018-0005, 2018.
62. Shelia, V., J. Šimůnek, K. Boote, and G. Hoogenbooom, Coupled DSSAT and HYDRUS-1D for simulations of soil water dynamics in the soil-plant-atmosphere system, Journal of Hydrology and Hydromechanics, 66(2), 232-245, doi: 10.1515/johh-2017-0055, 2018.
63. Karimov, A. K., M. A. Hanjra, J. Šimůnek, and M. Avliyakulov, Can a change in cropping pattern produce water savings and social gains: A case study from the Fergana Valley, Central Asia, Journal of Hydrology and Hydromechanics, 66(2), 189-201, 2018.
64. Šimůnek, J., M. Šejna, and M. Th. van Genuchten, New Features of the Version 3 of the HYDRUS (2D/3D) Computer Software Package, Journal of Hydrology and Hydromechanics, 66(2), 129-132, doi: 10.1515/johh-2017-0050, 2018.
65. Jacques, D., J. Šimůnek, D. Mallants, and M. Th. van Genuchten, The HPx software for multicomponent reactive transport during variably-saturated flow: Recent developments and applications, Journal of Hydrology and Hydromechanics, 66(2), 211-226, doi: 10.1515/johh-2017-0049, 2018.
66. Arthur, J. D., N. W. Mark, S. Taylor, J. Šimůnek, M. L. Brusseau, and K. M. Dontsova, Dissolution and transport of insensitive munitions formulations IMX-101 and IMX-104 in saturated soil columns, Science of Total Environment, 624, 758-768, doi: 10.1016/j.scitotenv.2017.11.307, 2018.
67. Darzi-Naftchali, A., F. Karandish, and J. Šimůnek, Numerical modeling of soil water dynamics in subsurface drained paddies with midseason drainage or alternate wetting and drying management, Agricultural Water Management, 197, 67-78, doi: 10.1016/j.agwat.2017.11.017, 2018.
68. 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, 17(1), 170040, 16 p., doi: 10.2136/vzj2017.02.0040, 2018.

1. Karandish, F., A. Darzi-Naftchali, and J. Šimůnek, Application of HYDRUS (2D/3D) for predicting the influence of subsurface drainage on soil water dynamics in a rainfed-canola cropping system, Irrigation and Drainage Journal, 67, Supplement 2, 29-39, doi: 10.1002/ird.2194, 2018.

69. Diamantopoulos, E., J. Šimůnek, C. Oberdörster, K. Hammel, B. Jene, T. Schröder, and T. Harter, Assessing the potential risk of groundwater to pesticides – a model comparison, Vadose Zone Journal, 16(11), pp. 13, doi: 10.2136/vzj2017.04.0070, 2017.
70. Sasidharan, S., S. A. Bradford, J. Šimůnek, S. Torkzaban, and J. Vanderzalm, Transport and fate of viruses in sediment and stormwater from a Managed Aquifer Recharge site, Journal of Hydrology, 555, 724-735, Journal of Hydrology, 2017.
71. Brunetti, G., H. Saito, T. Saito, and J. Šimůnek, A computationally efficient pseudo-3D model for the numerical analysis of borehole heat exchangers, Applied Energy, 208, 113-1127, doi.: 10.1016/j.apenergy.2017.09.042, (2017) (IF=7.18).
72. Karandish, F., and J. Šimůnek, Two-dimensional modelling of nitrogen and water dynamics under various N-managed water saving irrigation strategies using HYDRUS, Agricultural Water Management, 193, 174-190, doi: 10.1016/j.agwat.2017.07.023, 2017.
73. Mallmann, F. J. K., D. R. dos Santos, M. A. Bender, E. Gubiani, M. da Veiga, J. P. G. Minella, F. van Oort, and J. Šimůnek, Modeling zinc and copper movement in an Oxisol contaminated by long-term pig slurry amendments, Vadose Zone Journal, Special issue "Soil Variability and Biogeochemical Fluxes", 16, pp. 14, doi: 10.2136/vzj2017.01.0011, 2017.
74. Li, Y., J. Šimůnek, S. Wang, W. Zhang, and J. Yuan, Simulating the effects of lake wind waves on water and solute exchange across the lakeshore using Hydrus-2D, Water, 9(8), 566, 18 pp., doi: 10.3390/w9080566, 2017.
75. Phogat, V., N. J. Potter, J.W. Cox, and J. Šimůnek, Long-term quantification of stream-aquifer exchange in a variably saturated heterogeneous environment, Water Resources and Management, 31(13), 4353-4366, doi: 10.1007/s11269-017-1752-0, 2017.
76. Slimene, E. B., L. Lassabatere, J. Šimůnek, T. Winiarski, and R. Gourdon, The role of heterogeneous lithology in a glaciofluvial deposit on unsaturated preferential flow – a numerical study, Journal of Hydrology and Hydromechanics, 65(3), 209-221, doi: 10.1515/johh-2017-0004, 2017.
77. Liang, J., S. A. Bradford, J. Šimůnek, A. Hartmann, Adapting HYDRUS-1D to simulate overland flow and reactive transport during sheet flow deviations, Vadose Zone Journal, 16(6), pp. 18, doi: 10.2136/vzj2016.11.0113, 2017.
78. Mallants, D., J. Šimůnek, M. Th. van Genuchten, and D. Jacques, Simulating the fate and transport of coal seam gas chemicals in variably-saturated soils using HYDRUS, Water, 9, 385, doi:10.3390/w9060385, 2017.
79. Mallants, D., J. Šimůnek, and D. Torkzaban, Determining water quality requirements of coal seam gas produced water for sustainable irrigation, Agricultural Water Management, 189, 52-69, doi: 10.1016/j.agwat.2017.04.011, 2017.
80. Brunetti, G., J. Šimůnek, 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.
81. Arthur, J. D., N. W. Mark, S. Taylor, J. Šimůnek, M. L. Brusseau, and K. M. Dontsova, Batch soil adsorption and column transport studies of 2,4-dinitroanisole (DNAN) in soils, Journal of Contaminant Hydrology, 199, 14-23, doi: 10.1016/j.jconhyd.2017.02.004, 2017.
82. Li, Y., J. Šimůnek, S. Wang, J. Yuan, and W. Zhang, Modeling of soil water regime and water balance in a transplanted rice field experiment with reduced irrigation, Water, 9(4), 248, 14 pp, doi: 10.3390/w9040248, 2017.
83. Lamorski, K., J. Šimůnek, C. Sławiński, and J. Lamorska, Estimation of the main wetting branch of soil water retention curve based on the main drying branch using the machine learning method, Water Resources Research, 53, pp. 14, doi:10.1002/2016WR019533, 2017.
84. Aggarwal, P., R. Bhattacharyya, A. K. Mishra, T. K. Das, J. Šimůnek, P. Pramanik, S. Sudhishri, A. Vashisth, P. Krishnan, D. Chakraborty, and K. H. Kamble, Modelling soil water balance and root water uptake in cotton grown under different soil conservation practices in the Indo-Gangetic Plain, Agriculture, Ecosystems & Environment, 240, 287-299, doi: 10.1016/j.agee.2017.02.028, 2017.
85. Zhang, M., I. Engelhardt, J. Šimůnek, S. A. Bradford, D. Kasel, A. E. Berns, H. Vereecken, and E. Klumpp, Co-transport of chlordecone and sulfadiazine in the presence of functionalized multi-walled carbon nanotubes in soils, Environmental Pollution, 221, 470-479, doi: 10.1016/j.envpol.2016.12.018, 2017.
86. Mark, N., J. D. Arthur, K. Dontsova, M. Brusseau, S. Taylor, and J. Šimůnek, Column transport studies of 3-nitro-1,2,4-triazol-5-one (NTO) in soils, Chemosphere, 171, 427-434, doi: 10.1016/j.chemosphere.2016.12.067, 2017.
87. Zhang, M, S. A. Bradford, J. Šimůnek, H. Vereecken, and E. Klumpp, Roles of cation valance and exchange on the retention and colloid-facilitated transport of functionalized multi-walled carbon nanotubes in a natural soil, Water Research, 109, 358-366, doi: 10.1016/j.watres.2016.11.062, 2017.
88. Li, X., J. Šimůnek, H. Shi, J. Yan, Z. Peng, and X. Gong, Spatial distribution of soil water, soil temperature, and plant roots in a drip-irrigated intercropping field with plastic mulch, European Journal of Agronomy 83, 47-56, doi: 10.1016/j.eja.2016.10.015, 2017.
89. Phogat, V., M. A. Skewes, M. G. McCarthy, J. W. Cox, J. Šimůnek, and P. Petrie, Evaluation of crop coefficients, water productivity, and water balance components for wine grapes irrigated at different deficit levels by a sub-surface drip, Agricultural Water Management, 180, 22-34, doi: 10.1016/j.agwat.2016.10.016, 2017.
90. Karandish, F., and J. Šimůnek, Numerical and machine-learning modeling of soil water content for sustainable water management in agriculture under water stress, Journal of Hydrology, 543, 892-909, doi: 10.1016/j.jhydrol. 2016.11.007, 2016.
91. Zhang, M, S. A. Bradford, J. Šimůnek, H. Vereecken, and E. Klumpp, Do goethite surfaces really control the transport and retention of multi-walled carbon nanotubes in chemically heterogeneous porous media? Environmental Science & Technology, 50, 12713-12721, doi: 10.1021/acs.est.6b03285, 2016.
92. Karandish, F., and J. Šimůnek, A field-modeling study for assessing temporal variations of soil-water-crop interactions under water-saving irrigation strategies, Agricultural Water Management, 178, 291-303, doi: 10.1016/j.agwat.2016.10.009, 2016.
93. Phogat, V., J. Šimůnek, M. A. Skewes, J. W. Cox, and M. G. McCarthy, Improving the estimation of evaporation by the FAO-56 dual crop coefficient approach under subsurface drip irrigation, Agricultural Water Management, 178(12), 189-200, doi: 10.1016/j.agwat.2016.09.022, 2016.
94. Raij, I., J. Šimůnek, A. Ben-Gal, and N. Lazarovitch, Water flow and multicomponent solute transport in drip irrigated lysimeters: Experiments and modeling, Water Resources Research, 52, 6557-6574, doi: 10.1002/2016WR018930, 2016.
95. 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.
96. 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.
97. 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. (Hot paper according to Web of Knowledge (ISI))
98. Hlaváčiková, H., V. Novák, and J. Šimůnek, The effects of rock fragment shapes and positions on modeled hydraulic conductivities of stony soils, Geoderma, 281, 39-48, doi: 10.1016/j.geoderma.2016.06.034, 2016.
99. Phogat, V., M. A. Skewes, J. W. Cox, and J. Šimůnek, Statistical assessment of a numerical model simulating agro hydro-chemical processes in soil under drip fertigated mandarin tree, Irrigation & Drainage System Engineering, 5(1), pp. 9, ISSN: 2168-9768, doi:10.4172/2168-9768.1000155, 2016.
100. Vereecken, H., A. Schnepf, J. W. Hopmans, M. Javaux, D. Or, T. Roose, J. Vanderborght, M. H. Young, W. Amelung, M. Aitkenhead, S. D. Allisson, S. Assouline, P. Baveye, M. Berli, N. Brüggemann, P. Finke, M. Flury, T. Geiser, G. Govers, T. Ghezzehei, P. Hallett, H. J. Hendricks Franssen, J. Heppel, R. Horn, J. A. Huisman, D. Jacques, F. Jonard, S. Kollet, F. Lafolie, K. Lamorsky, D. Leitner, A. McBratney, B. Minasny, C. Montzka, W. Nowak, Y. Pachepsky, J. Padarian, N. Romano, K. Roth, Y. Rothfuss, E. C. Rowe, A. Schwen, J. Šimůnek, A. Titak, J. van Dam, S. E. A. T. M. van der Zee, H. J. Vogel, J. A. Vrugt, T. Wöhling, and I. M. Young, Modelling soil processes: Review, key challenges, and new perspectives, Vadose Zone Journal, 15(5), pp. 57, doi: 10.2136/vzj2015.09.0131, 2016. (Highly cited paper according to Web of Knowledge (ISI))
101. Dafny, E., and J. Šimůnek, Infiltration in unsaturated layered loess deposits: Revised numerical simulations and recharge assessment, Journal of Hydrology, 518, 339-354, doi:10.1016/j.jhydrol.2016.04.029, 2016.
