Journal Publications

• Lucas, L.V., Koseff, J.R., Monismith, S.G., and Thompson, J.K., " Shallow water processes govern system-wide phytoplankton bloom dynamics: A modeling study," Journal of Marine Systems, doi:10.1016/j.jmarsys.2008.07.011, 2008.

• Rosman, J.H., Hench, J.L., Koseff, J.R., and Monismith, S.G., "Extracting Reynolds stresses from acoustic Doppler current profiler measurements in wave-dominated environments", Jouranl of Atmospheric and Oceanic Technology, 25, 2, Feb. 2008,  286-306.

• Ivey, G.N., Winters, K.B., and Koseff, J.R., "Density stratification, turbulence, but how much is mixing," Annual Review of Fluid Mechanics, 40, 2008, 169-184.

• Thompson, J.K., Koseff, J.R., Monismith, S.G., and Lucas, L.V., "Shallow water processes govern system-wide phytoplankton bloom dynamics: A field study," Journal of Marine Systems, doi:10.1016/j.jmarsys.2007.12.006, 2007.

• Reidenbach M.A., Koseff J.R.,  and Monismith S.G., "Laboratory experiments of fine-scale mixing and mass transport within a coral canopy", Physics of Fluids, 19, 2007,  075107.

• Gaylord, B., Rosman, J.H., Reed, D.C., Koseff, J.R., Fram, J., MacIntyre, S., Arkema, K., McDonald, C., Brzezinski, M. A., Largier, J.L., Monismith, S.G., Raimondi, P.T., Mardian, B., "Spatial patterns of flow and their modification within and around a giant kelp forest", Limnology and Oceanography, 52(5), September, 2007, 1838-1852.

• Koehl, M.A.R., Strother, J.A., Reidenbach, M.A., Koseff, J.R., and Hadfield, M.G.," Individual-based model of larval transport to coral reefs in turbulent, wave-driven flow: behavioral responses to dissolved settlement inducer", Marine Ecology-Progress Series, 335, 2007, 1-18.

• Lowe, R. J., Falter, J.L., Koseff, J.R., Monismith, S.G., and  Atkinson, M.J.,  "Spectral wave flow attenuation within submerged canopies: Implications for wave energy dissipation,"  Journal of Geophysical Research, 112, C05018, 2007, doi:10.1029/2006JC003605.(pdf)

• Crimaldi, J.P., Koseff, J.R., and Monismith, S.G., "Structure of mass and momentum fields over a model aggregation of benthic filter feeders," Biogeosciences , 2007, in press.

• Koehl, M. A. R., Strother, J.A., Reidenbach, M.A., Koseff, J.R.,   and M. G. Hadfield, "Individual-based model of larval transport to coral reefs in turbulent, wave-driven flow: Effects of behavioral responses to dissolved settlement inducer,"   Marine Ecology Progress Series , 335, 2007,   1-18.

• Rosman, J. H., Koseff, J.R., Monismith, S.G., and Grover, J. ,   "A field investigation into the effects of a kelp forest ( Macrocystis pyrifera ) on coastal hydrodynamics and transport", Journal of Geophysical Research , 112, C02016, 2007, doi:10.1029/2005JC003430. (pdf)

• Falter, J. L.,   Atkinson, M.J., Lowe, R.J., Monismith, S.G., and Koseff, J.R., "Effects of nonlocal turbulence on the mass transfer of dissolved species to reef corals",   Limnology and Oceanography . 52, 2007, 274-285.

• Crimaldi, J.P., and Koseff, J.R., "Structure of turbulent plumes from a momentumless source in a smooth bed", Environmental Fluid Mechancis 6 (6), December, 2006, 573-592.

• Hult, E.L, Troy, C.D., and Koseff, J.R., "Laboratory images of breaking internal waves," Physics of Fluids , 18, September, 2006, 091107.

