USGS - science for a changing world

Environmental Health - Toxic Substances

Bibliography

Development of Computer Simulation Models and Statistical Analysis Software, Publications, and Documentation

Sorted by Author Sort by Year Sort by Title Sort by Publication Type Only On-Line Reports Search the Toxics Program Bibliography Go to Contents of the Toxics Program Bibliography

This crosscutting topic bibliography is a subcategory of the following bibliography:

A | B | C | D | E | F | G | H | J | K | L
M | N | O | P | R | S | T | U | V | W | Z

A

Abrams, R.H., 1999,
A compartmentalized approach to simulating redox zones in contaminated aquifers: Stanford, Calif., Stanford University, Department of Geological and Environmental Sciences, unpublished Ph.D. thesis, 182 p.
Abrams, R.H., and Loague, K., 2000,
A compartmentalized solute transport model for redox zones in contaminated aquifers--1, Theory and development: Water Resources Research, v. 36, no. 8, p. 2001-2013, 2000WR900110, doi:10.1029/2000WR900110.
Abrams, R.H., and Loague, K., 2000,
A compartmentalized solute transport model for redox zones in contaminated aquifers--2, Field-scale simulations: Water Resources Research, v. 36, no. 8, p. 2015--2029, 10.1029/2000WR900111, doi:10.1029/2000WR900111.
Abrams, R.H., Loague, K., and Kent, D.B., 1998,
Development and testing of a compartmentalized reaction network model for redox zones in contaminated aquifers: Water Resources Research, v. 34, no. 6, p. 1531-1541, 98WR00485, doi:10.1029/98WR00485.
Alexander, S.C., and Saar, M.O., 2012,
Improved characterization of small “u” for Jacob pumping test analysis methods: Ground Water, v. 50, no. 2, p. 256-265, doi:10.1111/j.1745-6584.2011.00839.x.
Anderman, E.R., 1996,
The use of advective-transport observations to improve ground-water flow parameter estimation: Golden, Colorado School of Mines, Department of Geology and Geological Engineering, unpublished Ph.D. thesis, 277 p.
Anderman, E.R., and Hill, M.C., 1998,
Improving ground-water flow model calibration with the advective-transport observation (ADV) package to MODFLOWP: U.S. Geological Survey Fact Sheet FS-059-98, 2 p.
Anderman, E.R., and Hill, M.C., 1997,
Advective-transport observation (ADV) package, a computer program for adding advective-transport observations of steady-state flow fields to the three-dimensional ground-water-flow parameter-estimation model MODFLOWP: U.S. Geological Survey Open-File Report 97-14, 67 p.
Anderman, E.R., Hill, M.C., and Poeter, E.P., 1996,
Two-dimensional advective transport in ground-water flow parameter estimation: Ground Water, v. 34, no. 6, p. 1001-1009.
Anderman, E.R., Hill, M.C., and Poeter, E.P., 1994,
Two-dimensional advective transport in nonlinear regression--Sensitivities and uncertainty of plume-front observations, in Warner, J.W., and van der Heijde, P., eds., Proceedings, 1994 Groundwater Modeling Conference, Fort Collins, Colorado, August 10-12, 1994: Fort Collins, Colo., Colorado State University, p. 55-62.
Andraski, B.J., and Jacobson, E.A., 2000,
Testing a full-range soil-water retention function in modeling water potential and temperature: Water Resources Research, v. 36, no. 10, p. 3081-3089, 2000WR900193, doi:10.1029/2000WR900193.
Appelo, C.A.J., and Parkhurst, D.L., 1998,
Enhancements to the geochemical model PHREEQC-1D transport and reaction kinetics, in Arehart, G.B., and Hulston, J.R., eds., Proceedings of the 9th International Symposium on Water-Rock Interaction (WRI-9), Rottersam: A.A. Balkema, p. 873-876.