102. Deb, S. K., P. Sharma, M. K. Shukla, J. Ashigh, and J. Šimůnek, Numerical evaluation of nitrate distributions in the onion root zone under conventional furrow fertigation, Journal of Hydrologic Engineering, 21(2), 05015026-1-12, doi:10.1061/(ASCE)HE.1943-5584.0001304, 2016.
103. Šimůnek, J., K. L. Bristow, S. A. Helalia, and A. A. Siyal, The effect of different fertigation strategies and furrow surface treatments on plant water and nitrogen use, Irrigation Science, 34(1), 53-69, doi:10.1007/s00271-015-0487-z, 2016.
104. Šimůnek, J., Estimating groundwater recharge using HYDRUS-1D, (Bulgarian) Engineering Geology and Hydrogeology, 29, 25-36, ISSN 0204-7934, 2015.
105. Imran, M., A.-U. Hassan, M. Iqbal, E. Ullah, and J. Šimůnek, Assessment of actual evapotranspiration and yield of wheat under different irrigation regimes with potassium application, Soil & Environment (formerly Pakistan Journal of Soil Science), 34(2), 156-165, Print ISSN: 2074-9546, Online ISSN: 2075-1141, 2015.
106. Bradford, S. A., S. Torkzaban, F. J. Leij, and J. Šimůnek, Equilibrium and kinetic models for colloid release under transient solution chemistry conditions, Journal of Contaminant Hydrology, 181, 141-152, doi:10.1016/j.jconhyd.2015.04.003, 2015.
107. Han, M., C. Zhao, J. Šimůnek, and G. Feng, Evaluating the impact of groundwater on cotton growth and root zone water balance using Hydrus-1D coupled with a crop growth model, Agricultural Water Management, 160, 64-75, doi:10.1016/j.agwat.2015.06.028, 2015.
108. Xie, M., K. U. Mayer, F. Claret, P. Alt-Epping, D. Jacques, C. Steefel, C. Chiaberge, and J. Šimůnek, Implementation and evaluation of permeability-porosity and tortuosity-porosity relationships linked to mineral dissolution-precipitation, Computational Geosciences, 19(3), 65-671, doi:10.1007/s10596-014-9458-3, 2015.
109. Steefel, C. I., C. A. J. Appelo, B. Arora, D. Jacques, T. Kalbacher, O. Kolditz, V. Lagneau, P. C. Lichtner, K. U. Mayer, J. C. L. Meeussen, S. Molins, D. Moulton, H. Shao, J. Šimůnek, N. Spycher, S. B. Yabusaki, and G. T. Yeh, Reactive transport codes for subsurface environmental simulation, Computational Geosciences, 19(3), 445-478, doi:10.1007/s10596-014-9443-x, 2015. (Hot and highly cited paper according to Web of Knowledge (ISI))
110. Bradford, S. A., Y. Wang, S. Torkzaban, and J. Šimůnek, Modeling the release of E. coli D21g with transients in water content, Water Resources Research, 51(5), 3303-3316, doi:10.1002/2014WR016566, 2015.
111. Li, X., H. Shi, J. Šimůnek, X. Gong, and Z. Peng, Investigation of soil water dynamics in a drip irrigated strip intercropping field under plastic mulch, Irrigation Sciences, 33, 289-302, doi:10.1007/s00271-015-0466-4, 2015.
112. Chaganti, V. N., D. M. Crohn, and J. Šimůnek, Leaching and reclamation of a biochar and compost amended saline-sodic soil with moderate SAR reclaimed water, Agricultural Water Management, 158, 255-265, 2015.
113. Bradford, S. A., B. Headd, G. Arye, and J. Šimůnek, Transport of E. coli D21g with runoff water under different solution chemistry conditions and surface slopes, Journal of Hydrology, 525, 760-768, 2015.
114. Engelhardt, I., S. Sittig, J. Šimůnek, J. Groeneweg, T. Pütz, and H. Vereecken, Fate of the antibiotic sulfadiazine in natural soils: experimental and numerical investigations, Journal of Contaminant Hydrology, 177-178, 30-42, 2015.
115. Rashid, N. S. A., M. Askari, T. Tanaka, J. Šimůnek, and M. Th. van Genuchten, Inverse estimation of soil hydraulic properties under oil palm trees, Geoderma, 241-242, 306-312, doi:10.1016/j.geoderma.2014.12.00, 2015.
116. Li, Y., J. Šimůnek, L. Jing, Z. Zhang, Y. Chen, J. Hua, L. Ni, and L. Zhu, Water flow and nitrate transport through a lakeshore with different revetment materials, Journal of Hydrology, 520, 123-133, 10.1016/j.jhydrol.2014.11.045, 2015.
117. Li, Y., J. Šimůnek, Z. Zhang, L. Jing, and L. Ni, Evaluation of nitrogen balance in a direct-seeded-rice field experiment using Hydrus-1D, Agricultural Water Management, 148, 213-222, doi:10.1016/j.agwat.2014.10.010, 2015.
118. Lassabatere, L., D. Yilmaz, X. Peyrard, P. E. Peyneau, T. Lenoir, U. Pillai, J. Šimůnek, and R. Angulo-Jaramillo, Analytical and numerical modeling of cumulative infiltration into dual-permeability soils, Vadose Zone Journal, 13(12), doi:10.2136/vzj2013, 15 pp., 2014.
119. Wang, Y., S. A. Bradford, and J. Šimůnek, Release of E. coli D21g with transients in water content, Environmental Science & Technology, 48(16), 9349-9357, doi: 10.1021/es501956k, 2014.
120. Kool, D., A. Ben-Gal, N. Agam, J. Šimůnek, J. L. Heitman, T. J. Sauer, and N. Lazarovitch, Spatial and diurnal below canopy evaporation in a desert vineyard: measurements and modeling, Water Resources Research, 2014WR015409, doi:10.1002/2014WR015409, 2014.
121. Filipović, V., F. J. K. Mallmann, Y. Coquet, and J. Šimůnek, Numerical simulation of water flow in tile and mole drainage systems, Agricultural Water Management, 146, 105-114, http://dx.doi.org/10.1016/j.agwat.2014.07.020, 2014.
122. Mallmann, F. J. K., D. R. dos Santos, C. A. Ceretta, C. Cella, J. P. G. Minella, R. L. Guma, V. Filipović, F. van Oort, and J. Šimůnek, Soil tillage to reduce surface metal contamination - model development and simulations of zinc and copper concentration profiles in a pig slurry-amended soil, Agriculture, Ecosystems and Environment, 196, 59-68, doi: 10.1016/j.agee.2014.06.024, 2014.
123. Li, Y., J. Šimůnek, L. Jing, Z. Zhang, and L. Ni, Evaluation of water movement and water losses in a direct-seeded-rice field experiment using Hydrus-1D, Agricultural Water Management, 142, 38-46, doi 10.1016/j.agwat.2014.04.021, 2014.
124. Phogat, V., M. A. Skewes, J. W. Cox, G. Sanderson, J. Alam, and J. Šimůnek, Seasonal simulation of water, salinity, and nitrate dynamics under drip irrigated mandarin (Citrus reticulata) and assessing management options for drainage and nitrate leaching, Journal of Hydrology, 513, 504-516, 2014.
125. Wang, Y., S. A. Bradford, and J. Šimůnek, Estimation and upscaling of dual-permeability model parameters for the transport of E. coli D21g in soils with preferential flow, Journal of Contaminant Hydrology, 159, 57-66, 2014.
126. Bradford, S. A., Y. Wang, H. Kim, S. Torkzaban, and J. Šimůnek, Modeling microorganism transport and survival in the subsurface, Journal of Environmental Quality, 43(2), 421-440, doi:10.2134/jeq2013.05.0212, 2014.
127. Teijón, G., L. Candela, J. Šimůnek, K. Tamoh, and J. Valdes-Abellán, Fate and transport of Naproxen in a sandy aquifer material: Saturated column studies and model evaluation, Soil and Sediment Contamination: An International Journal, 23(7), 736-750, doi: 10.1080/15320383.2014.869194, 2014.
128. Galeandro, A., A. Doglioni, V. Simeone, and J. Šimůnek, Analysis of infiltration processes into fractured and swelling soils as triggering factors of landslides, Environmental Earth Sciences, 71(6), 2911-2923doi:10.1007/s12665-013-2666-7, 2014.
129. El-Nesr, M. N. B., A. Alazba, and J. Šimůnek, PHYDRUS simulations of the effects of dual-drip subsurface irrigation and a physical barrier on water movement and solutes transport in soils, Irrigation Science, 32(2), 11-125, doi:10.1007/s00271-013-0417-x, 2014.
130. Nakhaei, M., and J. Šimůnek, Parameter estimation of soil hydraulic and thermal property functions for unsaturated porous media using the HYDRUS-2D code, Journal of Hydrology and Hydromechanics, 62(1), 7-15, doi:10.2478/johh-2014-0008, 2014.
131. Wang, Y., S. A. Bradford, and J. Šimůnek, Physicochemical factors influencing the preferential transport of Escherichia coli in soils, Vadose Zone Journal, 13(1), doi:10.2136/vzj2013.07.0120, 10 pp., 2014.
132. Wang, Z.., M. Jin, J. Šimůnek, and M. Th. van Genuchten, Evaluation of mulched drip irrigation for cotton in arid Northwest China, Irrigation Science, 32(1), 15-27, doi:10.1007/s00271-013-0409-x, 2014.
133. Karimov, A. K. J. Šimůnek, M. A. Hanjra, M. Avliakulov, and I. Forkutsa, Effects of the shallow water table on water use of winter wheat and ecosystem health: Implications for unlocking the potential of groundwater in the Fergana Valley (Central Asia), Agricultural Water Management, 131, 57-69, doi:10.1016/j.agwat.2013.09.010, 2014.
134. Amin, M. G., J. Šimůnek, and M. Lægdsmand, Simulation of the redistribution and fate of contaminants from soil-injected animal slurry, Agricultural Water Management, 131, 17-29, 10.1016/j.agwat.2013.09.002, 2014.
135. Rings, J., T. Kamai, M. Kandelous, P. Hartsough, J. Šimůnek, J. A. Vrugt, and J. W. Hopmans, Bayesian inference of tree water relations using a soil-tree-atmosphere continuum model, Procedia Environmental Sciences, 19, 26-36, doi:10.1016/j.proenv.2013.06.004, 2013.
136. Saito, H., M. Sakai, N. Toride, and J. Šimůnek, HYDRUS-1D: Software package for simulating water, heat, and solutes in variably-saturated soils (in Japanese), Water, Land and Environmental Engineering, 81(12), 993-996, 2013.
137. Galeandro, A., J. Šimůnek, and V. Simeone, Analysis of rainfall infiltration effects on the stability of pyroclastic soil veneer affected by vertical drying shrinkage fractures, Bulletin of Engineering Geology and the Environment, 72(3-4), 447-455, doi:10.1007/s10064-013-0492-5, 2013.
138. Liang, Y., S. A. Bradford, J. Šimůnek, M. Heggen, H. Vereecken, and E. Klumpp, Retention and remobilization of stabilized silver nanoparticles in an undisturbed loamy sandy soil, Environmental Science & Technology, 47(21), 12229-12237, doi:10.1021/es402046u, 2013.