• Crimaldi, J.P., Koseff, J.R., and Monismith, S.G., "A mixing-length formulation for the turbulent Prandtl number in wall-bounded flows with bed roughness and elevated scalar sources," Physics of Fluids , 18 (9), September, 2006, 095102-095110. (pdf)

• Reidenbach, M. A., Monismith, S.G., Koseff, J.R., Yahel, G., and Genin. A., "Boundary layer turbulence and flow structure over a fringing coral reef."  Limnology and Oceanography, 51, 2006, 1956-1968 (pdf)

• Falter, J.L., Atkinson, M.J., Fleming, J.H., Bos, M., Lowe, R.J., Koseff, J.R., and Monismith, S.G., "A new mesocosm for simulating the effects of wave-driven water motion on the biogeochemistry of benthic reef communities, Limnology and Oceanography: Methods , 4, 2006, 68-79.

• Troy, C.D., and Koseff, J.R., "The viscous decay of progressive interfacial waves," Physics of Fluids, 18, 2006 , 026602.

• McDonald, C. B., Koseff, J.R., and Monismith, S.G., "Effects of the depth to coral height ratio on drag coefficients for unidirectional flow over coral," Limnology and Oceanography, 51, 2006, 1294-1301. (pdf)

• Monismith, S.G., Genin, A., Reidenbach, M.A., Yahel, G., and Koseff, J.R., "Thermally Driven Exchanges Between a Coral Reef and the Adjoining Ocean", Journal of Physical Oceanography , Vol. 36, No. 7, 2006, 1332-1347. (pdf)

• Reidenbach M.A., Koseff J.R., Monismith S.G., Steinbuck J.V., and Genin A., "The effects of waves and morphology on mass transfer within branched reef corals", Limnology and Oceanography , 51(2), 2006,   1134-1141. (pdf)

• Troy, C.D., and Koseff, J.R., "The generation and quantitative visualization of breaking internal waves," Experiments in Fluids , 38(5), May, 2005, pp. 549-562

• Troy, C.D., and Koseff, J.R., "The instability and breaking of long internal waves,"   Journal of Fluid Mechanics , 543, 2005, pp. 107-136.

• Lowe, R.J., Koseff, J.R., and Monismith, S.G., "Oscillatory flow through submerged canopies Part 1. Velocity structure, " Journal of Geophysical Research, 110, C10016, 2005, doi:10.1029/2004JC002788 (pdf)

• Lowe, R.J., Koseff, J.R., Monismith, S.G., and Falter, J.L., "Oscillatory flow through submerged canopies. Part 2. Canopy mass transfer, " Journal of Geophysical Research , 110, C10017, 2005, doi:10.1029/2004JC002789 (pdf)

• Lowe, R.J., Falter, J.L., Bandet, M.D., Pawlak, G., Atkinson, M.J., Monismith, S.G., and Koseff, J.R., "Spectral wave dissipation over a barrier reef", Journal of Geophyical Research-Oceans , 110, C04001, 2005, doi:10.1029/2004JC002711 (pdf)

• Holzman, R.,   Reidenbach, M.A., Monismith, S.G., Koseff, J.R., and Genin, A.,   "Near-bottom depletion of zooplankton over a coral reef: II. Relationships with zooplankton swimming ability", Coral Reefs , 24,1, 2005, pp. 87-94. (pdf)

• Shih, L.H., Koseff, J.R., Ivey, G.N., and J.H. Ferziger,   "Parameterization of turbulent fluxes and scales using homogeneous sheared stably- stratified turbulence simulations", Journal of Fluid Mechanics , 525, 2005, pp. 193-214.

• Rehmann, C.R. and Koseff, J.R.,   "Mean potential energy change in weakly and strongly stratified turbulent flow,"   Dynamics Atmospheres and Oceans , 37, 2004, pp. 271-294.

• Venayagamoorthy, S.K., Koseff, J.R., Ferziger, J.H, and L.H. Shih, 2003. Testing of RANS turbulence models for stratified flows based on DNS data, Center for Turbulence Research, Stanford University, Annual Research Briefs - 2003, pp. 127-138.

