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Home / About us / People / J. Simunek

Jirka Simunek

Jirka Simunek Professor and Hydrologist
Department of Environmental Sciences
University of California Riverside
Riverside, CA 92521, USA
Tel. +1-951-827-7854
e-mail: Jiri.Simunek@ucr.edu

  • Other WEB sites: UCR web page
  • Citation Report, June 2011: h-factor = 35
  • HYDRUS Textbook from CRC Press: Soil Physics with HYDRUS
  • Silverman 2008 - HYDRUSing will make you strong!
  • Desert Triathlon 2009
  • Tour de Palm Springs 2010

Academic Degrees:

  • Ph.D. 1993, Czech Academy of Sciences, Prague, Czech Republic.
  • M.S. 1984, Czech Technical University, Faculty of Civil Engineering, Prague, Czechoslovakia.

Awards:

  • Don and Betty Kirkham Award (awarded by the Soil Science Society of America for a mid career scientist who has made outstanding scholarly achievements and educational contributions in soil physics), 2005.
  • ESR (Institute of Environmental Science & Research, Christchurch, New Zealand) International Fellow 2006.
  • CRCIF (Cooperative Research Center Irrigation Futures, Australia) Visiting Fellow, July 1-14 2007.
  • Fellowship from the Japan Society for the Promotion of Science, Tokyo, Japan, 2008.
  • Distinguished Visitor of the Blaustein Center for Scientific Cooperation of the Sede Boqer Campus, 2008.
  • Soil Science Society of America Fellow, 2010.
  • American Geophysical Union Fellow, 2012.

Research Interests:

  • Water flow and solute transport processes in soils and groundwater
  • Numerical modeling
  • Characterization and measurement of the unsaturated soil hydraulic properties
  • Use on inverse methods to estimate flow and solute transport parameters
  • Preferential flow in macroporous soils and unsaturated fractured rock
  • Nonequilibrium transport of contaminants
  • Computer software development

Peer-reviewed journal articles:

