Michael L. MacWilliams, Ph.D.

Dr. MacWilliams has more than twenty years of experience in the field of numerical modeling and seventeen years of experience in computational fluid dynamics. His primary field of study is the application of state-of-the-art three-dimensional numerical models to environmental flows. His Ph.D. research focused on the application of detailed three-dimensional hydrodynamic models to flow in river channels and on floodplains. In addition, Dr. MacWilliams has more than thirteen years of experience working as an environmental consultant using three-dimensional hydrodynamic models in estuarine systems. This work includes conducting detailed hydrodynamic and salinity modeling related to a large-scale restoration project of salt ponds in San Francisco Bay and hydrodynamic and salinity modeling in Suisun Bay to investigate the potential mechanisms underlying the relationships of fish abundance to flow, "Fish-X2," which form the basis for the current salinity standard for the San Francisco estuary.

Dr. MacWilliams is the primary developer of the UnTRIM San Francisco Bay-Delta model, a three-dimensional hydrodynamic model of San Francisco Bay, which has been used in studies of San Francisco Bay and the Sacramento-San Joaquin Delta for California DWR, USBR, USGS, and the US Army Corps of Engineers. Recent projects include the application of the UnTRIM model to San Francisco Bay and the Sacramento-San Joaquin Delta to assess potential impacts of sea level rise, Delta levee failures, the effects of Delta operations on delta smelt entrainment, and the potential water quality impacts of deepening the Sacramento and San Francisco Bay to Stockton Deep Water Ship Channels.


Education

Ph.D., Stanford University, Environmental Fluid Mechanics & Hydrology with a
Ph.D. Minor in Geological & Environmental Sciences, 2004

M.S., Stanford University, Civil and Environmental Engineering, 1998

B.S., University of Notre Dame, Engineering and Environmental Science, 1997

B.A., University of Notre Dame, English, 1997


Professional History

Delta Modeling Associates, Inc., 2011 - present

Environmental Consultant, May 2001 - present

Consulting Assistant Professor, June 2004 - August 2013
Dept. of Civil and Environmental Engineering, Stanford University


Awards

Lorenz G. Straub Award, 2004
This award is presented annually by the St. Anthony Falls Laboratory at the University of Minnesota for the most meritorious thesis in hydraulic engineering or related fields.


Recent Publications

Kimmerer, W.J., E.S. Gross, and M.L. MacWilliams, 2014. Tidal migration and retention of estuarine zooplankton investigated using a particle-tracking model, Limnology and Oceanography, 59(3), 901-916.

Kimmerer, W.J., M.L. MacWilliams, and E.S. Gross, 2013. Variation of fish habitat and extent of the low-salinity zone with freshwater flow in the San Francisco Estuary, San Francisco Estuary and Watershed Science, 11(4).

MacWilliams, M.L., and E.S. Gross, 2013. Hydrodynamic Simulation of Circulation and Residence Time in Clifton Court Forebay, San Francisco Estuary and Watershed Science, 11(2).

Bever, A.J., and M.L. MacWilliams, 2013. Simulating sediment transport processes in San Pablo Bay using coupled hydrodynamic, wave, and sediment transport models, Marine Geology, 345, 235-253.

Andes, L., F. Wu, J. Lo, M. MacWilliams, C. Lu, and R. Dean, 2012. Estimate of Coastal Flood Statistics for the Far South San Francisco Bay, Proceedings of the 10th Intl. Conf.on Hydroscience & Engineering, Nov. 4-7, 2012, Orlando, Florida, U.S.A.

MacWilliams, M.L., M.R. Tompkins, R.L. Street, G.M. Kondolf, and P.K. Kitanidis, 2010. An assessment of the effectiveness of a constructed compound channel river restoration project on an incised stream. Journal of Hydraulic Engineering, Volume 136, Issue 12, pp. 1042-1052. (click here for pdf)

Gross, E.S., M.L. MacWilliams, C.D. Holleman, and T.A. Hervier, 2010. Particle Tracking Model Testing and Applications Report, POD 3-D Particle Tracking Modeling Study, Prepared for Interagency Ecological Program, May 11, 2010, 109 p.