• Mead, K.S., Wiley, M.B., Koehl, M.A.R., and Koseff, J.R., "Fine-scale patterns of odor encounter by the antennules of Mantis Shrimp tracking turbulent plumes in wave-affected and unidirectional flow", Journal of Experimental Biology , 206, 1, 2003, pp. 181-193.

• May, C.L.,   Koseff, J.R.., Lucas, L.V., Cloern, J.E., and Schoellhammer, D.H., "Effects of spatial and temporal variability of turbidity on phytoplankton blooms", Marine Ecology Progress Series , 254, 2003, pp. 111-128.

• Genin, A., Yahel, G., Reidenbach, M.A., Monismith, S.G., and Koseff, J.R., "Intense benthic grazing on phytoplankton in coral reefs revealed using the Control Volume approach", Oceanography, 15, 2, 2002, pp. 90-96. (pdf)

• Ferziger, J.H., Koseff, J.R., and Monismith, S.G., "Numerical simulation of geophysical turbulence," Computers & Fluids , v31(#4-7), pp. 557-568, May- Sept 2002. (pdf)

• Crimaldi, J.P., Thompson, J.K., Rosman, J.H., Lowe, R.J., and Koseff, J.R., "Hydrodynamics of larval settlement: the influence of turbulent stress events at potential recruitment sites," Limnology and Oceanography , 47, 2002,   pp. 1137-1151.

• Crimaldi, J.P,   Koehl, M.A.R., and Koseff, J.R., "Effects of the resolution and kinematics of olfactory appendages on the interception of chemical signals in a turbulent odor plume, " Environmental Fluid Mechanics , 2, 2002, pp. 35-63.

• Crimaldi, J.P., Wiley, M.B., and Koseff, J.R., "The relationship between mean and instantaneous structure in turbulent passive scalar plumes,"   Journal of Turbulence , 3 (014) 2002,   http://stacks.iop.org/JoT/3/014

• Koehl, M.A. R., Koseff, J.R., Crimaldi, J.P., McCay, M.G., Cooper, T., Wiley, M. B., and Moore, P.A., "Lobster Sniffing: Antennule Design and Hydrodynamic Filtering of Information in an Odor Plume," Science ,   Volume 294, pages 1948-1952,   November 30, 2001.

• Calhoun, R.J., Street, R.L., and Koseff, J.R., "Turbulent Flow over a Wavy Surface. Part 2: Stratified Case," Journal of Geophysical Research , 106, C5, May 15, 2001, pp. 9295-9310.

• Crimaldi, J.P., and Koseff, J.R., "High-Resolution Measurements of the Spatial and Temporal Scalar Structure of a Turbulent Plume," Experiments in Fluids , 31-1, 2001, pp 90-102.

• Garg, R. P., Ferziger, J. H., Monismith, S. G., and Koseff, J. R., "Stably Stratified Turbulent Channel Flows. Part I: Stratification Regimes and Turbulence Suppression Mechanisms," Physics of Fluids , 12,10, 2000, pp. 2569-2594. (pdf)

• Stacey, M.T., Cowen, E.A., Powell, T.M., Monismith, S.G., Koseff, J.R., and Dobbins, E., "Plume Dispersion in a Stratified, Near Coastal Flow: Measurements and Modeling," Continental Shelf Research , 20(6), 2000, pp. 637-663.

• Shih, L.H., Koseff, J.R., Ferziger, J.H., and Rehmann, C.R., "Scaling and Parameterization of Stratified Homogeneous Turbulent Shear Flow," Journal of Fluid Mechanics , 412, 1-20,2000.