139. Rasouli, F., A. K. Pouya, and J. Šimůnek, Modeling the effects of saline water use in wheat-cultivated lands using the UNSATCHEM model, Irrigation Science, 31(5), 1009-1024, doi:10.1007/s00271-012-0383-8, 2013.
140. Bradshaw, J. K., D. E. Radcliffe, J. Šimůnek, A. Wunsch, and J. E. McCray, Nitrogen fate and transport in a conventional onsite wastewater treatment system installed in a clay soil: A nitrogen chain model, Vadose Zone Journal, 12(3), doi:10.2136/vzj2012.0150, 20 pp., 2013.
141. Rudiyanto, N. Toride, M. Sakai, and J. Šimůnek, A hysteretic model of hydraulic properties for dual-porosity soils, Soil Science Society of America Journal, 77(4), 1182-1188, doi: 10.2136/sssaj2012.0339n, 2013.
142. Deb, S. K., M. K. Shukla, J. Šimůnek, and John G. Mexal, Evaluation of spatial and temporal root water uptake patterns of a flood–irrigated pecan tree using the HYDRUS (2D/3D) model, ASCE Journal of Irrig. and Drain. Eng., 139(8), 599-611, 2013.
143. Šimůnek, J., D. Jacques, G. Langergraber, S. A. Bradford, M. Šejna, and M. Th. van Genuchten, Numerical modeling of contaminant transport with HYDRUS and its specialized modules, Invited paper for the Special Issue "Water Management in Changing Environment", Editor M. S. Mohan Kumar, Journal of the Indian Institute of Science, 93(2) 265-284, ISSN: 0970-4140 Coden-JIISAD, 2013.
144. Wang, Y., S. A. Bradford, and J. Šimůnek, Transport and fate of microorganisms in soils with preferential flow under different solution chemistry conditions, Water Resources Research, 49(5), 2424-2436, doi:10.1002/wrcr.20174, 2013.
145. Phogat, V., M. A. Skewes, J. W. Cox, J. Alam, G. Grigson, and J. Šimůnek, Evaluation of water movement and nitrate dynamics in a lysimeter planted with an orange tree, Agricultural Water Management, 127, 74-84, 2013.
146. Kasel, D., S. A. Bradford, J. Šimůnek, T. Pütz, H. Vereecken, and E. Klumpp, Limited transport of functionalized multi-walled carbon nanotubes in two natural soils, Environmental Pollution, 180, 152-158, http://dx.doi.org/10.1016/j.envpol.2013.05.031, 2013.
147. Spurlock, F., J. Šimůnek, B. Johnson, and, A. Tuli, Sensitivity analysis of soil fumigant transport and volatilization to the atmosphere, Vadose Zone Journal, 12(2), doi:10.2136/vzj2012.0130, 12 pp., 2013.
148. Liu, X., J. Šimůnek, L. Li, and J. He, Identification of sulfate sources in groundwater using isotope analysis and modeling of flood irrigation with waters of different quality in the Jinghuigu district of China, Environmental Earth Science, 69(5), 1589-1600, doi:10.1007/s12665-012-1993-4, 2013.
149. Liang, Y. S. A. Bradford, J. Šimůnek, H. Vereecken, and E. Klumpp, Sensitivity of the transport an retention of stabilized silver nanoparticles to physicochemical factors, Water Research, 47, 2572-2582, doi:10.1016/j.watres.2013.02.025, 2013.
150. Kasel, D., S. A. Bradford, J. Šimůnek, M. Heggen, H. Vereecken, and E. Klumpp, Transport and retention of multi-walled carbon nanotubes in saturated porous media: Effects of input concentration and grain size, Water Research, 47(2), 933-944, 2013.
151. Dabach, S., N. Lazarovitch, J. Šimůnek, and U. Shani, Numerical investigation of irrigation scheduling based on soil water status, Irrigation Science, 31(1), 27-36, doi:10.1007/s00271-011-0289-x, 2013.
152. Liu, X., S. Sun, P. Ji, and J. Šimůnek, Evaluation of historical nitrate sources in groundwater and impact of current irrigation practices on groundwater quality, J. Hydrol. Sci., 58(1), 1–15, doi:10.1080/02626667.2012.745937, 2013.
153. Luo, L., D. J. Ashworth, J. Šimunek, R. Xuan, and S. R. Yates, Assessment of various methods for methyl iodide emission reduction and pest control using simulation model, Atmospheric Environment, 66, 33-40, doi:10.1016/j.atmosenv.2012.03.080, 2013.
154. Mallmann, F. J. K., D. R. dos Santos, C. A. Ceretta, C. Cella, J. Šimůnek, and F. van Oort, Modeling field-scale vertical movement of zinc and copper in a pig slurry-amended soil in Brazil, Journal of Hazardous Materials, 243, 223-231, doi: 10.1016/j.jhazmat.2012.10.022, 2012.
155. Nasta, P, L. Lassabatere, M. M. Kandelous, J. Šimůnek, and R. Angulo-Jaramillo, Analysis of the role of tortuosity and infiltration constants in the Beerkan method, Soil Physics Note, Soil Science Society of America, 76, 1999-2005, 2012.
156. Siyal, A. A., K. L. Bristow, and J. Šimůnek, Minimizing nitrogen leaching from furrow irrigation through novel fertilizer placement and soil management strategies, Agricultural Water Management, 115, 242-251, 2012
157. Bradford, S. A., S. Torkzaban, H. Kim, and J. Šimůnek, Modeling colloid and microorganism transport and release with transients in solution ionic strength, Water Resour. Res., 48, W09509, doi: 10.1029/2012WR012468, 10 pp., 2012.
158. Jacques, D., C. Smith, J. Šimůnek, and D. Smiles, Inverse optimization of hydraulic, solute transport, and cation exchange parameters using HP1 and UCODE to simulate cation exchange, J. Contaminant Hydrology, 142-143, 109-125, 2012.
159. van Genuchten, M. Th., J. Šimůnek, F. L. Leij, N. Toride, and M. Šejna, STANMOD: Model use, calibration and validation, Special issue Standard/Engineering Procedures for Model Calibration and Validation, Transactions of the ASABE, 5(4), 1353-1366, 2012.
160. Šimůnek, J., M. Th. van Genuchten, and M. Šejna, HYDRUS: Model use, calibration and validation, Special issue on Standard/Engineering Procedures for Model Calibration and Validation, Transactions of the ASABE, 55(4), 1261-1274, 2012.
161. Ramos, T. B., J. Šimůnek, M. C. Gonçalves, J. C. Martins, A. Prazeres, and L. S. Pereira, Two-dimensional modeling of water and nitrogen fate from sweet sorghum irrigated with fresh and blended saline waters, Agricultural Water Management, 111, 87-104, 2012.
162. Langergraber, G., and J. Šimůnek, Reactive transport modeling of subsurface flow constructed wetlands using the HYDRUS Wetland module, Special Issue "Reactive Transport Modeling", Vadose Zone Journal, 11(2), doi:10.2136/vzj2011.0104, 14 pp., 2012.
163. Seaman, J. C., H. Chang, S. Goldberg, and J. Šimůnek, Reactive Transport Modeling, Vadose Zone Journal, 11(2), doi:10.2136/vzj2012.0066, 7 pp., 2012.
164. Stumpp, C., W. Stichler, M. Kandolf, and J. Šimůnek, Effects of land cover and fertilization method on water flow and solute transport in five lysimeters: A long-term study using stable water isotopes, Vadose Zone Journal, 11(1), doi:10.2136/vzj2011.0075, 14 pp., 2012.
165. Kandelous, M. M., T. Kamai, J. A. Vrugt, J. Šimůnek, B. R. Hanson, and J. W. Hopmans, Evaluation of subsurface drip irrigation design and management parameters for alfalfa, Agric. Water Management, 109, 81-93, 2012.
166. Weihermüller, L., R. Kasteel, J. Vanderborght, J. Šimůnek, and H. Vereecken, Uncertainty in pesticide monitoring using suction cups: Evidence from numerical simulations, Vadose Zone Journal, 10(4), 1287-1298, 2011.
167. Bradford, S. A., S. Torkzaban, and J. Šimůnek, Modeling colloid transport and retention in saturated porous media under unfavorable attachment conditions, Water Resour. Res., 47, W10503, doi:10.1029/2011WR010812, 2011.
168. Yuan, F., T. Meixner, M. E. Fenn, and J. Šimůnek, Impact of transient soil water simulation on estimated nitrogen leaching and emission at high- and low-deposition forest sites in Southern California, Journal of Geophysical Research, 116, G03040, doi:10.1029/2011JG001644, 15 pp., 2011.
169. Jury, W. A., D. Or, Y. Pachepsky, H. Vereecken, J. W. Hopmans, L. R. Ahuja, B. E. Clothier, K. L. Bristow, G. J. Kluitenberg, P. Moldrup, J. Šimůnek, M. Th. van Genuchten, and R. Horton, Kirkham's legacy and contemporary challenges in soil physics research, Soil Sci. Soc. Am. J., special issue 75th anniversary of SSSAJ, 75(5), 1589-1601, 2011.
170. Neumann, L. E., J. Šimůnek, and F. J. Cook, Implementation of quadratic upstream interpolation schemes for solute transport into HYDRUS-1D, Environmental Modelling & Software, 26(11), 1298-1308, 2011.
171. Ramos, T. B., J. Šimůnek, M. C. Gonçalves, J. C. Martins, A. Prazeres, N. L. Castanheira, and L. S. Pereira, Field evaluation of a multicomponent solute transport model in soils irrigated with saline waters, J. of Hydrology, 407(1-4), 129-144, 2011.
172. Köhne, J. M., T. Wöhling, V. Pot, P. Benoit, S. Leguédois, Y. Le Bissonnais, and J. Šimůnek, Coupled simulation of surface runoff and soil water flow using multi-objective parameter estimation, J. of Hydrology, 403, 141-156, 2011.
173. Garcia, C. A., B. J. Andraski, D. A. Stonestrom, C. A. Cooper, J. Šimůnek, and S. W. Wheatcraft, Interacting vegetative and thermal contributions to water movement in desert soil, Vadose Zone Journal, 10(2), 552-564, 2011.
174. Ravikumar, V, G. Vijayakumar, J. Šimůnek, S. Chellamuthu, R. Santhi, and K. Appavu, Evaluation of fertigation scheduling for sugarcane using a vadose zone flow and transport model, Agricultural Water Management, 98, 1431-1400, 2011.
175. Kandelous, M. M., J. Šimůnek, M. Th. van Genuchten, and K. Malek, Soil water content distributions between two emitters of a subsurface drip irrigation system, Soil Science Society of America Journal, 75(2), 488497, 2011.
176. Shouse, P. J., J. E Ayars, and J. Šimůnek, Simulating Root Water Uptake From a Shallow Saline Groundwater Resource, Agricultural Water Manag., 98(5), 784-790, 2011.
177. Novák, V., K. Kňava, and J. Šimůnek, Assessing numerically the influence of stones on hydraulic conductivity of saturated soils, Geoderma, 161(3-4), 177-181, 2011.
178. Steenpass, C., J. Vanderborght, M. Herbst, J. Šimůnek, and H. Vereecken, Estimating soil hydraulic properties from infra-red measurements of soil surface temperatures and TDR data, Vadose Zone Journal, 9(4), 910-924, 2010.
179. Yakirevich, A., T. J. Gish, J. Šimůnek, M. Th. van Genuchten, Y. A. Pachepsky, T. J. Nicholson, and R. E. Cady, Potential impact of a seepage face on solute transport to a pumping well, Vadose Zone Journal, 9(3), 686-696, 2010.