  1. 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, (in press).
  2. Dabach, S., N. Lazarovitch, J. Šimůnek, and U. Shani, Numerical investigation of irrigation scheduling based on soil water status, Irrigation Science (in press).
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. Novák, V., Kňava, K., and J. Šimůnek, Assessing numerically the influence of stones on hydraulic conductivity of saturated soils, Geoderma, 161(3-4), 177-181, 2011.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. Pontedeiro, E. M., M. Th. van Genuchten, R. M. Cotta, J. Šimůnek, The effects of preferential flow and soil texture on the 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.
  25. 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.
  26. 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.
  27. Lassabatère, L., R. Angulo-Jaramillo, J. M. Soria Ugalde, J. Šimůnek, R. Haverkamp, Analytical and numerical modelling of water infiltration experiments, Water Resources Res., 45, W12415, doi:10.1029/2009WR007941, pp. 20, 2009.
  28. 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.
  29. 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.
  30. 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, Chemisphere, 77(4), 597-603, 2009.
  31. Twarakavi, N. K. C., J. Šimůnek, and H. S. Seo, Reply to Comment on 'Evaluating interactions between groundwater and vadose zone using HYDRUS-based flow package for MODFLOW', Vadose Zone Journal, 8(3), 820-821, 2009.
  32. 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.
  33. Twarakavi, N. K. C., J. Šimůnek, and M. Schaap, Support vector machine based pedotransfer functions for estimation of soil hydraulic parameters, Soil Sci. Soc. Am. J., 73(5), 2009.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. Saito, H., K. Seki, and J. Šimůnek, Alternative spatial interpolation method for water retention parameters, Hydrology and Earth Syst. Sci., 13, 453–465, 2009.
  39. Sakai, M., N. Toride, and J. Šimůnek, Water and vapor movement with condensation and evaporation in a sandy column subject to temperature gradient, Soil Sci. Soc. Am. J., 73(3), 707-717, 2009.
  40. 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.
  41. 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.
  42. 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)
  43. 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.
  44. 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.
  45. 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.
  46. De Wilde, T., J. Mertens, J. Šimůnek, K. Sniegowksi, J. Ryckeboer, P. Jaeken, D. Springael, and P. Spanoghe, Characterizing pesticide sorption and degradation in micro scale biopurification systems using column displacement experiment, Environmental Pollution, 157, 463-473, 2009.
  47. 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.
  48. Akay, O., G. A. Fox, and J. Šimůnek, Numerical simulation of water flow during macropore/subsurface drain interaction using HYDRUS, Vadose Zone Journal, 7(3), 909-918, 2008.
  49. 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.
  50. Sansoulet, J., Y.-M. Cabidoche, P. Cattan, S. Ruy, and J. Šimůnek, Spatially distributed water fluxes in an Andisol under banana plants: experiments and 3D modelling, Vadose Zone Journal, doi:10.2136/VZJ2007.0073, Special Issue “Vadose Zone Modeling”, 7(2), 819-829, 2008.
  51. Hanson, B. R., J. Šimůnek, and J. W. Hopmans, Leaching with subsurface drip irrigation under saline, shallow ground water 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)
  52. 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.
  53. Šimůnek, J. and M. Th. van Genuchten, Modeling nonequilibrium flow and transport with 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)
  54. 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.
  55. 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.
  56. 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.
  57. 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.
  58. 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.
  59. 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.
  60. 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.
  61. Gargiulo, G., S. A. Bradford, J. Šimůnek, P. Ustohal, H. Vereecken, and E. Klumpp, Bacteria transport and deposition under unsaturated conditions: the role of 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)
  62. 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.
  63. 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.
  64. Pang, L., M. McLeod, J. Aislabie, J. Šimůnek, M. Close, and R. Hector, Modeling transport of fecal coliforms and Salmonella bacteriophage in ten undisturbed New Zealand soils under dairy shed effluent irrigation, Vadose Zone Journal, 7(1), 97-111, 2008.
  65. 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.
  66. 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.
  67. 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.
  68. Srivastava, P., K. W. Migliaccio, and J. Šimunek, Centennial manuscript: Terrestrial models for simulating water quality at point, field, and watershed scales, Transactions of the ASAE, 50(5), 1683-1693, 2007.
  69. Corwin, D. L., J. D. Rhoades, J. Šimůnek, Leaching requirement for soil salinity control: Steady-state vs. transient-state models, Agric. Water Management, 90(3), 165-180, 2007.
  70. 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.
  71. Saito, H., J. Šimůnek, J. W. Hopmans, and A. Tuli, Numerical evaluation of the heat pulse probe for simultaneous estimation of water fluxes and soil hydraulic and thermal properties, Water Resour. Res., 43, W07408, doi:10.1029/2006WR005320, 2007.
  72. Zlotnik, V. A., T. Wang, J. 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.
  73. 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.
  74. 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)
  75. 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.
  76. 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.
  77. Wehrhan, A., R. Kasteel, J. Šimůnek, J. Groeneweg, H. Vereecken, Transport of sulfadiazine in soil columns – experiments and modeling approaches, J. Contam. Hydrology, 89(1-2), 107-135, 2007.
  78. 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.