B

Baehr, A.L., 1987,
Selective transport of hydrocarbons in the unsaturated zone due to aqueous and vapor phase partitioning: Water Resources Research, v. 23, no. 10, p. 1,926-1,938, doi:10.1029/WR023i010p01926.
Baehr, A.L., and Baker, R.J., 1995,
Use of a reactive gas transport model to determine rates of hydrocarbon biodegradation in unsaturated porous media: Water Resources Research, v. 31, no. 11, p. 2877-2882, 95WR02077, doi:10.1029/95WR02077.
Baehr, A.L., and Bruell, C.J., 1990,
Application of the Stefan-Maxwell equations to determine limitations of Fick's Law when modeling organic vapor transport in sand columns: Water Resources Research, v. 26, no. 6, p. 1155-1163, doi:10.1029/WR026i006p01155.
Baehr, A.L., and Corapcioglu, M.Y., 1987,
A compositional multiphase model for groundwater contamination by petroleum products--2, numerical solution: Water Resources Research, v. 23, no. 1, p. 201-213, doi:10.1029/WR023i001p00201.
Baehr, A.L., and Joss, C.J., 1995,
An updated model of induced airflow in the unsaturated zone: Water Resources Research, v. 31, no. 2, p. 417-421, 94WR02423, doi:10.1029/94WR02423.
Bahr, J.M., 1990,
Kinetically influenced terms for solute transport affected by heterogeneous and homogeneous classical reactions: Water Resources Research, v. 26, no. 1, p. 21-34, 89WR01545, doi:10.1029/WR026i001p00021.
Bahr, J.M., and Rubin, J., 1987,
Direct comparison of kinetic and local equilibrium formulations for solute transport affected by surface reactions: Water Resources Research, v. 23, no. 3, p. 438-452, 6W4566, doi:10.1029/WR023i003p00438.
Ball, J.W., and Nordstrom, D.K., 1991,
User's manual for WATEQ4F with revised thermodynamic data base and test cases for calculating speciation of major, trace and redoc elements in natural waters: U.S. Geological Survey Open-File Report 91-183, 185 p.
Battaglin, W.A., and Goolsby, D.A., 1998,
Regression models of herbicide concentrations in outflow from reservoirs in the midwestern USA, 1992-1993: Journal of the American Water Resources Association, v. 34, no. 6, p. 1369-1390, doi:10.1111/j.1752-1688.1998.tb05438.x.
Battaglin, W.A., Ulery, R.L., and Vowinkel, E.F., 1989,
Method for simulating water-table altitudes from stream and drainage-basin locations by use of a geographic information system, in Mallard, G.E., and Ragone, S.E., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the technical meeting, Phoenix, Arizona, September 26-30, 1988: U.S. Geological Survey Water-Resources Investigations Report 88-4220, p. 531-539.
Bekins, B.A., Cozzarelli, I.M., and Curtis, G.P., 2005,
A simple method for calculating growth rates of petroleum hydrocarbon plumes: Ground Water, v. 0, no. 0, doi:10.1111/j.1745-6584.2005.00093.x.
Bekins, B.A., Warren, E., and Godsy, E.M., 1998,
A comparison of zero-order, first-order, and Monod biotransformation models: Ground Water, v. 36, no. 2, p. 261-268, doi:10.1111/j.1745-6584.1998.tb01091.x.
Bekins, B.A., Warren, E., and Godsy, E.M., 1997,
Comparing zero and first order approximations to the Monod Model, in Alleman, B.C., and Leeson, A., eds., In Situ and On Site Bioremediation--Procedings of the Fourth International Symposium on In Situ And On-Site Bioremediation, New Orleans, La., April 28-May 1, 1997: Columbus, Ohio, Battelle Press, v. 5, p. 547-552 (Contact The Conference Group Inc. for information on the availability of the proceedings.).
Bencala, K.E., 1983,
Simulation of solute transport in a mountain pool and-riffle stream with a kinetic mass transfer model for sorption: Water Resources Research, v. 19, no. 3, p. 732-738, doi:10.1029/WR019i003p00732.
Bencala, K.E., and Walters, R.A., 2010,
Simulation of solute transport in a mountain pool-and-riffle stream--A transient storage model (Chap. F2), in Burt, T.P., Pinay, G., and Sabater, S., eds., Riparian Zone Hydrology and Biogeochemisty--IAHS Benchmark Papers in Hydrology Series no. 5: Wallingford, U.K., IAHS Press, ISBN:978-907161-09-4 (Reprinting of Bencala and Walters, 1983: Water Resources Research, v.19, p.718-724.).
Bencala, K.E., and Walters, R.A., 1983,
Simulation of solute transport in a mountain pool-and-riffle stream--A transient storage model: Water Resources Research, v. 19, no. 3, p. 718-724, doi:10.1029/WR019i003p00718.
Boyer, E.W., Hornberger, G.M., Bencala, K.E., and McKnight, D.M., 2000,
Effects of asynchronous snowmelt on flushing of dissolved organic carbon--A mixing model approach: Hydrological Processes, v. 14, no. 18, p. 3291-3308, doi:10.1002/1099-1085(20001230)14:18<3291::AID-HYP202>3.0.CO;2-2.
Boyer, E.W., Hornberger, G.M., Bencala, K.E., and McKnight, D.M., 1996,
Overview of a simple model describing variation of dissolved organic carbon in an upland catchment: Ecological Modeling, v. 86, p. 183-188, doi:10.1016/0304-3800(95)00049-6.
Broshears, R.E., Runkel, R.L., and Kimball, B.A., 1994,
Development and application of a reactive solute transport model for trace metals in mountain streams, in Dutton, A.R., ed., Toxic Substances and the Hydrologic Sciences--Proceedings of the conference, Austin, Texas, April 10-13, 1994: Minneapolis, Minn., American Institute of Hydrology, p. 19-34.
Brown, D.W., and Hem, J.D., 1984,
Development of a model to predict the adsorption of lead from solution on a natural streambed sediment: U.S. Geological Survey Water-Supply Paper 2187, 35 p.
Brown, J.G., Bassett, R.L., and Glynn, P.D., 2000,
Reactive transport of metal contaminants in alluvium--Model comparison and column simulation: Applied Geochemistry, v. 15, no. 1, p. 35-50, doi:10.1016/S0883-2927(99)00004-9.
Burkart, M.R., 1990,
Interagency research and technical integration, in Information exchange on models and data needs relating to the impact of agricultural practices on water quality--Workshop Proceedings, Reston, Virginia, February 5-8, 1990: U.S. Geological Survey, Office Water Data Coordination, p. 11-12.