• Lucas, L.V., Koseff, J.R., Monismith, S.G., Cloern, J.E., and Thompson, J.K., "Processes Governing Phytoplankton Blooms in Estuaries. I: The Local Production-Loss Balance," Marine Ecology Progress Series , 187, 1-15, 1999. (pdf)

• Lucas, L.V., Koseff, J.R., Monismith, S.G., Cloern, J.E., and Thompson, J.K., "Processes Governing Phytoplankton Blooms in Estuaries.   II:   The Role of Horizontal Transport," Marine Ecology Progress Series , 187, 17-30, 1999. (pdf)

• Gross, E.S., Koseff, J.R., and Monismith, S.G., "Three-Dimensional Salinity Simulations of South San Francisco," Journal of Hydraulic Engineering, 125,11, 1199-1209, 1999. (pdf)

• Gross, E.S., Koseff, J.R., and Monismith, S.G., "An Evaluation of Advective Schemes for Estuarine Salinity Simulations," Journal of Hydraulic Engineering, 125,1, 32-46, 1999. (pdf)

• Lin, C-L., Koseff, J.R., Ferziger, J.H., and Monismith, S.G., "Direct Numerical Simulation of Wave-Mean Flow and Wave-Wave Interactions: A Brief Perspective," Physical Processes in Lakes and Oceans (ed. J. Imberger), American Geophysical Union, 271-284, 1998.

• Ivey, G.N., Imberger, J., and Koseff, J.R., "Buoyancy Fluxes in a Stratified Fluid," Physical Processes in Lakes and Oceans (ed. J. Imberger), American Geophysical Union, 377-388, 1998.

• Lucas, L.V., Cloern, J.E., Koseff, J.R., Monismith, S.G., and Thompson, J.K., "Does the Sverdrup Critical Depth Model Explain Bloom Dynamics in Estuaries," Journal of Marine Research , 56,2, 375-415, 1998. (pdf)

• Gross, E.S., Casulli, V., Bonaventura, L., and Koseff, J.R., "A Semi-Implicit Method for Vertical Transport in Multidimensional Models," International Journal for Numerical Methods in Fluids , 28, 157-186, 1998.

• Briggs, D.A., Ferziger, J.H., Koseff, J.R., and Monismith, S.G., "Turbulent Mixing in a Shear-Free Stably Stratified Two-Layer Fluid," Journal of Fluid Mechanics , 354, 175-208, 1998.

• Jassby, A.D., Koseff, J.R., and Monismith, S.G., "Processes Underlying Phytoplankton Variability in San Francisco Bay," San Francisco Bay, The Ecosytem , (ed. T Hollibaugh), Pacific Division of AAAS, 325-350, 1996.

• O'Riordan, C.A., Monismith, S.G., Koseff, J.R., "The Effect Near-Bed Hydrodynamics on Model Bivalve Filtration Rates," Arch. Hydrobiol. Spec. Issues Advanc. Iimnol. , 47, 247-254, February, 1996.

• Prasad, A.K., and Koseff, J.R., "Combined Forced and Natural Convection Heat Transfer in a Deep Lid-Driven Cavity Flow," International Journal of Heat and Fluid Flow , 17,5, 460-467, 1996.

• Briggs, D.A., Ferziger, J.H., Koseff, J.R., and Monismith, S.G., "Entrainment in a Shear-Free Turbulent Mixing Layer," Journal of Fluid Mechanics , 310, 215-241, 1996.

• O'Riordan , C.A., Monismith, S.G., Koseff, J.R., "The Effect of Bivalve Excurrent Jet Dynamics on Mass Transfer in a Benthic Boundary Layer," Limnology and Oceanography, 40, 2, 330-344, 1995. (pdf)

• Lin, C-L., Koseff, J.R., and Ferziger, J.H., "On Triad Interactions in a Linearly Stratified Ocean," Journal of Physical Oceanography , 27, 1, 153-167, 1995.

• McDonald, E.T., and Koseff, J.R., "The Internal Structure of Lateral Intrusions in a Continuously Stratified Heat/Salt System," Physics of Fluids , 6,12, 3870-3883, 1994.

• Zang, Y., Street, R.L., and Koseff, J.R., "A Non-Staggered Grid, Fractional Step Method for Time-Dependent Incompressible Navier-Stokes Equations in General Curvilinear Coordinate Systems," Journal of Computational Physics , 114, 18-33, 1994.