180. Twarakavi, N. K. C., H. Saito, J. Šimůnek, and M. Th. van Genuchten, Inverse modeling of vadose zone flow processes using squared e-insensitivity loss function, Journal of Hydrology and Hydromechanics, 58(3), 188-200, 2010.
181. Kodešová, R., J. Šimůnek , A. Nikodem, and V. Jirků, Estimation of parameters of the radially-symmetric dual-permeability model using tension disk infiltrometer and Guelph permeameter experiments, Vadose Zone Journal, Special Issue: "Preferential and unstable flow in structured porous domains: From the pore to the catchment scale", doi:10.2136/vzj2009.0069, 9(2), 213-225, 2010.
182. Kandelous, M. M. and J. Šimůnek, Comparison of numerical, analytical and empirical models to estimate wetting pattern for surface and subsurface drip irrigation, Irrigation Sci., 10.1007/s00271-009-0205-9, 435-444, 2010.
183. Guan, H., J. Šimůnek, B. D. Newman, and J. L. Wilson, Modeling investigation of water partitioning at a semiarid ponderosa pine hillslope, Hydrological Processes, 24(9), 1095-1105, 2010.
184. Kandelous, M. M. and J. Šimůnek, Numerical simulations of water movement in a subsurface drip irrigation system under field and laboratory conditions using HYDRUS-2D, Agricultural Water Management, 97, 1070-1076, 2010.
185. Torkzaban, S., H. N. Kim, J. Šimůnek, and S. A. Bradford, Retention and release of colloids during transients in solution chemistry, Environ. Sci. and Technol., 44, 1662-1669, 2010.
186. Jiang, S., L. Pang, G. D. Buchan, J. Šimůnek, M. J. Noonan, M. E. Close, Modeling water flow and bacterial transport in undisturbed lysimeters under irrigations of dairy shed effluent and water using HYDRUS-1D, Water Research, special issue, doi:10.1016/j.watres.2009.08.039, 44, 1050-1061, 2010.
187. Pontedeiro, E. M., M. Th. van Genuchten, R. M. Cotta, and J. Šimůnek, The effects of preferential flow and soil texture on risk assessments of a NORM waste disposal site, Journal of Hazardous Materials, doi:10.1016/j.jhazmat.2009.09.100, 174(1-3), 648-655, 2010.
188. Twarakavi, N. K. C., J. Šimůnek, and M. G. Schaap, Can texture-based classification optimally classify soils with respect to soil hydraulics?, Water Resour. Res., 46, W02501, doi:10.1029/ 2009WR007939, pp. 11, 2010.
189. Paradelo, M., J. Šimůnek, J. C. Novoa-Muñoz, M. Arias-Estevez, and J. E. Lopez-Periago, Transport of copper oxychloride-based fungicide particles in saturated quartz sand, Environ. Sci. and Technol., 8(4), 8860-8866, 2009.
190. Lassabatère, L., R. Angulo-Jaramillo, J. M. Soria Ugalde, J. Šimůnek, R. Haverkamp, Numerical evaluation of a set of analytical infiltration equations, Water Resources Res., 45, W12415, doi:10.1029/2009WR007941, pp. 20, 2009.
191. Wöhling, T., N. Schütze B. Heinrich, J. Šimůnek, and G. F. Barkle, Three-dimensional modeling of multiple automated equilibrium tension lysimeters to measure vadose zone fluxes, Vadose Zone Journal, 8, 1051–1063, doi:10.2136/vzj2009.0040, 2009.
192. Twarakavi, N. K. C, M. Sakai, and J. Šimůnek, An objective analysis of the dynamic nature of field capacity, Water Resour. Res., 45, W10410, doi:10.1029/2009WR007944, pp. 9, 2009.
193. Dontsova, K. M., J. C. Pennington, C. Hayes, J. Šimůnek, and C. W. Williford, Dissolution and transport of 2,4-DNT and 2,6-DNT from M1 propellant in soil, Chemisphere, 77(4), 597-603, 2009.
194. Twarakavi, N. K. C., J. Šimůnek, and H. S. Seo, Reply to Comment on 'Evaluating interactions between groundwater and vadose zone using the HYDRUS-based flow package for MODFLOW', Vadose Zone Journal, 8(3), 820-821, 2009.
195. Unold, M., J. Šimůnek, R. Kasteel, J. Groeneweg, and H. Vereecken, Transport of manure-based applied sulfadiazine and its main transformation products in soil columns, Vadose Zone Journal, 8(3), 677-689, 2009.
196. Twarakavi, N. K. C., J. Šimůnek, and M. G. Schaap, Support vector machine based pedotransfer functions for estimation of soil hydraulic parameters, Soil Sci. Soc. Am. J., 73(5), 2009.
197. Saito, H., and J. Šimůnek, Effects of meteorological models on the solution of the surface energy balance and soil temperature variations in bare soils, J. Hydrology, doi:10.1016/j.jhydrol.2009.05.019, 373(3-4), 545-561, 2009.
198. Hanson, B. R., D. E. May, J. Šimůnek, J. W. Hopmans, and R. B. Hutmacher, Drip irrigation provides the salinity control needed for profitable irrigation of tomatoes in the San Joaquin Valley, California Agriculture, 63(3), 131-136, 2009.
199. Šimůnek, J., D. Jacques, N. K. C. Twarakavi, and M. Th. van Genuchten, Modeling subsurface flow and contaminant transport as influenced by biological processes at various scales using selected HYDRUS modules, Biologia, 64(3), 465-469, doi:10.2478/s11756-009-0106-7, 2009.
200. Wang, T., V. A. Zlotnik, J. Šimůnek, and M. G. Schaap, Using pedotransfer functions in vadose zone models for estimating groundwater recharge in semiarid regions, Water Resour. Res., 45, W04412, doi:10.1029/2008WR006903, 12 pp., 2009.
201. Saito, H., K. Seki, and J. Šimůnek, An alternative deterministic method for the spatial interpolation of water retention parameters, Hydrology and Earth Syst. Sci., 13, 453–465, 2009.
202. Sakai, M., N. Toride, and J. Šimůnek, Water and vapor movement with condensation and evaporation in a sandy column, Soil Sci. Soc. Am. J., 73(3), 707-717, 2009.
203. Bradford, S. A., S. Torkzaban, F. J. Leij, J. Šimůnek, and M. Th. van Genuchten, Modeling the coupled effects of pore space geometry and velocity on colloid transport and retention, Wat. Resour. Res., 45, W02414, doi:10.1029/2008WR007096, 15 pp., 2009.
204. Guber, A. K., Y. A. Pachepsky, M. Th. van Genuchten, J. Šimůnek, D. Jacques, A. Nemes, T. J. Nicholson, and R. E. Cady, Multimodel simulation of water flow in a field soil using pedotransfer functions, Vadose Zone Journal, 8(1), 1-10, 2009.
205. 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. (download selected HYDRUS projects used in the paper here for 1D and here for 2D)
206. Kodešová,R., N. Vignozzi, M. Rohošková, T. Hájková, M. Kočárek, M. Pagliai, J. Kozák, and J. Šimůnek, Impact of varying soil structure on transport processes in soils, J. Contam. Hydrology9, Special Issue “Flow Domains”, doi:10.1016/j.jconhyd.2008.10.008, 104(1-4), 107-125, 2009.
207. Köhne, J. M., S. Köhne, and J. Šimůnek, A review of model applications for structured soils: a) Water flow and tracer transport, J. Contam. Hydrology, Special Issue “Flow Domains”, doi:10.1016/j.jconhyd.2008.10.002, 104(1-4), 4-35, 2009.
208. Köhne, J. M., S. Köhne, and J. Šimůnek, A review of model applications for structured soils: b) Pesticide transport, J. Contam. Hydrology, Special Issue “Flow Domains”, doi:10.1016/j.jconhyd.2008.10.003, 104(1-4), 36-60, 2009.
209. De Wilde, T., J. Mertens, J. Šimůnek, K. Sniegowksi, J. Ryckeboer, P. Jaeken, D. Springael, and P. Spanoghe, Characterizing pesticide sorption and degradation in microscale biopurification systems using column displacement experiment, Environmental Pollution, 157, 463-473, 2009.
210. Buchner, J. S., J. Šimůnek, J. Lee, D. E. Rolston, J. W. Hopmans, A. P. King, and J. Six, Evaluation of CO2 fluxes from an agricultural field using a process-based numerical model, J. Hydrology, doi: 10.1016/j.jhydrol.2008.07.035, 361(1-2), 131– 143, 2008.
211. Akay, O., G. A. Fox, and J. Šimůnek, Numerical simulation of water flow dynamics during macropore/subsurface drain interaction using HYDRUS, Vadose Zone Journal, 7(3), 909-918, 2008.
212. Jacques, D., J. Šimůnek, D. Mallants and M. Th. van Genuchten, Modelling coupled water flow, solute transport and geochemical reactions affecting heavy metal migration in a Podzol soil, Geoderma, doi:10.1016/j.geoderma.2008.01.009, 145, 449-461, 2008.
213. Sansoulet, J., Y.-M. Cabidoche, P. Cattan, S. Ruy, and J. Šimůnek, Spatially distributed water fluxes in an Andisol under banana plants: Experiments and three-dimensional modelling, Vadose Zone Journal, doi:10.2136/VZJ2007.0073, Special Issue “Vadose Zone Modeling”, 7(2), 819-829, 2008.
214. Hanson, B. R., J. Šimůnek, and J. W. Hopmans, Leaching with subsurface drip irrigation under saline, shallow groundwater conditions, Vadose Zone Journal, doi:10.2136/VZJ2007.0053, Special Issue “Vadose Zone Modeling”, 7(2), 810-818, 2008. (download selected HYDRUS projects used in the paper here)
215. Kodešová, R., M. Kočárek, V. Kodeš, J. Šimůnek, and J. Kozák, Impact of soil micromorphological features on water flow and herbicide transport in soils, Vadose Zone Journal, doi:10.2136/VZJ2007.0079, Special Issue “Vadose Zone Modeling”, 7(2), 798-809, 2008.
216. Šimůnek, J. and M. Th. van Genuchten, Modeling nonequilibrium flow and transport processes using HYDRUS, Vadose Zone Journal, doi:10.2136/VZJ2007.0074, Special Issue “Vadose Zone Modeling”, 7(2), 782-797, 2008. (download selected HYDRUS projects used in the paper here)
217. Twarakavi, N. K. C., J. Šimůnek, and H. S. Seo, Evaluating interactions between groundwater and vadose zone using HYDRUS-based flow package for MODFLOW, Vadose Zone Journal, doi:10.2136/VZJ2007.0082, Special Issue “Vadose Zone Modeling”, 7(2), 757-768, 2008.
218. 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, doi:10.2136/VZJ2007.0084, Special Issue “Vadose Zone Modeling”, 7(2), 698-711, 2008.
219. 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. (Highly cited paper according to Web of Knowledge (ISI))
220. Šimůnek, J. and S. A. Bradford, Vadose Zone Modeling: Introduction and importance, Vadose Zone Journal, doi:10.2136/VZJ2008.0012, Special issue “Vadose Zone Modeling”, 7(2), 581-586, 2008.
221. Šimůnek, J. J. M. Köhne, R. Kodešová, and M. Šejna, Simulating nonequilibrium movement of water, solutes, and particles using HYDRUS: A review of recent applications, Soil and Water Research, 3(Special Issue 1), S42-S51, 2008.
222. Herbst, M., H. J. Hellebrand, J. Bauer, J. A. Huisman, J. Šimůnek, L. Weihermüller, A. Graf, J. Vanderborght, and H. Vereecken, Multiyear heterotrophic soil respiration: Evaluation of a coupled CO2 transport and carbon turnover model, Ecological Modelling, 214, 271-283, 2008.