C

Cabaniss, S.E., Zhou, Q., Maurice, P.A., Chin, Y., and Aiken, G.R., 2000,
A log-normal distribution model for the molecular weight of aquatic fulvic acids: Environmental Science and Technology, v. 34, no. 6, p. 1103-1109, doi:10.1021/es990555y.
Casulli, V., Bertolazzi, E., and Cheng, R.T., 1993,
TRIM_3D--A three-dimensional model for accurate simulation of shallow water flow, in 1993 National Conference on Hydraulic Engineering, Proceedings, San Francisco, California, July, 1993: American Society of Civil Engineers, p. 1988-1993.
Casulli, V., and Cheng, R.T., 1994,
Solutions of primitive equations for three-dimensional tidal circulation, in Proceedings of the Third International Conference on Estuarine and Coastal Modeling, Chicago, Ill., September, 1993: American Society of Civil Engineers, p. 396-406.
Chapelle, F.H., Robertson, J.F., Landmeyer, J.E., and Bradley, P.M., 2000,
Methodology for applying monitored natural attenuation to petroleum hydrocarbon-contaminated ground-water systems with examples from South Carolina: U.S. Geological Survey Water-Resources Investigations Report 00-4161, 47. A 3 1/2" disk is included p.
Chapelle, F.H., Widdowson, M.A., Brauner, J.S., Mendez, E., and Casey, C.C., 2003,
Methodology for estimating times of remediation associated with monitored natural attenuation: U.S. Geological Survey Water-Resources Investigations Report 03-4057, 51 p.
Chapra, S.C., and Runkel, R.L., 1999,
Modeling impact of storage zones on stream dissolved oxygen: Journal of Environmental Engineering, v. 125, no. 5, p. 415-419.
Charlton, S.R., Macklin, C.L., and Parkhurst, D.L., 1997,
PHREEQCI - A graphical user interface for the geochemical computer program PHREEQC: U.S. Geological Survey Water-Resources Investigations Report 97-4222, 9 p.
Charlton, S.R., and Parkhurst, D.L., 2011,
Modules based on the geochemical model PHREEQC for use in scripting and programming languages: Computers and Geosciences, v. 37, no. 10, p. 1653-1663, doi:10.1016/j.cageo.2011.02.005.
Charlton, S.R., and Parkhurst, D.W., 2012,
PHAST4 Windows--A 3D graphical user interface for the reactive-transport simulator PHAST: Ground Water, v. 51, no. 4, p. 623-628, doi:10.1111/j.1745-6584.2012.00993.x.
Cheng, R.T., Casulli, V., and Gartner, J.W., 1993,
Tidal, residual, intertidal mudflat (TRIM) model and its applications to San Francisco Bay, California: Estuarine, Coastal and Shelf Science, v. 36, p. 235-280, doi:10.1006/ecss.1993.1016.
Cheng, R.T., Smith, P.E., and Casulli, V., 1993,
Recent development in three-dimensional numerical estuarine models, in Proceedings, 1993 National Conference on Hydraulic Engineering, San Francisco, California, July, 1993: American Society of Civil Engineers, p. 1982-1987.
Cheng, R.T., and Smith, R.E., 1998,
A NOWCAST model for tides and tidal currents in San Francisco Bay, California, in Ocean Community Conference ‘98, Marine Technology Society, Baltimore, Maryland, November 15-19, 1998: Marine Technology Society, v. I, p. 537-543.
Chin, U.P., Weber, W.J., Jr., and Chiou, C.T., 1991,
A thermodynamic partition model for binding of nonionic organic compounds by organic colloids and implications for their sorption to soils and sediment, in Baker, R.A., ed., Humics and soils, v. 1 of Organic substances and sediments in water: Chelsea, Mich., Lewis Publishers, p. 251-273.
Chiou, C.T., Schmedding, D.W., and Manes, M., 2005,
Improved prediction of octanol--water partition coefficients from liquid-solute water solubilities and molar volumes: Environmental Science and Technology, v. 39, no. 22, p. 8840-8846, doi:10.1021/es050729d.
Chiou, C.T., Sheng, G., and Manes, M., 2001,
A partition-limited model for the plant uptake of organic contaminants from soil and water: Environmental Science and Technology, v. 35, no. 7, p. 1437-1444, doi:10.1021/es0017561.
Christian, S.B., 1992,
Well test analysis in a two-zone aquifer using the boundary integral method: Stanford, Calif., Stanford University, M.S. thesis.
Cloern, J.E., Grenz, C., and Vidergar-Lucas, L., 1995,
An empirical model of the phytoplankton chlorophyll/carbon ratio--The conversion factor between productivity and growth rate: Limnology and Oceanography, v. 40, no. 7, p. 1313-1321.
Cole, B.E., and Cloern, J.E., 1987,
An empirical model for estimating phytoplankton productivity in estuaries: Marine Ecology Progress Series, v. 36, p. 299-305.
Corapcioglu, M.Y., and Baehr, A.L., 1987,
A compositional multiphase model for groundwater contamination by petroleum products--1, Theoretical considerations: Water Resources Research, v. 23, no. 1, p. 191-200, 6W4404, doi:10.1029/WR023i001p00191.
Cox, T.J., and Runkel, R.L., 2008,
Eulerian-Lagrangian numerical scheme for simulating advection, dispersion, and transient storage in streams and a comparison of numerical methods: Journal of Environmental Engineering, v. 134, no. 12, p. 996-1005, doi:10.1061/(ASCE)0733-9372(2008)134:12(996).
Cravotta, C.A., III, Parkhurst, D.L., Means, B., McKenzie, R., Morris, H., and Arthur, W., 2010,
A geochemical module for "AMDTreat" to compute caustic quantity, effluent quality, and sludge volume, in Barnhisel, R.I., ed., Bridging Reclamation, Science and Community--2010 National Meeting of the American Society of Mining and Reclamation, Pittsburgh, Pa., June 5-11, 2010: Lexington, Ky., American Society of Mining and Reclamation, p. 1413-1436.
Cunningham, K.M., and Goldberg, M.C., 1989,
A model for photolytic decomposition of toxic materials adsorbed onto iron oxyhydroxides in surface waters, in Mallard, G.E., and Ragone, S.E., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the technical meeting, Phoenix, Arizona, September 26-30, 1988: U.S. Geological Survey Water-Resources Investigations Report 88-4220, p. 608.
Curtis, G.P., 2003,
Comparison of approaches for simulating reactive solute transport involving organic degradation reactions by multiple terminal electron acceptors: Computers and Geosciences, v. 29, no. 3, p. 319-329, doi:10.1016/S0098-3004(03)00008-6.
Curtis, G.P., Cozzarelli, I.M., Baedecker, M.J., and Bekins, B.A., 1999,
Coupled biogeochemical modeling of ground water contamination at the Bemidji, Minnesota, crude oil spill site, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999--Volume 3 of 3--Subsurface Contamination from Point Sources: U.S. Geological Survey Water-Resources Investigations Report 99-4018C, p. 153-158.
Curtis, G.P., Fox, P., Kohler, M., and Davis, J.A., 2004,
Comparison of in situ uranium K D values with a laboratory determined surface complexation model: Applied Geochemistry, v. 19, p. 1643-1653, doi:10.1016/j.apgeochem.2004.03.004.