• Koseff, J.R., Holen, J.K., Monismith, S.G., and Cloern, J.E., "Coupled Effects of Vertical Mixing and Benthic Grazing on Phytoplankton Populations in Shallow, Turbid Estuaries," J. Marine Res. , 51,4, 1993, pp. 1-26. (pdf)

• O'Riordan , C.A., Monismith, S.G., Koseff, J.R., "A Study of Concentration Boundary Layer Formation over a Bed of Model Bivalves," Limnology and Oceanography , 38(8), 1993, pp. 1712-1729.

• Zang, Y., Street, R.L., Koseff, J.R., "A Dynamic Mixed Subgrid-Scale Model and its Application to Turbulent Recirculating Flows," Physics of Fluids A , 5 (12), 1993, pp.3186-3196.

• Itsweire, E.C., Koseff, J.R., Briggs, D.A., and Ferziger, J.H., "Turbulence in Stratified Shear Flows: Implications for Interpreting Shear-Induced Mixing in the Ocean," Journal of Physical Oceanography, 23(7), 1993, pp. 1508-1522 .

• Lin, C-L., Ferziger, J.H., Koseff, J.R., and Monismith, S.G., "Simulation and Stability of Two-Dimensional Internal Gravity Waves in a Stratified Shear Layer," Dynamics of Atmospheres and Oceans , 19, 1993, pp. 325-366.

• Holt, S.E., Koseff, J.R., and Ferziger, J.H., "A Numerical Study of the Evolution & Structure of Homogeneous Stably Stratified Sheared Turbulence," Journal of Fluid Mechanics , 237, 1992, pp. 449-539.

• Schladow, S.G., Thomas, E., and Koseff, J.R., "The Dynamics of Lateral Intrusions in a Thermohaline Stratification," Journal of Fluid Mechanics , 237, 1992, pp. 127-165.

• Monismith, S.G., Koseff, J.R., Thompson, J., O'Riordan, C., and Nepf, H.M., "A Study of Model Bivalve Siphon Currents," Limnology and Oceanography , 35(3), 1990, pp. 680-696.

• Koseff, J.R., Prasad, A.K., Perng, C-Y., and Street, R.L., "Complex Cavities:   How Many Dimensions are Sufficient for Simulation?" Physics of Fluids , 2(4), April 1990, pp. 619-622.

• Prasad, A.K., and Koseff, J.R., "Reynolds Number and End-Wall Effects on a Lid-Driven Cavity Flow," Physics of Fluids , A, Vol. 1, No. 2, pp. 208-218, 1989.

• Koseff, J.R., and Street, R.L., "Circulation Structure in a Stratified Lid-Driven Cavity Flow," Jour. Hydr. Div. , ASCE, 111(2), February 1985.

• Freitas, C.J., Street, R.L., Findikakis, A.N., and Koseff, J.R., "A Successful Numerical Simulation of a Three-Dimensional Cavity Flow," International Journal for Numerical Methods in Fluids , 5, pp. 561-575, 1985.

• Rhee, H., Koseff, J.R., and Street, R.L., "Flow Visualization of a Recirculating Flow by Rheoscopic and Liquid Crystal Techniques," Experiments in Fluids , 2, pp. 57-64, 1984.

• Koseff, J.R., and Street, R.L., "Visualization Studies of a Shear Driven Three-Dimensional Recirculating Flow," Jour. Fluid Engineering , ASME, 106, pp. 21-29, 1984.

• Koseff, J.R., and Street, R.L., "The Lid-Driven Cavity Flow: A Synthesis of Qualitative and Quantitative Observations," Jour. Fluids Eng ., ASME, 106, December, pp. 390-389, 1984.

• Koseff, J.R., and Street, R.L., "On End-Wall Effects in a Lid-Driven Cavity Flow," Jour. Fluids Eng ., ASME, 106, December, pp. 385-389, 1984.

• Cheung, T.K., and Koseff, J.R., "Simultaneous Backward-Scatter Forward-Scatter Laser-Doppler Anemometer Measurements in an Open Channel Flow," DISA Information , 28, pp. 3-9, 1983.   (Also ASCE EMD Specialty Conference on Measurement Techniques and Prediction Methods in Turbulent Flow, Purdue, May 23-25, 1983.)