223. De Silva, M.S., M. H. Nachabe, J. Šimůnek, and R. Carnahan, Simulating root water uptake from a heterogeneous vegetative cover, J. Irrig. Drain. Engin.-ASCE, 134(2), 167-174, doi:10.1061/(ASCE)0733-9437(2008)134:2(167), 2008.
224. Gargiulo, G., S. A. Bradford, J. Šimůnek, P. Ustohal, H. Vereecken, and E. Klumpp, Bacteria transport and deposition under unsaturated flow conditions: The role of water content and bacteria surface hydrophobicity, Vadose Zone Journal, 7(2), doi:10.2136/vzj2007.0068, 406-419, 2008. (download selected HYDRUS projects used in the paper here)
225. Haruta, S., W. Chen, J. Gan, J. Šimůnek, A. C. Chang, and L. Wu, Leaching risk of N-nitrosodimethylamine (NDMA) in soil receiving reclaimed wastewater, Highlighted article in Ecotoxicology and Environmental Safety, 69, 374–380, 2008.
226. Twarakavi, N. K. C., H. Saito, J. Šimůnek, and M. Th. van Genuchten, A new approach to estimate soil hydraulic parameters using only soil water retention data, doi:10.2136/sssaj2006.0342, Soil Sci. Soc. Am. J., 72(2), 471-479. 2008.
227. Pang, L., M. McLeod, J. Aislabie, J. Šimůnek, M. Close, and R. Hector, Modeling transport of microbes in ten undisturbed soils under effluent irrigation, Vadose Zone Journal, 7(1), 97-111, 2008.
228. Gonçalves, M. C., T. B. Ramos, J. Šimunek, J. M. J. Neves, J. C. Martins, F. P. Pires, and P. Leitão, Modelação da dinâmica da água e dos sais num Aluviossolo regado com águas de diferente qualidade: ensaio de validação do modelo Hydrus-1D com observações em monólitos (Water and solute transport simulation in a Fluvisol irrigated with waters of different quality: testing the Hydrus-1D model with observations in soil monoliths) (in Portugeese with English abstract), Rev. de Ciências Agrárias, 30(2), ISSN 0871-018X, 38-52, 2007.
229. Saito, H., J. Šimůnek, and N. Toride, Prediction of long-term changes in soil water content and temperature in bare soils: Determining surface boundary conditions from estimated meteorological information, J. Jpn. Soc. Soil Physics, 107, 79-96, 2007.
230. Dousset, S., M. Thevenot, V. Pot, J. Šimůnek, and F. Andreux, Evaluating equilibrium and non-equilibrium transport of bromide and isoproturon in disturbed and undisturbed soil columns, J. Contam. Hydrol., 94, 261-276, 2007.
231. Srivastava, P., K. W. Migliaccio, and J. Šimunek, Landscape models for simulating water quality at point, field, and watershed scales, Transactions of the ASAE, 50(5), 1683-1693, 2007.
232. Corwin, D. L., J. D. Rhoades, J. Šimůnek, Leaching requirement for soil salinity control: Steady-state versus transient models, Agric. Water Management, 90(3), 165-180, 2007.
233. Watanabe, K., N. Toride, M. Sakai, and J. Šimůnek, Numerical modeling of water, heat, and solute transport during soil freezing, J. Jpn. Soc. Soil Physics, 106, 21-32, 2007.
234. Saito, H., J. Šimůnek, J. W. Hopmans, and A. Tuli, Numerical evaluation of alternative heat pulse probe designs and analyses, Water Resour. Res., 43, W07408, doi:10.1029/2006WR005320, 2007.
235. Zlotnik, V. A., T. Wang, J. L. Nieber, and J. Šimůnek, Verification of numerical solutions of the Richards equation using a traveling wave solution, Advances in Water Resources, 30, 1973-1980, 2007.
236. Gargiulo, G., S. A. Bradford, J. Šimůnek, P. Ustohal, H. Vereecken, and E. Klumpp, Bacteria transport and deposition under unsaturated conditions: The role of the matrix grain size and the bacteria surface protein, J. Contam. Hydrology, 92 doi: 10.1016/j.jconhyd.2007.01.009, 255-273, 2007.
237. Gargiulo, G., S. A. Bradford, J. Šimůnek, P. Ustohal, H. Vereecken, and E. Klumpp, Transport and deposition of metabolically active and stationary phase Deinococcus Radiodurans in unsaturated porous media, Environ. Sci. and Technol., 41(4), 1265-1271, 2007. (download selected HYDRUS projects used in the paper here)
238. Lazarovitch, N., A. Ben-Gal, J. Šimůnek, and U. Shani, Uniqueness of soil hydraulic parameters determined by a combined Wooding inverse approach, Soil Science Society of America Journal, 71(3), doi:10.2136/sssaj2005.0420, 860-865, 2007.
239. Lazarovitch, N., A. W. Warrick, A. Furman, and J. Šimůnek, Subsurface water distribution from drip irrigation described by moment analyses, Vadose Zone Journal, 6(1), 116-123, 2007.
240. Wehrhan, A., R. Kasteel, J. Šimůnek, J. Groeneweg, and H. Vereecken, Transport of sulfadiazine in soil columns – Experiments and modeling approaches, J. Contam. Hydrology, 89(1-2), 107-135, 2007.
241. Saito, H., M. Sakai, J. Šimůnek, and N. Toride, Boundary conditions for numerical analysis of variably-saturated water flow in soils, J. Jpn. Soc. Soil Physics, 104, 63-73, 2006.
242. Schwärzel, K., J. Šimůnek, M. Th. van Genuchten, and G. Wessolek, Measurement and modeling of soil water dynamics and evapotranspiration in drained peatland soils, Journal of Plant Nutrition and Soil Science, 169, 762-774, 2006.
243. Bradford, S. A., J. Šimůnek, and S. L. Walker, Transport and straining of E. coli O157:H7 in saturated porous media, Water Resour. Res., 42, W12S12, doi:10.1029/2005WR004805, 12 pp., 2006.
244. Bradford, S. A., J. Šimůnek, M. Bettahar, M. Th. van Genuchten, and S. R. Yates, Significance of straining in colloid deposition: Evidence and implications, Water Resour. Res., 42, W12S15, doi:10.1029/2005WR004791, 16 pp., 2006.
245. Dontsova, K. M., S. L. Yost, J. Šimůnek, J. C. Pennington, C. Williford, Dissolution and transport of TNT, RDX, and Composition B in saturated soil columns, J. of Environ. Quality, 35, 2043-2054, 2006.
246. 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.
247. Pang, L. and J. Šimůnek, Evaluation of bacteria-facilitated cadmium transport in gravel columns using the HYDRUS colloid-facilitated solute transport model, Water Resour. Res., 42, W12S10, doi:10.1029/2006WR004896, 2006. (download selected HYDRUS projects used in the paper here)
248. Kodešová, R., V. Kodeš, A. Žigová and J. Šimůnek, Impact of plant roots and soil organisms on soil micromorphology and hydraulic properties, Biologia, 61/Suppl. 19, S339-S343, 2006.
249. Hanson, B. R., J. Šimůnek, and J. W. Hopmans, Numerical modeling of urea-ammonium-nitrate fertigation with drip irrigation using numerical modeling, Agric. Water Management, 86, 102-113, 2006. (download selected HYDRUS projects used in the paper here)
250. Gonçalves, M. C., J. Šimůnek, T. B. Ramos, J. C. Martins, M. J. Neves, and F. P. Pires, Multicomponent solute transport in soil lysimeters irrigated with waters of different quality, Water Resour. Res., 42, W08401, doi:10.1029/2006WR004802, 17 pp., 2006.
251. Carrillo-González, R., J. Šimůnek, S. Sauve, and D. Adriano, Mechanisms and pathways of trace element mobility in soils, Advances in Agronomy, 91, 111-178, 2006.
252. Gärdenäs, A., J. Šimunek, N. Jarvis, and M. Th. van Genuchten, Two-dimensional modelling of preferential water flow and pesticide transport from a tile-drained field, J. Hydrology, 329, 647-660, 2006.
253. Šimůnek, J., D. Jacques, M. Th. van Genuchten, and D. Mallants, Multicomponent geochemical transport modeling using HYDRUS and HP1, J. Am. Water Resour. Assoc., 42(6), 1537-1547, 2006.
254. Šimůnek, J., Changming He, J. L. Pang, and S. A. Bradford, Colloid-facilitated solute transport in variably saturated porous media: Numerical model and experimental verification, Vadose Zone Journal, 5, 1035-1047, 2006. (download selected HYDRUS projects used in the paper here)
255. Pachepsky, Y., A. Guber, D. Jacques, J. Šimůnek, M. Th. van Genuchten, T. Nicholson, R. Cady, Information content and complexity of simulated soil water fluxes, Geoderma, 134, 253-266, 2006.
256. Bahaminyakamwe, L., J. Šimůnek, J. Dane, J. F. Adams, and J. W. Odom, Copper mobility in soils as affected by sewage sludge and low molecular weight organic acids, Soil Sci., 171(1), 29-38, 2006.
257. Boivin, A., J. Šimůnek, M. Schiavon and M. Th. van Genuchten, Comparison of pesticide transport processes in three tile-drained field soils using Hydrus-2D, Vadose Zone Journal, 5, 838–849, 2006.
258. Saito, H., J., J. Šimůnek, and B. Mohanty, Numerical analyses of coupled water, vapor, and heat transport in the vadose zone, Vadose Zone Journal, 5, 784–800, 2006.
259. Schwärzel, K., J. Šimůnek, H. Stoffregen, G. Wessolek, and M. Th. van Genuchten, Estimation of the unsaturated hydraulic conductivity of peat soils: Laboratory versus field data, Vadose Zone Journal, 5, 628-640, 2006.
260. Pang, L., C. Nokes, J. Šimůnek, H. Kikkert, and R. Hector, Modeling the impact of clustered septic tank systems on groundwater quality, Vadose Zone Journal, 5, 599-609, 2006.
261. Kodešová, R., J. Kozák, and J. Šimůnek, Numerical study of macropore impact on ponded infiltration in clay soils, Soil and Water Research, 1(1), ISBN 1801-5395, 16-22, 2006.
262. Köhne, J. M., S. Köhne, and J. Šimůnek, Multi-process herbicide transport in structured soil columns: Experiments and model analysis, J. Contam. Hydrology, 85, 1-32, 2006.
263. Köhne, S., B. Lennartz, J. M. Köhne, and J. Šimůnek, Bromide transport at a tile-drained field site: experiment, and one- and two-dimensional equilibrium and non-equilibrium numerical modeling, J. Hydrology, 321(1-4), 390-408, 2006.
264. Guber, A. K., Ya. A. Pachepsky, M. Th. van Genuchten, W. J. Rawls, J. Šimůnek, D. Jacques, T. J. Nicholson, and R. E. Cady, Field-scale water flow simulations using ensembles of pedotransfer functions for soil water retention, Vadose Zone Journal, 5, 234–247, 2006.
265. Decker, D. L., J. Šimůnek, S. W. Tyler, Ch. Papelis, and M. J. Logsdon, Variably saturated reactive transport of arsenic in heap leach facilities, Vadose Zone Journal, 5, 430-444, 2006.
266. Decker, D. L., Ch. Papelis, S. W. Tyler, M. Logsdon, and J. Šimůnek, Arsenate and arsenite sorption on carbonate hosted precious metals ore, Vadose Zone Journal, 5, 419-429, 2006.
267. Köhne, J. M., B. P. Mohanty, and J. Šimůnek, Inverse dual-permeability modeling of preferential water flow in a soil column and implications on field-scale solute transport prediction, Vadose Zone Journal, 5, 59-76, 2006.
268. Hansson, K., L.-Ch. Lundin, and J. Šimůnek, Modeling water flow patterns in flexible pavements, Transportation Research Record: Journal of the Transportation Research Board, 1936, 133-141, 2005.