D

Davis, J.A., Fuller, C.C., and Cook, A.D., 1987,
A model for trace metal sorption processes at the calcite surface--Adsorption of Cd and subsequent solid solution formation: Geochimica et Cosmochimica Acta, v. 51, no. 6, p. 1,477-1,490, doi:10.1016/0016-7037(87)90330-9.
Davis, J.A., Meece, D.E., Kohler, M., and Curtis, G.P., 2004,
Approaches to surface complexation modeling of uranium(VI) adsorption on aquifer sediments: Geochimica et Cosmochimica Acta, v. 68, p. 3621-3641, doi:10.1016/j.gca.2004.03.003.
Day-Lewis, F.D., Johnson, C.D., Paillet, F.L., and Halford, K.J., 2011,
A computer program for flow-log analysis of single holes (FLASH): Ground Water, v. 49, no. 6, p. 926-931, doi:10.1111/j.1745-6584.2011.00798.x.
Day-Lewis, F.D., Person, M.A., and Konikow, L.F., 1995,
A computer program (MACPUMP) for interactive aquifer-test analysis: U.S. Geological Survey Water-Resources Investigations Report 95-4012, 32 p.
Deng, F.-W., Cushman, J.H., and Delleur, J.W., 1993,
A fast Fourier transform stochastic analysis of the contaminant transport problem: Water Resources Research, v. 29, no. 9, p. 3241-3248, 93WR01236, doi:10.1029/93WR01236.
Dillard, L.A., and Blunt, M.J., 2000,
Development of a pore network simulation model to study nonaqueous phase liquid dissolution: Water Resources Research, v. 36, no. 2, p. 439-454, 1999WR900301, doi:10.1029/1999WR900301.
Dillard, L.A., Essaid, H.I., and Blunt, M.J., 2001,
A functional relation for field-scale nonaqueous phase liquid dissolution developed using a pore network model: Journal of Contaminant Hydrology, v. 48, no. 1-2, p. 89-119, doi:10.1016/S0169-7722(00)00171-6.
Dillard, L.A., Essaid, H.I., and Herkelrath, W.N., 1997,
Multiphase flow modeling of a crude-oil spill site with a bimodal permeability distribution: Water Resources Research, v. 33, no. 7, p. 1617-1632, 97WR00857, doi:10.1029/97WR00857.
Diodato, D.M., 1999,
Simulation of mass transport using the FracTran98 Module of FracSys2000, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999--Volume 3 of 3--Subsurface Contamination from Point Sources: U.S. Geological Survey Water-Resources Investigations Report 99-4018C, p. 833-840.
du Bray, E.A., ed., 1995,
Preliminary compilation of descriptive geoenvironmental mineral deposit models: U.S. Geological Survey Open-File Report 95-0831, Online Version 1.0.

E

El-Kadi, A.I., Plummer, L.N., and Aggarwal, P., 2011,
NETPATH-WIN--An interactive user version of the mass-balance model, NETPATH: Ground Water, v. 49, no. 4, p. 593-599, doi:10.1111/j.1745-6584.2010.00779.x.
Ellefsen, K.J., 2003,
seg2_edit--A program for editing and manipulating SEG-2 files: U.S. Geological Survey Open-File Report 03-141, 11 p.
Ellefsen, K.J., 2000,
check_picks_x -- A program for checking the travel time picks of crosswell seismic and radar data: U.S. Geological Survey Open-File Report 00-109.
Ellefsen, K.J., 1999,
pick_xwell -- A program for interactive picking of crosswell seismic and radar data: U.S. Geological Survey Open-File Report 99-534.
Engesgaard, P., and Kipp, K.L., 1992,
A geochemical transport model for redox-controlled movement of mineral fronts in groundwater flow systems--A case of nitrate removal by oxidation of pyrite: Water Resources Research, v. 28, no. 10, p. 2829-2843, 92WR01264, doi:10.1029/92WR01264.
Essaid, H.L., and Bekins, B.A., 1998,
Modeling solute-transport and biodegradation with BIOMOC: U.S. Geological Survey Fact Sheet 095-98, 4 p.

F

Francy, D.S., Stelzer, E.A., Duris, J.W., Brady, A.M.G., Harrison, J.H., Johnson, H.E., and Ware, M.W., 2013,
Predictive models for Escherichia coli concentrations at inland lake beaches and relationship of model variables to pathogen detection: Applied and Environmental Microbiology, v. 79, no. 5, p. 1676-1688, doi:10.1128/aem.02995-12.
Friedel, M.J., 2001,
Documentation and verification of VST2D--A model for simulating transient, variably saturated, coupled water-heat-solute transport in heterogeneous, anisotropic, 2-dimensional, ground-water systems with variable fluid density: U.S. Geological Survey Water-Resources Investigations Report 00-4105, 2 fold-in oversize sheets and 124 p.