  79. Schwärzel, K., J. Šimůnek, M. Th. van Genuchten, and G. Wessolek, Measurement and modeling of soil water dynamics and evapotranspiration in disturbed peatland soils, Journal of Plant Nutrition and Soil Science, 169, 762-774, 2006.
  80. 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.
  81. 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.
  82. 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.
  83. 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.
  84. 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)
  85. 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.
  86. Hanson, B. R., J. Šimůnek, and J. W. Hopmans, Numerical modeling of urea-ammonium-nitrate fertigation under microirrigation, Agric. Water Management, 86, 102-113, 2006. (download selected HYDRUS projects used in the paper here)
  87. 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.
  88. 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.
  89. 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.
  90. Šimůnek, J., D. Jacques, M. Th. van Genuchten, and D. Mallants, Multicomponent geochemical transport modeling using the HYDRUS computer software packages, J. Am. Water Resour. Assoc., 42(6), 1537-1547, 2006.
  91. Šimůnek, J., Changming He, J. L. Pang, and S. A. Bradford, Colloid-facilitated 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)
  92. 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.
  93. 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.
  94. Boivin, A., J. Šimůnek, M. Schiavon and M. Th. van Genuchten, A comparison of pesticides transport processes in three contrasting field soils using Hydrus-2D, Vadose Zone Journal, 5, 838–849, 2006.
  95. 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.
  96. 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.
  97. 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.
  98. 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.
  99. Köhne, J. M., S. Köhne, and J. Šimůnek, Multi-process herbicide transport in structured soil columns: Experiment and model analysis, J. Contam. Hydrology, 85, 1-32, 2006.
  100. Köhne, S., B. Lennartz, J. M. Köhne, and J. Šimůnek, Bromide transport at a tile-drained field site: experiment, one- and two-dimensional equilibrium and non-equilibrium numerical modeling, J. Hydrology, 321(1-4), 390-408, 2006.
  101. 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.
  102. Decker, D. L., J. Šimůnek, S. W. Tyler, Ch. Papelis, and M. Logsdon, Variably saturated reactive transport of arsenic in heap leach facilities, Vadose Zone Journal, 5, 430-444, 2006.
  103. 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.
  104. 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.
  105. 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.
  106. 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.
  107. 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.
  108. 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.
  109. Bradford, S. A., J. Šimůnek, M. Bettahar, Yadata 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.
  110. 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.
  111. 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.
  112. 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.
  113. 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.
  114. 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.
  115. 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.
  116. Kelleners, T. J., R. W. O. Soppe, J. E. Ayars, T. H. Skaggs, and J. Šimůnek, Inverse analysis of upward water flow in a groundwater table lysimeter, Vadose Zone Journal, 4, 558–572, 2005.
  117. Gärdenäs, A., 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.
  118. 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.
  119. 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.
  120. 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.
  121. 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.
  122. 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.
  123. 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.
  124. 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)
  125. 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.
  126. Casey, F. X. M., G. L. Larsen, H. Hakk, and J. Šimůnek. Fate and transport of testosterone in agriculturally significant soils. Environ. Sci. Technol., 38(3), 790-798, 2004.
  127. Abbasi, F., D. Jacques, J. Šimůnek, J. Feyen, and M. Th. van Genuchten, Inverse estimation of the soil hydraulic and solute transport parameters from transient field experiments: Heterogeneous soil, Transactions of ASAE, 46(4), 1097-1111, 2003.
  128. 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.
  129. 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.
  130. 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.
  131. Scanlon, B., K. Keese, R. C. Reedy, J. Šimůnek, and B. Andraski, Variations in flow and transport in thick desert vadose zones in response to paleoclimatic forcing (0 – 90 kyr): Monitoring, modeling, and uncertainties, Water Resour. Res. 39(7), 1179, doi:10.1029/2002WR001604, 13.1-13.7, 2003.
  132. 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: Theory and experimental evidence, Vadose Zone Journal, 2, 212-221, 2003.
  133. Abbasi, F., J. Šimůnek, M. Th. van Genuchten, J. Feyen, F. J. Adamsen, D. J. Hunsaker, T. S. Strelkoff, and P. Shouse, Overland water and solute transport: Model development and field data analysis, Journal of Irrig. and Drainage ASCE, 129(2), 71-81, 2003.
  134. 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)
  135. Scanlon, B. R., M. Christman, R. Reedy, I. Porro, J. Šimůnek, and G. 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.
  136. 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.
  137. 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.
  138. 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.
  139. 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.
  140. Novák, V., J. Šimůnek, and M. Th. van Genuchten, Infiltration into a swelling, cracked clay soil, J. Hydrol. Hydromech., 50(1), 3-19, 2002.
  141. 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.
  142. 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.