269. Pot, V., J. Šimůnek, P. Benoit, Y. Coquet, A. Yra, and M.-J. Martínez-Cordón, Impact of rainfall intensity on the transport of two herbicides in undisturbed grassed filter strip soil cores, J. of Contaminant Hydrology, 81, 63-88, 2005.
270. Mortensen, A, P., J. W. Hopmans, Y. Mori, and J. Šimůnek, Inverse modeling of water, heat, and solute transport in the vadose zone using data collection with a multi-functional heat pulse technique, Advances in Water Resources, 29, 250-267, 2006.
271. Haws, N. W., P. S. C. Rao, J. Šimůnek, and I. C. Poyer, Single-porosity and dual-porosity modeling of water flow and solute transport in subsurface-drained fields using effective field-scale parameters, J. of Hydrology , 313(3-4), 257-273, 2005.
272. Bradford, S. A., J. Šimůnek, M. Bettahar, Y. F. Tadassa, M. Th. van Genuchten, and S. R. Yates, Straining of colloids at textural interfaces, Water Resour. Res., 41, W10404, doi:10.1029/2004WR003675, 17 pp, 2005.
273. 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.
274. Coquet, Y., J. Šimůnek, C. Coutadeur, M. Th. van Genuchten, V. Pot, and J. Roger-Estrade, Water and solute transport in a cultivated silt loam soil: 2. Numerical analyses, Vadose Zone Journal, 4, 587-601, 2005.
275. Coquet, Y., C. Coutadeur, C. Labat, P. Vachier, M. Th. van Genuchten, J. Roger-Estrade, and J. Šimůnek, Water and solute transport in a cultivated silt loam soil: 1. Field Observations, Vadose Zone Journal, 4, 573-586, 2005.
276. Casey, F. X. M., J. Šimůnek, J. Lee, G. L. Larsen, and H. Hakk, Sorption, mobility, and transformation of estrogenic hormones in natural soil, J. of Environ. Quality, 34, 1372-1379, 2005.
277. Šimůnek, J. and J. R. Nimmo, Estimating soil hydraulic parameters from transient flow experiments in a centrifuge using parameter optimization technique, Water Resour. Res., 41(4), W04015, doi:10.1029/2004WR003379, 2005.
278. Kodešová, R., J. Kozák, J. Šimůnek, and O. Vacek, Single and dual-permeability models of chlorotoluron transport in the soil profile, Plant, Soil and Environment, 51(7), ISSN 1214-1178, 310-315, 2005.
279. Kelleners, T. J., R. W. O. Soppe, J. E. Ayars, J. Šimůnek, and T. H. Skaggs, Inverse analysis of upward water flow in a groundwater table lysimeter, Vadose Zone Journal, 4, 558–572, 2005.
280. Gärdenäs, A. I., Hopmans, J. W., B. R. Hanson, and J. Šimůnek, Two-dimensional modeling of nitrate leaching for various fertigation scenarios under micro-irrigation, Agric. Water Management, 74, 219-242, 2005.
281. Lazarovitch, N., J. Šimůnek, and U. Shani, System-dependent boundary condition for water flow from subsurface source, Soil Sci. Soc. Am. J., 69(1), 46-50, 2005.
282. Köhne, J. M., S. Köhne, B. P. Mohanty, and J. Šimůnek, Inverse mobile-immobile modeling of transport during transient flow: Effect of between-domain transfer and initial water content, Vadose Zone Journal, 3(4), 1309-1321, 2004.
283. Köhne, J. M., B. Mohanty, J. Šimůnek, and H. H. Gerke, Numerical evaluation of a second-order water transfer term for variably saturated dual-permeability models, Water Resour. Res., 40, doi:10.1029/2004WR00385, 2004.
284. Coquet, Y., C. Desbourdes-Coutadeur, P. Vachier, J. Šimůnek, and J. Roger-Estrade, Influence de la variabilité spatiale de la structure des sols cultivés ser les transferts de l’eau et de l’ion bromure, Étude et Gestion des Sols, 11(1), 81-92, 2004.
285. Zhang, P., J. Šimůnek, and R. S. Bowman, Nonideal transport of solute and colloidal tracers through reactive zeolite/iron pellets, Water Resour. Res., 40, doi:10.1029/2003WR002445, 2004.
286. Hansson, K., J. Šimůnek, M. Mizoguchi, L.-Ch. Lundin, M. Th. van Genuchten, Water flow and heat transport in frozen soil: Numerical solution and freeze-thaw applications, Vadose Zone Journal, 3(2), 693-704, 2004.
287. Skaggs, T. H., T. J. Trout, J. Šimůnek, and P. J. Shouse, Comparison of Hydrus-2D simulations of drip irrigation with experimental observations, J. of Irrigation and Drainage Engineering, 130(4), 304-310, 2004. (download selected HYDRUS projects used in the paper here)
288. Bradford, S. A., M. Bettehar, J. Šimůnek, and M. Th. van Genuchten, Straining and attachment of colloids in physically heterogeneous porous media, Vadose Zone Journal, 3(2), 384-394, 2004.
289. Casey, F. X. M., G. L. Larsen, H. Hakk, and J. Šimůnek, Fate and transport of testosterone in agricultural soils, Environ. Sci. Technol., 38(3), 790-798, 2004.
290. Abbasi, F., D. Jacques, J. Šimůnek, J. Feyen, and M. Th. van Genuchten, Inverse estimation of soil hydraulic and solute transport parameters from transient field experiments: Heterogeneous soil, Transactions of ASAE, 46(4), 1097-1111, 2003.
291. Abbasi, F., J. Šimůnek, J. Feyen, M. Th. van Genuchten, P. J. Shouse, Simultaneous inverse estimation of soil hydraulic and solute transport parameters from transient field experiments: Homogeneous soil, Transactions of ASAE, 46(4), 1085-1095, 2003.
292. Casey, F. X. M., G. L. Larsen, H. Hakk, and J Šimůnek, Fate and transport of 17β-Estradiol in soil-water systems, Environ. Sci. Technol., 37(11), 2400-2409, 2003.
293. Bradford, S. A., J. Šimůnek, M. Bettehar, M. Th. van Genuchten, and S. R. Yates, Modeling colloid attachment, straining, and exclusion in saturated porous media, Environ. Sci. Technol., 37(10), 2242-2250, 2003.
294. Scanlon, B., K. Keese, R. C. Reedy, J. Šimůnek, and B. J. Andraski, Variations in flow and transport in thick desert vadose zones in response to paleoclimatic forcing (0 – 90 kyr): Field measurements, modeling, and uncertainties, Water Resour. Res. 39(7), 1179, doi:10.1029/2002WR001604, 13.1-13.7, 2003.
295. Castiglione, P., B. P. Mohanty, P. J. Shouse, J. Šimůnek, M. Th. van Genuchten, and A. Santini, Lateral water diffusion in an artificial macroporous system: Modeling and experimental evidence, Vadose Zone Journal, 2, 212-221, 2003.
296. Abbasi, F., J. Šimůnek, M. Th. van Genuchten, J. Feyen, F. J. Adamsen, D. J. Hunsaker, T. S. Strelkoff, and P. Shouse, Overland water flow and solute transport: Model development and field data analysis, Journal of Irrig. and Drainage ASCE, 129(2), 71-81, 2003.
297. 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. (download selected HYDRUS projects used in the paper here)
298. Scanlon, B. R., M. Christman, R. C. Reedy, I. Porro, J. Šimůnek, and G. F. Flerchinger, Intercode comparisons for simulating water balance of surficial sediments in semiarid regions, Water Resour. Res., 38(12), 1323, doi:10.1029/2001WR001233, 59.1-59.16, 2002.
299. Bradford, S. A., S. R. Yates, M. Bettehar, and J. Šimůnek, Physical factors affecting the transport and fate of colloids in saturated porous media, Water Resour. Res., 38(12), 1327, doi:10.1029/2002WR001340, 63.1-63.12, 2002.
300. Yeh, T-C. J., and J. Šimůnek, Stochastic fusion of information for characterizing and monitoring the vadose zone, Vadose Zone Journal, 1, 207-221, 2002.
301. Ferré, T. P.A., H. H., Nissen, and J. Šimůnek, The effect of the spatial sensitivity of TDR on inferring soil hydraulic properties from water content measurements made during the advance of a wetting front, Vadose Zone Journal, 1, 281-288, 2002.
302. Seuntjens, P., D. Mallants, J. Šimůnek, J. Patyn, and D. Jacques, Sensitivity analysis of physical and chemical properties affecting field-scale cadmium transport in a heterogeneous soil profile, J. of Hydrology, 264, 185-200, 2002.
303. Novák, V., J. Šimůnek, and M. Th. van Genuchten, Infiltration into a swelling, cracked clay soil, J. Hydrol. Hydromech., 50(1), 3-19, 2002.
304. Ishizaki, T., T. Nishiura, J. Šimůnek, and M. Th. van Genuchten, Numerical analysis of the water regime of Budha monuments in Skhothai, Thailand, Science for Conservation, 39, 43-50, in Japanese with English summary, 2000.
305. Jandl, R., H. Spögler, J. Šimůnek, and L. K. Heng, Simulation of soil hydrology and establishment of a nitrogen budget of a mountain forest, Environmental Science & Pollution Research, 9(Special Issue 2), 42-45, 2002.
306. Timlin, D. J., Y. Pachepsky, B. A. Acock, J. Šimůnek, G. Flerchinger, and F. Whisler, Error analysis of soil temperature simulations using measured and estimated hourly weather data with 2DSOIL, Agricultural Systems, 72, 215-239, 2002.
307. Jacques, D., J. Šimůnek, A. Timmerman, and J. Feyen, Calibration of Richards' and convection-dispersion equations to field-scale water flow and solute transport under rainfall conditions, J. of Hydrology, 259, 15-31, 2002.
308. Hopmans, J. W., J. Šimůnek, and K. L. Bristow, Indirect estimation of soil thermal properties and water flux using heat pulse prove measurements: Geometry and dispersion effects, Water Resour. Res., 38(1), 10.1029/2000WR000071, 7.1-7.14, 2002.
309. Schijven, J., and J. Šimůnek, Kinetic modeling of virus transport at the field scale, J. of Contam. Hydrology, 55(1 2), 113 135, 2002.
310. Young, M. H., A. Karagunduz, J. Šimůnek, and K. D. Pennell, A modified upward infiltration method for characterizing soil hydraulic properties, Soil Sci. Soc. Am. J., 66, 57-64, 2002.
311. Silliman, S. E., B. Berkowitz, J. Šimůnek, and M. Th. van Genuchten, Fluid flow and solute migration within the capillary fringe, Ground Water, 40(1), 76-84, 2002.
312. Abbaspour, K. C., A. Kohler, J. Šimůnek, M. Fritsch, and R. Schulin, Application of a two-dimensional model to simulate flow and transport in a macroporous agricultural soil with tile drains, European J. of Soil Sci., 52(3), 433-447, 2001.
313. Vrugt, J.A., M. T. van Wijk, J. W. Hopmans, and J. Šimůnek, One-, two-, and three-dimensional root water uptake functions for transient modeling, Water Resour. Res., 37(10), 2457-2470, 2001.
314. Casey, F. X. M., and J. Šimůnek, Inverse analyses of transport of chlorinated hydrocarbons subject to sequential transformation reactions, J. of Environ. Quality, 30(4), 1354-1360, 2001.
315. Rupp, D. E., J. S. Selker, and J. Šimůnek, A modification to the Bouwer and Rice method of slug-test analysis for large-diameter, hand-dug wells, Ground Water, 39(2), 308-314, 2001.
316. Seuntjens, P., K. Tirez, J. Šimůnek, M. Th. van Genuchten, C. Cornelis, and P. Geuzens. Aging effects on cadmium transport in undisturbed contaminated sandy soil columns. Journal of Environmental Quality, 30, 1040-1050, 2001.