G

Gandhi, N., Bhavsar, S.P., Diamond, M.L., Kuwabara, J.S., Marvin-DiPasquale, M., and Krabbenhoft, D.P., 2007,
Development of a mercury speciation, fate and biotic uptake (BIOTRANSPEC) model--Application to Lahontan Reservoir (Nevada, USA): Environmental Toxicology and Chemistry, v. 26, no. 11, p. 2,260-2,273, doi:10.1897/06-468R.1.
Garabedian, S.P., and Konikow, L.F., 1983,
Front-tracking model for convective transport in flowing ground water: U.S. Geological Survey Water-Resources Investigations Report 83-4034, 55 p.
Glynn, P.D., 2003,
Modeling Np and Pu transport with a surface complexation model and spatially variant sorption capacities--implications for reactive transport modeling and performance assessments of nuclear waste disposal sites: Computers and Geosciences, v. 29, no. 3, p. 331-349, doi:10.1016/S0098-3004(03)00009-8.
Glynn, P.D., 1991,
MBSSAS--A code for the computation of Margules parameters and equilibrium relations in binary solid-solution aqueous-solution systems: Computers and Geosciences, v. 17, no. 7, p. 907-966.
Glynn, P.D., Engesgaard, P., and Kipp, K.L., 1991,
Use and limitations of two computer codes for simulating geochemical mass transport at the Pinal Creek toxic-waste site, in Mallard, G.E., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the technical meeting, Monterey, California, March 11-15, 1991: U.S. Geological Survey Water-Resources Investigations Report 91-4034, p. 454-460.
Glynn, P.D., and Parkhurst, D.L., 1992,
Modeling non-ideal solid-solution aqueous-solution reactions in mass transfer computer codes, in Kharaka, Y.K., and Maest, A.S., eds., Low temperature environments, v. 1 of Water-rock interaction--Proceedings of the 7th International Symposium on Water-Rock Interaction--WRI-7, Park City, Utah, July 9-23, 1992: Rotterdam, Balkema, p. 175-179.
Goode, D.J., 1999,
Modifications to the solute-transport model MOC3D for simple reactions, double porosity, and age, with application at Mirror Lake, New Hampshire, and other sites, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999--Volume 3 of 3--Subsurface Contamination from Point Sources: U.S. Geological Survey Water-Resources Investigations Report 99-4018C, p. 821-832.
Goode, D.J., 1992,
Modeling transport in transient ground-water flow--An unacknowledged approximation: Ground Water, v. 30, no. 2, p. 257-261, doi:10.1111/j.1745-6584.1992.tb01798.x.
Goode, D.J., and Konikow, L.F., 1991,
Testing a method-of-characteristics model of three-dimensional solute transport in ground water, in Lennon, G.P., ed., Proceedings of the International Symposium on Ground Water in Practice, Nashville, Tenn., July 29-August 2, 1991: New York, American Society of Civil Engineers, p. 21-27.
Goode, D.J., and Konikow, L.F., 1990,
Re-evaluation of large-scale dispersivities for a waste chloride plume--Effects of transient flow, in Kovar, K., ed., Model CARE 90--Calibration and reliability in groundwater modeling: International Association of Hydrological Sciences 195, p. 417-426.
Goode, D.J., and Konikow, L.F., 1989,
Modification of a method-of-characteristics solute-transport model to incorporate decay and equilibrium-controlled sorption or ion exchange: U.S. Geological Survey Water-Resources Investigations Report 89-4030, 65 p.
Gooseff, M.N., Bencala, K.E., Scott, D.T., Runkel, R.L., and McKnight, D.M., 2005,
Sensitivity analysis of conservative and reactive stream transient storage models applied to field data from multiple-reach experiments: Advances in Water Resources, v. 28, no. 5, p. 479-492, doi:10.1016/j.advwatres.2004.11.012.
Granato, G.E., Konikow, L.F., and Srinivasan, P., 1993,
PREMOC (version 4.0), A preprocessor for the two-dimensional method of characteristics (MOC) solute-transport model: International Ground Water Modeling Center Report FOS 23, 22 p.
Green, T.R., Constantz, J.E., and Freyberg, D.L., 1996,
Upscaled soil-water retention using van Genuchten's function: Journal of Hydrologic Engineering, v. 1, no. 3, p. 123-130, doi:10.1061/(ASCE)1084-0699(1996)1:3(123).
Green, T.R., and Freyberg, D.L., 1995,
State-dependent anisotrophy--Comparison of quasi-analytical solutions with stochastic results for steady gravity drainage: Water Resources Research, v. 31, no. 9, p. 2201-2212, 95WR00790, doi:10.1029/95WR00790.
Grove, D.B., and Stollenwerk, K.G., 1984,
Computer model of one-dimensional equilibrium controlled sorption processes: U.S. Geological Survey Water-Resources Investigations Report 84-4059, 37 p.