  143. 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.
  144. 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.
  145. Hopmans, J. W., J. Šimůnek, and K. L. Bristow, Indirect estimation of soil thermal properties and water flux from heat pulse measurements: Geometry and Dispersion effects, Water Resour. Res., 38(1), 10.1029/2000WR000071, 7.1-7.14, 2002.
  146. Schijven, J., and J. Šimůnek, Kinetic modeling of virus transport at field scale, J. of Contam. Hydrology, 55(1 2), 113 135, 2002.
  147. Young, M. H., A. Karagunduz, J. Šimůnek, and K. D. Pennell, Modified upward infiltration method for characterizing soil hydraulic properties, Soil Sci. Soc. Am. J., 66, 57-64, 2002.
  148. Silliman, S., B. Berkowitz, J. Šimůnek, and M. Th. van Genuchten, Fluid flow and chemical migration within the capillary fringe, Ground Water, 40(1), 76-84, 2002.
  149. 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 field with tile drains, European J. of Soil Sci., 52(3), 433-447, 2001.
  150. 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.
  151. Casey, F. X. M., and J. Šimůnek, Inverse analyses of the transport of chlorinated hydrocarbons subject to sequential transformation reactions, J. of Environ. Quality, 30(4), 1354-1360, 2001.
  152. 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.
  153. 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.
  154. Šimůnek, J., O. Wendroth, N. Wypler, and M. Th. van Genuchten, Nonequilibrium water flow characterized from an upward infiltration experiment, European J. of Soil Sci., 52(1), 13-24, 2001.
  155. 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.
  156. 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.
  157. Novák, V., and J. Šimůnek, Modeling of water infiltration into soils with cracks, Acta Hydrologica Slovaca, 1, 119-125, in Slovak with English summary, 2000.
  158. 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.
  159. 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.
  160. Inoue, M., J. Šimůnek, S. Shiozawa, and J. W. Hopmans, Estimation of soil hydraulic and solute transport parameters from transient infiltration experiments, Advances in Water Resources, 23, 677-688, 2000.
  161. Hollenbeck, K., J. Šimůnek, and M. Th. van Genuchten, RETCML: Incorporating maximum-likelihood estimation principles in the hydraulic parameter estimation code RETC, Computer & Geosciences, 26(3), 319-327, 2000.
  162. 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.
  163. 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.
  164. 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.
  165. 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.
  166. 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.
  167. Vaughan, P. J., D. L. Suarez, J. Šimůnek, D. L. Corwin, and J. D. Rhoades, Role of groundwater flow in variation of discharge from tile drain systems, J. Environ. Qual., 28, 403-410, 1999.
  168. 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.
  169. Šimůnek, J., D. Wang, P. J. Shouse, and M. Th. van Genuchten, Analysis of a field tension disc infiltrometer experiment by parameter estimation, Intern. Agrophysics, 12, 167-180, 1998.
  170. Gribb, M. M., J. Šimůnek, and M. F. Leonard, Development of a cone penetrometer method to determine soil hydraulic properties, ASCE J. of Geotech. and Geoenviron. Eng., 124(9), 820-829, 1998.
  171. 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.
  172. Kodešová, R., M. M. Gribb, and J. Šimůnek, Estimating soil hydraulic properties from transient cone permeameter data, Soil Science, 163(6), 436-453, 1998.
  173. Šimůnek, J., O. Wendroth, and M. Th. van Genuchten, A parameter estimation analysis of the evaporation method for determining soil hydraulic properties, Soil Sci. Soc. Am. J., 62(4), 894-905, 1998.
  174. 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.
  175. 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.
  176. Inoue, M., J. Šimůnek, J. W. Hopmans, and V. Clausnitzer, In-situ estimation of soil hydraulic functions using a multi-step soil water extraction technique, Water Resour. Rer., 34(5), 1035-1050, 1998.
  177. 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.
  178. Šimůnek, J., and D. L. Suarez, Sodic soil reclamation using multicomponent transport modeling, ASCE J. Irrig. and Drain. Engineering, 123(5), 367-376, 1997.
  179. 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.
  180. 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.
  181. 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.
  182. 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.
  183. 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.
  184. Šimůnek, J., Numerical model for simulating the movement of water, heat and multiple solutes in variably saturated porous media, J. Hydrol. Hydromech., 42(1-2), 66-88, 1994.
  185. 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.
  186. 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.
  187. 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.
  188. 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.
  189. 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.
  190. Šimůnek, J., Numerical simulation of the transport processes in soil (in Czech, English abstract), Vodohosp. Čas., 39(1), 20 34, 1991.
  191. 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.
  192. Šimůnek, J., Analysis of spatial dependence and soil properties interrelations (in Czech, English abstract), Vodohosp. Čas., 38(5), 559 576, 1990.
  193. Šimůnek, J., Transport and ion exchange of cations solutes in porous media (in Czech, English abstract), Vodohosp. Čas., 37(4), 441 454, 1989.
  194. 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.
  195. Šimůnek, J., Infiltration - numerical simulation (in Czech, English abstract), Vodohosp. Čas., 36(4), 407 420, 1988.
  196. 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.
  197. 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.

Selected Other Publications:

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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:

  • 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.
 

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