317. Šimůnek, J., O. Wendroth, N. Wypler, and M. Th. van Genuchten, Non-equilibrium water flow characterized by means of upward infiltration experiments, European J. of Soil Sci., 52(1), 13-24, 2001.
318. Vrugt, J. A., J. W. Hopmans, and J. Šimůnek, Calibration of a two-dimensional root water uptake model, Soil Sci. Soc. Am. J., 65(4), 1027-1037, 2001.
319. Wildenschild, D., J. W. Hopmans, and J. Šimůnek, Flow rate dependence of soil hydraulic characteristics, Soil Sci. Soc. Am. J., 65(1), 35-48, 2001.
320. Novák, V., and J. Šimůnek, Infiltration modeling into soils with cracks, Acta Hydrologica Slovaca, 1, 119-125, in Slovak with English summary, 2000.
321. Šimůnek, J., J. W. Hopmans, D. R. Nielsen, and M. Th. van Genuchten, Horizontal infiltration revisited using parameter estimation, Soil Sci., 165(9), 708-717, 2000.
322. Ventrella, D., B. P. Mohanty, J. Šimůnek, N. Losavio, and M. Th. van Genuchten, Water and chloride transport in a fine-textured soil: Field experiments and modeling, Soil Sci., 165(8), 624-631, 2000.
323. Inoue, M., J. Šimůnek, S. Shiozawa, and J. W. Hopmans, Simultaneous estimation of soil hydraulic and solute transport parameters from transient infiltration experiments, Advances in Water Resources, 23, 677-688, 2000.
324. Hollenbeck, K., J. Šimůnek, and M. Th. van Genuchten, RETCML: Incorporating maximum-likelihood estimation principles in the RETC soil hydraulic parameter estimation code, Computer & Geosciences, 26(3), 319-327, 2000.
325. Novák, V., J. Šimůnek, and M. Th. van Genuchten, Infiltration of water into soils with cracks, ASCE J. Irrig. and Drain. Engineering, 126(1), 41-47, 2000.
326. Schaerlaekens, J., D. Mallants, J. Šimůnek, M. Th. van Genuchten, and J. Feyen, Numerical simulation of transport and sequential biodegradation of chlorinated aliphatic hydrocarbons using CHAIN_2D, J. of Hydrological Processes, 13(17), 2847-2859, 1999.
327. Ishizaki, T., N. Kuchitsu, T. Nishiura, and J. Šimůnek, Analysis of water regime in historical brick buildings in Ayutthaya, Thailand, Science for Conservation, 38, 154-163, in Japanese with English summary, 1999.
328. Šimůnek, J., O. Wendroth, and M. Th. van Genuchten, Estimating unsaturated soil hydraulic properties from laboratory tension disc infiltrometer experiments, Water Resour. Res., 35(10), 2965-2979, 1999.
329. Kodešová, R., S. E. Ordway, M. M. Gribb, and J. Šimůnek, Estimation of soil hydraulic properties with the cone permeameter: Field studies, Soil Science, 164(8), 527-541, 1999.
330. Vaughan, P. J., D. L. Suarez, J. Šimůnek, D. L. Corwin, and J. D. Rhoades, Role of groundwater flow in tile drain discharge, J. Environ. Qual., 28, 403-410, 1999.
331. Šimůnek, J., R. Kodešová, M. M. Gribb, and M. Th. van Genuchten, Estimating hysteresis in the soil water retention function from cone permeameter experiments, Water Resour. Res., 35(5), 1329-1345, 1999.
332. Šimůnek, J., D. Wang, P. J. Shouse, and M. Th. van Genuchten, Analysis of field tension disc infiltrometer data by parameter estimation, Intern. Agrophysics, 12, 167-180, 1998.
333. Gribb, M. M., J. Šimůnek, and M. F. Leonard, Development of cone penetrometer method to determine soil hydraulic properties, ASCE J. of Geotech. and Geoenviron. Eng., 124(9), 820-829, 1998.
334. Šimůnek, J., R. Angulo-Jaramillo, M. Schaap, J.-P. Vandervaere, and M. Th. van Genuchten, Using an inverse method to estimate the hydraulic properties of crusted soils from tension-disc infiltrometer data, Geoderma, 86(1-2), 61-81, 1998.
335. Kodešová, R., M. M. Gribb, and J. Šimůnek, Estimating soil hydraulic properties from transient cone permeameter data, Soil Science, 163(6), 436-453, 1998.
336. Šimůnek, J., O. Wendroth, and M. Th. van Genuchten, Parameter estimation analysis of the evaporation method for determining soil hydraulic properties, Soil Sci. Soc. Am. J., 62(4), 894-905, 1998.
337. Šimůnek, J., M. Th. van Genuchten, M. M. Gribb, and J. W. Hopmans, Parameter estimation of unsaturated soil hydraulic properties from transient flow processes, Soil & Tillage Research, 47/1-2, Special issue "State of the art in soil physics and in soil technology of antrophic soils", 27-36, 1998.
338. Mohanty, B. P., R. S. Bowman, J. M. H. Hendrickx, J. Šimůnek, and M. Th. van Genuchten, Preferential transport of nitrate to a tile drain in an intermittent-flood-irrigated field: Model development and experimental evaluation, Water Resour. Rer., 34(5), 1061-1076, 1998.
339. Inoue, M., J. Šimůnek, J. W. Hopmans, and V. Clausnitzer, In situ estimation of soil hydraulic functions using a multistep soil-water extraction technique, Water Resour. Rer., 34(5), 1035-1050, 1998.
340. Suarez, D. L., and J. Šimůnek, UNSATCHEM: Unsaturated water and solute transport model with equilibrium and kinetic chemistry, Soil Sci. Soc. Am. J., 61, 1633-1646, 1997.
341. Šimůnek, J., and D. L. Suarez, Sodic soil reclamation using multicomponent transport modeling, ASCE J. Irrig. and Drain. Engineering, 123(5), 367-376, 1997.
342. Wang, D., S. R. Yates, J. Šimůnek, and M. Th. van Genuchten, Solute transport in simulated conductivity fields under different irrigations, ASCE J. Irrig. and Drain. Engineering, 123(5), 336-343, 1997.
343. Šimůnek, J., and M. Th. van Genuchten, Estimating unsaturated soil hydraulic properties from multiple tension disc infiltrometer data, Soil Science, 162(6), 383-398, 1997.
344. Huang, K., J. Šimůnek, and M. Th. van Genuchten, A third-order numerical scheme with upwind weighting for solving the solute transport equation, Int. J. for Num. Methods in Eng., 40, 1623-1637, 1997.
345. Šimůnek, J., and M. Th. van Genuchten, Estimating unsaturated soil hydraulic properties from tension disc infiltrometer data by numerical inversion, Water Resour. Res., 32(9), 2683-2696, 1996.
346. Šimůnek, J., and D. L. Suarez, Two-dimensional transport model for variably saturated porous media with major ion chemistry, Water Resour. Res., 30(4), 1115-1133, 1994.
347. Šimůnek, J., Numerical model for simulating movement of water, heat and multiple solutes in variably saturated porous media, J. Hydrol. Hydromech., 42(1-2), 66-88, 1994.
348. Suarez, D. L., and J. Šimůnek, Modeling of carbon dioxide transport and production in soil: 2. Parameter selection, sensitivity analysis, and comparison of model predictions to field data, Water Resour. Res., 29(2), 499-513, 1993.
349. Šimůnek, J., and D. L. Suarez, Modeling of carbon dioxide transport and production in soil: 1. Model development, Water Resour. Res., 29(2), 487-497, 1993.
350. Šimůnek, J., Numerical model of two-dimensional water movement and solute transport in variably saturated porous media (in Czech, English abstract), J. Hydrol. Hydromech., 41(4-5), 305-330, 1993.
351. Petrie, C. L., Z. J. Kabala, A. E. Hall, and J. Šimůnek, Water transport in an unsaturated medium to roots with differing local geometries, Soil Sci. Soc. Am. J., 56, 1686-1694, 1992.
352. Šimůnek, J., Lagrangian approach to the solution of the advection-dispersion equation for porous media unsaturated by water (in Czech, English abstract), Vodohosp. Čas., 39(2), 154 164, 1991.
353. Šimůnek, J., Numerical simulation of the transport processes in soil (in Czech, English abstract), Vodohosp. Čas., 39(1), 20 34, 1991.
354. Šimůnek, J., T. Vogel, and M. Soukup, Numerical solution of the function of regulation drainage (in Czech, English abstract), Vodohosp. Čas., 38(6), 628 644, 1990.
355. Šimůnek, J., Analysis of spatial dependence and soil properties interrelations (in Czech, English abstract), Vodohosp. Čas., 38(5), 559 576, 1990.
356. Šimůnek, J., Transport and ion exchange of cations solutes in porous media (in Czech, English abstract), Vodohosp. Čas., 37(4), 441 454, 1989.
357. Semotán, J., and J. Šimůnek, The application of non-equilibrium transport model for describing practical miscible flow experiments (in Czech, English abstract), Vodohosp. Čas., 37(4), 425 440, 1989.
358. Šimůnek, J., Infiltration - numerical simulation (in Czech, English abstract), Vodohosp. Čas., 36(4), 407 420, 1988.
359. Císlerová, M., J. Šimůnek, and T. Vogel, Changes of steady-state infiltration rates in recurrent ponding infiltration experiments, J. of Hydrology, 104(1-4), 1-16, 1988.
360. Šimůnek, J., and J. Semotán, Numerical simulation of the solute transport in porous media (in Czech, English abstract), Vodohosp. Čas., 36(2), 186 198, 1988.

Books:

1. Šimůnek, J., M. Th. van Genuchten, and R. Kodešová (eds.), Proc. of the 4th International Conference "HYDRUS Software Applications to Subsurface Flow and Contaminant Transport Problems", March 21-22, 2013, Dept. of Soil Science and Geology, Czech University of Life Sciences, Prague, Czech Republic, ISBN: 978-80-213-2380-3, pp. 404, 2013. (PDF, 16 MB)
2. Radcliffe, D., and J. Šimůnek, Soil Physics with HYDRUS: Modeling and Applications, CRC Press, Taylor & Francis Group, Boca Raton, FL, ISBN: 978-1-4200-7380-5, pp. 373, 2010.
3. Saito, H., M. Sakai, N. Toride, and J. Šimůnek, (eds.), Proc. of The Third HYDRUS Workshop, June 28, 2008, Dept. of Ecoregion Science, Tokyo University of Agriculture & Technology, Fuchu Tokyo, Japan, ISBN: 978-4-9901192-5-6, pp. 160, 2008. (PDF, 7.2MB )
4. Šimůnek, J. and R. Kodešová (eds.), Proc. of The Second HYDRUS Workshop, March 28, 2008, Dept. of Soil Science and Geology, Czech University of Life Sciences, Prague, Czech Republic, ISBN: 978-80-213-1783-3, pp. 110, 2008. (PDF, size 3.3MB )
5. Rassam, D., J. Šimůnek, and M. Th. van Genuchten, HYDRUS-2Dによる土中の 不飽和流れの計算 (Modeling Variably Saturated Flow with HYDRUS-2D, Japanese translation, edited by N. Toride, and M. Inoue), Japanese Irrigation and Drainage Society, Soil Physics Section, Tokyo, Japan, 2004.
6. Rassam, D., J. Šimůnek, and M. Th. van Genuchten, Modeling Variably Saturated Flow with HYDRUS-2D , ND Consult, Brisbane, Australia, 261pp., ISBN 0-646-42309-6, 2003.