H

Haverkamp, R., Nimmo, J.R., and Reggiani, P., 2002,
Property-transfer models, in Dane, J.H., and Topp, G.C., eds., Methods of Soil Analysis, Part 4, Physical Methods: Madison, Wisconsin, Soil Science Society of America, p. 759-761.
Healy, R.W., and Ronan, A.D., 1996,
Documentation of computer program VS2DH for simulation of energy transport in variably saturated porous media--modification of the U.S. Geological Survey's computer program VS2DT: U.S. Geological Survey Water-Resources Investigations Report 96-4230, 36 p.
Healy, R.W., and Russell, T.F., 2000,
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Prediction of stream volatilization coefficients: American Society of Civil Engineers Journal of Environmental Engineering, v. 116, no. 3, p. 615-631.
Rehmann, L.L.C., Welty, C., and Harvey, R.W., 1999,
Stochastic analysis of virus transport in aquifers: Water Resources Research, v. 35, no. 7, p. 1987-2006, 1999WR900059, doi:10.1029/1999WR900059.
Reinfelder, J.R., Fischer, N.S., Luoma, S.N., Nichols, J.W., and Wang, W.X., 1998,
Trace element trophic transfer in aquatic organisms--A critique of the kinetic model approach: The Science of the Total Environment, v. 219, no. 2-3, p. 117-135, doi:10.1016/S0048-9697(98)00225-3.
Rubin, J., 1990,
Solute transport with multisegment, equilibrium-controlled reactions--A feed forward simulation method: Water Resources Research, v. 26, no. 9, p. 2029-2055, doi:10.1029/WR026i009p02029.
Runkel, R.L., 2010,
One-dimensional transport with equilibrium chemistry (OTEQ)--A reactive transport model for streams and rivers: U.S. Geological Survey Techniques and Methods book 6, chapter B6, 102 p.
Runkel, R.L., 2000,
Using OTIS to model solute transport in streams and rivers: U.S. Geological Survey Fact Sheet 138-99, 4 p.
Runkel, R.L., 1998,
One dimensional transport with inflow and storage (OTIS)--A solute transport model for streams and rivers: U.S. Geological Survey Water-Resources Investigations Report 98-4018, 73 p.
Runkel, R.L., 1995,
Simulation models for conservative and nonconservative solute transport in streams, in Osterkamp, W.R., ed., Effects of scale on interpretation and management of sediment and water quality--Proceedings of the 1995 Meeting of the International Association of Hydrological Sciences, Boulder, Colorado, July 3-14, 1995: International Association of Hydrological Sciences IAHS Publication 225, p. 153-159.
Runkel, R.L., 1993,
Development and application of an equilibrium-based simulation model for reactive solute transport in small streams: Boulder, University of Colorado, unpublished Ph.D. dissertation, 202 p.
Runkel, R.L., Bencala, K.E., and Broshears, R.E., 1996,
An equilibrium-based simulation model for reactive solute transport in small streams, in Morganwalp, D.W., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the technical meeting, Colorado Springs, Colorado, September 20-24, 1993: U.S. Geological Survey Water-Resources Investigations Report 94-4015, v. 2, p. 775-780.
Runkel, R.L., Bencala, K.E., Broshears, R.E., and Chapra, S.C., 1996,
Reactive solute transport in streams--1, Development of an equilibrium-based model: Water Resources Research, v. 32, no. 2, p. 409-418, 95WR03106, doi:10.1029/95WR03106.
Runkel, R.L., Bencala, K.E., and Kimball, B.A., 1999,
Modeling solute transport and geochemistry in streams and rivers using OTIS and OTEQ, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999--Volume 1 of 3--Contamination from Hardrock Mining: U.S. Geological Survey Water-Resources Investigations Report 99-4018A, p. 109-118.
Runkel, R.L., and Broshears, R.L., 1992,
One-dimensional transport with inflow and storage (OTIS)--A solute transport model for small streams: Boulder, Colo., CADSWES, 1 p.
Runkel, R.L., and Chapra, S., 1993,
An efficient numerical solution of the transient storage equations for solute transport in small streams: Water Resources Research, v. 29, no. 1, p. 211-215, 92WR02217, doi:10.1029/92WR02217.
Runkel, R.L., and Chapra, S.C., 1994,
Reply to "Comment on an efficient numerical solution of the transient storage equations for solute transport in small streams" by Dawes and Short: Water Resources Research, v. 30, no. 10, p. 2863-2865, 94WR00986, doi:10.1029/94WR00986.
Runkel, R.L., Kimball, B.A., McKnight, D.M., and Bencala, K.E., 1999,
Reactive solute transport in streams--A surface complexation approach for trace metal sorption: Water Resources Research, v. 35, no. 12, p. 3829-3840, 1999WR900259, doi:10.1029/1999WR900259.
Runkel, R.L., Kimball, B.A., Walton-Day, K., and Verplanck, P.L., 2007,
A simulation-based approach for estimating premining water quality--Red Mountain Creek, Colorado: Applied Geochemistry, v. 22, no. 9, p. 1899-1918, doi:10.1016/j.apgeochem.2007.03.054.
Runkel, R.L., McKnight, D.M., and Andrews, E.D., 1998,
Analysis of transient storage subject to unsteady flow--Diel flow variation in an Antarctic stream: Journal of North American Benthological Society, v. 17, no. 2, p. 143-154.
Runkel, R.L., McKnight, D.M., Bencala, K.E., and Chapra, S.C., 1996,
Reactive solute transport in streams--2, Simulation of a pH modification experiment: Water Resources Research, v. 32, no. 2, p. 419-430, 95WR03107, doi:10.1029/95WR03107.
Runkel, R.L., and Restrepo, P.J., 1993,
Solute transport modeling under unsteady flow regimes--An application of the Modular Modeling Sytem, in Hon, K., ed., Water management in the `90s--A Time for Innovation--Proceedings of the 20th Anniversary Conference of the Water Resource Planning and Management Division of the American Society of Civil Engineers, Seattle, Wash., May 1-5, 1993: Washington, D.C., American Society of Civil Engineers, p. 256-259.
Russell, T.F., Heberton, C.I., Konikow, L.F., and Hornberger, G.Z., 2003,
A finite-volume ELLAM for three-dimensional solute-transport modeling: Ground Water, v. 41, no. 2, p. 258-272, doi:10.1111/j.1745-6584.2003.tb02589.x.
Rutledge, A.T., and Helgesen, J.O., 1991,
A steady-state unsaturated-zone model to simulate pesticide transport: U.S. Geological Survey Water-Resources Investigations Report 90-4164, 13 p.
Rutledge, A.T., and Helgesen, J.O., 1989,
Use of a simplified transport model for pesticides in the unsaturated zone, in Mallard, G.E., and Ragone, S.E., eds., U.S. Geological Survey Toxic-Substances Hydrology Program--Proceedings of the technical meeting, Phoenix, Arizona, September 26-30, 1988: U.S. Geological Survey Water-Resources Investigations Report 88-4220, p. 523-530.

S

Sanford, W.E., Wood, W.W., and Councell, T.B., 1992,
Calcium chloride-dominated brines--An ion-exchange model, in Kharaka, Y.K., and Maest, A.S., eds., Low temperature environments, v. 1 of Water-rock interaction--Proceedings of the 7th International Symposium on Water-Rock Interaction--WRI-7, Park City, Utah, July 13-18, 1992: Rotterdam, A.A. Balkema, p. 669-672.
Scott, D.T., Gooseff, M.N., Bencala, K.E., and Runkel, R.L., 2003,
Automated calibration of a stream solute transport model--Implications for interpretation of biogeochemical parameters: Journal of the North American Benthological Society, v. 22, no. 4, p. 492-510.
See, R.B., Naftz, D.L., and Qualls, C.L., 1992,
GIS-assisted regression analysis to identify sources of selenium in streams: Water Resources Bulletin, v. 28, no. 2, p. 315-330, doi:10.1111/j.1752-1688.1992.tb03997.x.
Smith, P.E., 1994,
San Francisco Bay test case for 3-D model verification, in 1994 National Conference on Hydraulic Engineering, Proceedings, Buffalo, N.Y., August 1-5, 1994: American Society of Civil Engineers, v. 2, p. 885-889.
Smith, P.E., and Larock, B.E., 1993,
A finite-difference model for 3-D flows in bays and estuaries, in 1993 National Conference on Hydraulic Engineering, Proceedings, San Francisco, Calif., July 25-30, 1993: American Society of Civil Engineers, p. 6.
Solomon, D.K., Cook, P.G., and Plummer, L.N., 2006,
Models of groundwater ages and residence times (chapter 6), in IAEA, ed., Use of chlorofluorocarbons in hydrology--A guidebook: Vienna, International Atomic Energy Agency, p. 73-88.
Solomon, D.K., Genereux, D.P., Plummer, L.N., and Busenberg, E., 2010,
Testing mixing models of old and young groundwater in a tropical lowland rain forest with environmental tracers: Water Resources Research, v. 46, no. 4, W04518, doi:10.1029/2009wr008341.
Stackelberg, P.E., and Siwiec, S.F., 1992,
Evaluation of statistical models to predict chemical quality of shallow ground water in the pine barrens of Suffolk County, Long Island, New York: U.S. Geological Survey Water-Resources Investigations Report 92-4100, 22 p.
Stannard, D.I., 1993,
Comparison of Penman-Monteith, Shuttleworth-Wallace, and modified Priestley-Taylor evapotranspiration models for wildland vegetation in semiarid rangeland: Water Resources Research, v. 29, no. 5, p. 1379-1392, 93WR00333, doi:10.1029/93WR00333.

T

Thompson, K.D., 1993,
The stochastic characterization of glacial aquifers using geologic information: Cambridge, Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, unpublished Ph.D. thesis, 309 p.
Thorstenson, D.C., and Parkhurst, D.L., 2004,
Calculation of individual isotope equilibrium constants for geochemical reactions: Geochimica et Cosmochimica Acta, v. 68, no. 11, p. 2449-2465, doi:10.1016/j.gca.2003.11.027.
Tiedeman, C.R., Hill, M.C., D'Agnese, F.A., and Faunt, C.C., 2001,
Identifying model parameters important to preductions for guiding hydrogeologic data collection, in Proceedings, MODFLOW-2001, Golden, Colorado, September 2001: p. 195-201.
Tiedeman, C.R., Lacombe, P.J., and Goode, D.J., 2010,
Multiple well-shutdown tests and site-scale flow simulation in fractured rocks: Ground Water, v. 48, no. 3, p. 401-415, doi:10.1111/j.1745-6584.2009.00651.x.
Tiedeman, C.R., and M.C., H., 2007,
Model calibration and issues related to validation, sensitivity analysis, post-audit, uncertainty evaluation, and assessment of prediction data needs, in Thangarajan, M., ed., Groundwater--Resource Evaluation, Augmentation, Contamination, Restoration, Modeling and Management: Berlin, Springer, p. 237-282, ISBN:978-90-481-7435-5 (originally published in 2006 in Thangarajan, M., Groundwater--Resource Evaluation, Augmentation, Contamination, Restoration, Modeling and Management: Capital Publishing, New Delhi, Chap. 9.).
Troutman, B.M., and Karlinger, M.R., 1986,
Averaging properties of channel networks using methods in stochastic branching theory, in Gupta, V.K., Rodriguez-Iturbe, I., and Wood, E.F., eds., Scale problems in hydrology--Runoff generation and basin response, Symposium, Proceedings, Princeton, New Jersey, October 30-November 3, 1984: Dordrecht, Netherlands, D. Reidel Publishing Co., p. 185-216.

U

Uncles, R.J., and Peterson, D.H., 1995,
A computer model of long-term salinity in San Francisco Bay--Sensitivity to mixing and inflows: Environmental International, v. 21, no. 5, p. 647-656.

V

Voss, C., Simmons, C., and Robinson, N., 2010,
Three-dimensional benchmark for variable-density flow and transport simulation--Matching semi-analytic stability modes for steady unstable convection in an inclined porous box: Hydrogeology Journal, v. 18, no. 1, p. 5-23, doi:10.1007/s10040-009-0556-6.
Voss, C.E., 1984,
SUTRA, A finite-element simulation model for saturated-unsaturated, fluid-density-dependent ground-water flow with energy transport or chemically-reactive single-species solute transport: U.S. Geological Survey Water-Resources Investigations Report 84-4369, 409 p.
Voss, C.I., and Provost, A.M., 2002,
SUTRA--A model for 2D or 3D saturated-unsaturated, variable-density ground-water flow with solute or energy transport: U.S. Geological Survey Water-Resources Investigations Report 2002-4231, 250 p.
Vrabel, J., and Glynn, P.D., 1998,
PHRQCGRF - A computer program for graphical interpretation of PHREEQC geochemical transport simulations: U.S. Geological Survey Open-File Report 98-281, 30 p.