Selected Other Publications:

1. Šimůnek, J., D. Jacques, T. B. Ramos, and B. Leterme, The Use of Multicomponent Solute Transport Models in Environmental Analyses, Chapter 16, in "Application of Soil Physics in Environmental Analyses: Measuring, Modelling and Data Integration", eds. W. G. Teixeira, M. B. Ceddia, M. V. Ottoni, and G. K. Donnagema, ISBN 978-3-319-06012-5, doi: 10.1007/978-3-319-06013-2, Springer, Heidelberg, Germany, 377-402, 2014.
2. Radcliffe, D., and J. Šimůnek, Soil Physics with HYDRUS: Modeling and Applications, CRC Press, Taylor & Francis Group, ISBN-10: 142007380X, ISBN-13: 9781420073805, pp. 373, 2010.
3. Šimůnek, J., M. Th. van Genuchten, and M. Šejna, Modeling Subsurface Water Flow and Solute Transport with HYDRUS and Related Numerical Software Packages, In: Garcia-Navarro & Playán (eds.), Numerical Modelling of Hydrodynamics for Water Resources, An International Workshop, Centro Politecnico Superior, University of Zaragoza Spain, June 18-21 2007. Taylor & Francis Group, London, ISBN 978-0-415-44056-1, 95-114, 2007.
4. Šimůnek, J., Models for Soil Pollution Risk Assessment, Proc. of NATO Advanced Research Workshop “Air, Water and Soil Quality Modelling for Risk and Impact Assessment”, Eds. A. Ebel and T. Davitashvili, NATO Security through Science Series – C: Environmental Security, Springer, ISBN-10 1-4020-5876-4 (PB), 221-233, 2007.
5. Šimůnek, J., and M. Th. van Genuchten, Contaminant Transport in the Unsaturated Zone: Theory and Modeling, Chapter 22 in The Handbook of Groundwater Engineering, Ed. Jacques Delleur, Second Edition, CRC Press, pp. 22.1-22.46, 2006.
6. Šimůnek, J., Chapter 78: Models of Water Flow and Solute Transport in the Unsaturated Zone, In: M. G. Anderson and J. J. McDonnell (Editors), Encyclopedia of Hydrological Sciences, John Wiley & Sons, Ltd., Chichester, England, 1171-1180, 2005.
7. van Genuchten, M. Th., and J. Šimůnek, Integrated modeling of vadose zone flow and transport processes (Color pages), Proc. Unsaturated Zone Modelling: Progress, Challenges and Applications, Eds. R. A. Feddes, G. H. de Rooij, and J. C. van Dam, Wageningen UR Frontis Series, Vol. 6, Chapter 2, pp. 37- 69, x-xi, Kluwer Academic Publishers, Dordrecht, The Netherlands, 2004.
8. Šimůnek, J., and J. W. Hopmans, Parameter Optimization and Nonlinear Fitting, In: Methods of Soil Analysis, Part 1, Physical Methods, Chapter 1.7, Eds. J. H. Dane and G. C. Topp, Third edition, SSSA, Madison, WI, 139-157, 2002.
9. 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.
10. 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.
11. Šimůnek, J. and A. J. Valocchi, Geochemical Transport, In: Methods of Soil Analysis, Part 1, Physical Methods, Chapter 6.9, Eds. J. H. Dane and G. C. Topp, Third edition, SSSA, Madison, WI, 1511-1536, 2002.
12. Šimůnek, J., and J. A. de Vos, Inverse optimization, calibration and validation of simulation models at the field scale, in J. Feyen and K. Wiyo (eds.) Modelling of Transport Process in Soils at Various Scales in Time and Space, Proc. of Intern. Workshop of EurAgEng's Field of Interest on Soil and Water, Leuven, Belgium, 24-26 November, pp. 431-445, Wageningen Pers, Wageningen, The Netherlands, 1999.
13. van Genuchten, M. Th., and J. Šimůnek, Evaluation of pollutant transport in the unsaturated zone, In P. E. Rijtema and V. Eliáš (eds.), Regional Approaches to Water Pollution in the Environment, NATO ASI Series: 2. Environment, 139-172, Kluwer, Dordrecht, The Netherlands, 1996.

Selected Programs:

• Brunetti, G., J. Šimůnek, and M. Šejna, The Furrow Module for HYDRUS (2D/3D) Simulating Water Flow and Solute Transport in a Pseudo-Three-Dimensional Furrow Irrigation System, Version 1.0, PC Progress, Prague, Czech Republic, 43 pp., 2019.
• 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, 78 pp., 2012. (pdf 2.0MB)
• Šimůnek, J., M. Šejna, and M. Th. van Genuchten, The C-Ride Module for HYDRUS (2D/3D) Simulating Two-Dimensional Colloid-Facilitated Solute Transport in Variably-Saturated Porous Media, Version 1.0, PC Progress, Prague, Czech Republic, 45 pp., 2012. (pdf0.75MB)
• 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, 54 pp., 2012. (pdf 1.1MB)
• 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., 2012. (pdf 0.6MB)
• 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 Media, Technical Manual, Version 2.0, PC Progress, Prague, Czech Republic, pp. 258, 2011. (PDF 3.6MB)
• Šejna, M., J. Šimůnek, and M. Th. van Genuchten, The HYDRUS Software Package for Simulating Two- and Three-Dimensional Movement of Water, Heat, and Multiple Solutes in Variably-Saturated Media, User Manual, Version 2.0, PC Progress, Prague, Czech Republic, pp. 280, 2011. (PDF 7.4MB)
• 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. (PDF 1.4MB)
• 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.
• 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 Media, Version 4.0, HYDRUS Software Series 3, Department of Environmental Sciences, University of California Riverside, Riverside, California, USA, pp. 315, 2008.
• Seo, H. S., J. Šimůnek, and E. P. Poeter, Documentation of the HYDRUS Package for MODFLOW-2000, the U.S. Geological Survey Modular Ground-Water Model, GWMI 2007-01, International Ground Water Modeling Center, Colorado School of Mines, Golden, Colorado, 96 pp., 2007.
• 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.
• Šimůnek, J., M. Šejna, and M. Th. van Genuchten, The HYDRUS Software Package for Simulating Two- and Three-Dimensional Movement of Water, Heat, and Multiple Solutes in Variably-Saturated Media, User Manual, Version 1.0, PC Progress, Prague, Czech Republic, pp. 161, 2006.
• 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 Media, Technical Manual, Version 1.0, PC Progress, Prague, Czech Republic, pp. 241, 2006.
• 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.
• Šimůnek, J., M. Th. van Genuchten, and M. Šejna, The Hydrus-1D software package for simulating the one-dimensional movement of water, heat, and multiple solutes in variably-saturated media. Version 3.0, HYDRUS Software Series 1, Department of Environmental Sciences, University of California Riverside, Riverside, CA, 270 pp., 2005.
• Šimůnek, J., and M. Th. van Genuchten, The DISC (10.6Mb) computer software for analyzing tension disc infiltrometer data by parameter estimation. Versions 1.0, Research Report No. 145, U.S. Salinity Laboratory, USDA, ARS, Riverside, California, 34 pp., 2000. (Download PDF, 0.4Mb)
• Šimůnek, J., M. Th. van Genuchten, M. Šejna, N. Toride, and F. J. Leij, The STANMOD computer software for evaluating solute transport in porous media using analytical solutions of convection-dispersion equation. Versions 1.0 and 2.0, IGWMC - TPS - 71, International Ground Water Modeling Center, Colorado School of Mines, Golden, Colorado, 32 pp., 1999. (Download PDF, 0.3Mb)
• Šimůnek, J., M. Šejna, and M. Th. van Genuchten, The Hydrus-2D software package for simulating two-dimensional movement of water, heat, and multiple solutes in variably saturated media. Version 2.0, IGWMC - TPS - 53, International Ground Water Modeling Center, Colorado School of Mines, Golden, Colorado, 251 pp., 1999.
• Šimůnek, J., M. Šejna, and M. Th. van Genuchten, The Hydrus-1D software package for simulating the one-dimensional movement of water, heat, and multiple solutes in variably-saturated media. Version 2.0, IGWMC - TPS - 70, International Ground Water Modeling Center, Colorado School of Mines, Golden, Colorado, 202 pp., 1998.
• Šimůnek, J., K. Huang, and M. Th. van Genuchten, The HYDRUS code for simulating the one-dimensional movement of water, heat, and multiple solutes in variably-saturated media. Version 6.0, Research Report No. 144, U.S. Salinity Laboratory, USDA, ARS, Riverside, California, 164 pp., 1998. (Download PDF, 13.6Mb)
• Šimůnek, J., K. Huang, M. Šejna, and M. Th. van Genuchten, The Hydrus-1D software package for simulating the one-dimensional movement of water, heat, and multiple solutes in variably-saturated media. Version 1.0, IGWMC - TPS - 70, International Ground Water Modeling Center, Colorado School of Mines, Golden, Colorado, 186 pp., 1998.
• Vaughan, P. J., D. L. Suarez, J. Šimůnek, and J. D. Rhoades, UnsatchemGeo geographic information system software package for simulating one-dimensional water flow, heat transport, carbon dioxide production and transport, and multicomponent solute transport in a geographic area, Version 1.0, Research Report No. 142, U.S. Salinity Laboratory, USDA, ARS, Riverside, California, 71 pp., 1997.
• Šimůnek, J., D. L. Suarez, and M. Šejna, The UNSATCHEM software package for simulating one-dimensional variably saturated water flow, heat transport, carbon dioxide production and transport, and multicomponent solute transport with major ion equilibrium and kinetic chemistry, Version 2.0, Research Report No. 141, U.S. Salinity Laboratory, USDA, ARS, Riverside, California, 186 pp., 1996. (Download PDF, 3.5Mb)
• Šimůnek, J., M. Šejna, and M. Th. van Genuchten, The Hydrus-2D software package for simulating water flow and solute transport in two-dimensional variably saturated media. Version 1.0, IGWMC - TPS - 53, International Ground Water Modeling Center, Colorado School of Mines, Golden, Colorado, 167 pp., 1996.
• Šimůnek, J., K. Huang, and M. Th. van Genuchten, The SWMS_3D code for simulating water flow and solute transport in three-dimensional variably saturated media. Version 1.0, Research Report No. 139, U.S. Salinity Laboratory, USDA, ARS, Riverside, California, 155 pp., 1995. (Download PDF, 2.7Mb)
• Šimůnek, J., and M. Th. van Genuchten, The CHAIN_2D code for simulating two-dimensional movement of water flow, heat, and multiple solutes in variably-saturated porous media, Version 1.1, Research Report No 136, U.S. Salinity Laboratory, USDA, ARS, Riverside, California, 205 pp., 1994. ( Download PDF, 19.5Mb)
• Šimůnek, J., T. Vogel, and M. Th. van Genuchten, The SWMS_2D code for simulating water flow and solute transport in two-dimensional variably saturated media. Version 1.2, Research Report No. 132, U.S. Salinity Laboratory, USDA, ARS, Riverside, California, 196 pp., 1994. (Download PDF, 12Mb)
• Šimůnek, J., and D. L. Suarez, The UNSATCHEM-2D code for simulating two-dimensional variably saturated water flow, heat transport, carbon dioxide transport, and solute transport with major ion equilibrium and kinetic chemistry, Version 1.1, Research Report No. 128, U.S. Salinity Laboratory, USDA, ARS, Riverside, California, 218 pp., 1993.
• Šimůnek, J., and D. L. Suarez, The SOILCO2 code for simulating one-dimensional carbon dioxide production and transport in variably saturated porous media, Version 1.1, Research Report No. 127, U.S. Salinity Laboratory, USDA, ARS, Riverside, California, 162 pp., 1993.
• Šimůnek, J., T. Vogel, and M. Th. van Genuchten, The SWMS_2D code for simulating water flow and solute transport in two-dimensional variably saturated media. Version 1.1, Research Report No. 126, U.S. Salinity Laboratory, USDA, ARS, Riverside, California, 169 pp., 1992.