W

Waddill, D.W., and Widdowson, M.A., 1997,
SEAM3D--A numerical model for three-dimensional solute transport and sequential electron acceptor-based bioremediation in groundwater: Virginia Polytechnic Institute and State University Final Technical Report, prepared for the U.S. Army Corps of Engineers, 336-344 p.
Wang, Y.S., Miller, D.R., Anderson, D.E., and McManus, M.L., 1995,
A lagrangian stochastic model for aerial spray transport above an oak forest: Agricultural and Forest Meteorology, v. 76, no. 3-4, p. 277-291, doi:10.1016/0168-1923(95)02221-I.
Weatherill, D., Simmons, C.T., Voss, C.I., and Robinson, N.I., 2004,
Testing density-dependent groundwater models--Two-dimensional steady state unstable convection in infinite, finite and inclined porous layers: Advances in Water Resources, v. 27, no. 5, p. 547-562, doi:10.1016/j.advwatres.2004.01.003.
Wellman, T.P., Shapiro, A.M., and Hill, M.C., 2009,
Effects of simplifying fracture network representation on inert chemical migration in fracture-controlled aquifers: Water Resources Research, v. 45, no. 1, W01416, doi:10.1029/2008WR007025.
Welty, C., and Baehr, A.L., Joss, C.J., and Dillow, J.J.A., 1991,
Use of mathematical programming coupled with a transport model to optimize the design of vapor-extraction systems, in Mallard, G.E., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the technical meeting, Monterey, California, March 11-15, 1991: U.S. Geological Survey Water-Resources Investigations Report 91-4034, p. 276-279.
Wente, S.P., 2004,
A statistical model and national data set for partioning fish-tissue mercury concentration variation between spatiotemporal and sample characteristic effects: U.S. Geological Survey Scientific Investigations Report 2004-5199, 15 p.
Wershaw, R.L., 1993,
Model for humus in soils and sediments: Environmental Science and Technology, v. 27, no. 5, p. 814-816, doi:10.1021/es00042a603.
Wershaw, R.L., 1992,
Membrane-micelle model for humus in soils and sediments and its relation to humification: U.S. Geological Survey Open-File Report 91-513, 64 p.
Willis, C., and Rubin, J., 1987,
Transport of reacting solutes subject to a moving dissolution boundary--Numerical methods and solutions: Water Resources Research, v. 28, no. 8, p. 1,561-1,574, 6W4588, doi:10.1029/WR023i008p01561.
Winfield, K.A., 2005,
Development of property-transfer models for estimating the hydraulic properties of deep sediments at the Idaho National Engineering and Environmental Laboratory, Idahy: U.S. Geological Survey Scientific Investigations Report 2005-5114, 59 p.
Winston, R.B., 2006,
GoPhast--A graphical user interface for PHAST: U.S. Geological Survey Techniques and Methods 6-A20, 98 p.
Winston, R.B., 2001,
MODFLOW GUI and GW-Chart--Tools for building and interpreting MODFLOW models, in Seo, Poeter, and Zheng, eds., Proceedings MODFLOW 2001 and Other Modeling Odysseys Conference, Ground Water Modeling Center, Colorado School of Mines, Golden, Colorado, September 2001: p. 723-727.
Winston, R.B., 2001,
Programs for simplifying the analysis of geographic information in U.S. Geological Survey ground-water models: U.S. Geological Survey Open-File Report 01-392, 67 p.
Winston, R.B., 2000,
Graphical user interface for MODFLOW, version 4: U.S. Geological Survey Open-File Report 00-315, 27 p.
Winston, R.B., 1999,
Upgrade to MODFLOW-GUI--Addition of MODPATH ZONEBUDGET, and additional MODFLOW packages to the U.S. Geological Survey MODFLOW-96 graphical-user interface: U.S. Geological Survey Open-File Report 99-184, 64 p.
Winston, R.B., and Voss, C.I., 2004,
SutraGUI--A graphical user interface for SUTRA, a model for ground-water flow with solute or energy transport: U.S. Geological Survey Open-File Report 03-285.
Winston, R.B., and Voss, C.I., 2003,
SutraGUI, a graphical interface for SUTRA, a model for ground-water flow with solute or energy transport: U.S. Geological Survey Open-File Report 2003-285, 114 p.
Wood, W.W., 1985,
Origin of caves and other solution openings in the unsaturated (vadose) zone of carbonate rocks--A model for C02 generation: Geology, v. 13, p. 822-824.
Wood, W.W., Kraemer, T.F., and Shapiro, A., 2004,
Radon (222Rn) in ground water of fractured rocks--A diffusion/ion exchange model: Ground Water, v. 42, no. 4, p. 552-567, doi:10.1111/j.1745-6584.2004.tb02624.x.
Worrall, F., 2001,
A molecular topology approach to predicting pesticide pollution of groundwater: Environmental Science and Technology, v. 35, no. 11, p. 2282-2287, doi:10.1021/es001593g.

Z

Zheng, C., Hill, M.C., and Hsieh, P.A., 2001,
MODFLOW-2000, the U.S. Geological Survey modular ground-water model--User guide to the LMT6 package, the linkage with MT3DMS for multi-species mass transport modeling: U.S. Geological Survey Open-File Report 01-82, 43 p.
Zhu, L., 2007,
The development of efficient numerical time-domain modeling methods for geophysical wave propagation: Storrs, University of Connecticut, PhD dissertation, 199 p.
Zinn, B.A., and Konikow, L.F., 2005,
MODFLOW data extractor program: U.S. Geological Survey Open-File Report 2005-1143, 7 p.

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