Gross, E.S., M.L. MacWilliams, and W.J. Kimmerer, 2009. Three-dimensional modeling of tidal hydrodynamics in the San Francisco Estuary, San Francisco Estuary and Watershed Science 7 (2).

Kimmerer, W.J., E.S. Gross, and M.L. MacWilliams, 2009. Is the response of the estuarine nekton to freshwater flow in the San Francisco Estuary explained by variation in habitat volume., Estuaries and Coasts, 32: 375-389, DOI 10.1007/s12237-008-9124-x.

MacWilliams, M.L., F.G. Salcedo, and E.S. Gross, 2008. San Francisco Bay-Delta UnTRIM Model Calibration Report, POD 3-D Particle Tracking Modeling Study, Prepared for California Department of Water Resources, December 19, 2008, 344 p.

MacWilliams, M.L., P.K. Kitanidis, and R.L. Street, 2008. Numerical simulation of flow in incised and compound channels for evaluation of river restoration design, Inaugural International Conference of the Engineering Mechanics Institute, EM08, Minneapolis, MN.

MacWilliams, M.L., E.S. Gross, J.F. DeGeorge, and R.R. Rachielle, 2007. Three-dimensional hydrodynamic modeling of the San Francisco Estuary on an unstructured grid, IAHR, 32nd Congress, Venice Italy, July 1-6, 2007.

Gross, E.S., N.J. Nidzieko, M.L. MacWilliams, and M.T. Stacey, 2007. Parameterization of estuarine mixing processes in the San Francisco Estuary based on analysis of three-dimensional hydrodynamic simulations, Proceedings of the Estuarine and Coastal Modeling Conference, ECM10, ASCE.

MacWilliams, M.L., Jr., J.M. Wheaton, G.B. Pasternack, R.L. Street, and P.K. Kitanidis, 2006. Flow convergence routing hypothesis for pool-riffle maintenance in alluvial rivers, Water Resour. Res., 42, W10427, doi:10.1029/2005WR004391. (click here for full pdf)

MacWilliams, M.L., and R.T. Cheng, 2006. Three-dimensional hydrodynamic modeling of San Pablo Bay on an unstructured grid, The 7th Int. Conf. on Hydroscience and Engineering (ICHE-2006), Sep. 10 - Sep. 13, Philadelphia, USA, 2006. (click here for full proceedings)

Gross, E.S., M.L. MacWilliams and W.Kimmerer, 2006. Simulating Periodic Stratification in San Francisco Bay, Proceedings of the Estuarine and Coastal Modeling Conference, ASCE.

MacWilliams, M.L., E.S. Gross, and W.Kimmerer, 2005. Simulating salt intrusion into Suisun Bay and the Western Delta, State of the Estuary.

MacWilliams, M.L., 2004. Three-dimensional Hydrodynamic Simulation of River Channels and Floodplains, Ph.D. Dissertation, Stanford University, 222 p.

MacWilliams, M.L., R.L. Street, and P.K. Kitanidis, 2004. Modeling Floodplain Flow on Lower Deer Creek, CA, River Flow 2004: Proceedings of the Second International Conference on Fluvial Hydraulics, Greco, Carravetta, & Della Morte (eds.), Vol. 2, 1429-1439, Balkema.

Gross, E.S., M.L. MacWilliams, and W.Kimmerer, 2004. Three-dimensional Hydrodynamic Modeling to Improve Understanding of Mechanisms Relating Flow to Abundance of Estuarine Biota, Proceedings of the 2004 CALFED Bay-Delta Program Science Conference.

Gross, E.S., M.L. MacWilliams, and D.Schaaf, 2004. Three-dimensional Salinity Simulations in Tidal Sloughs, Proceedings of the 2004 CALFED Bay-Delta Program Science Conference.

MacWilliams, M.L., R.L. Street, and P.K. Kitanidis, 2003. Modeling Floodplain Flow on Lower Deer Creek, CALFED Science Conference 2003: Advances in Science and Restoration in the Bay, Delta and Watershed, Abstract Volume, p.109, January 2003.

MacWilliams, M.L., R.L. Street, and P.K. Kitanidis, 2002. Numerical Simulation of Flow in Compound Channels, EOS Trans. AGU, 83(47), Fall Meet. Suppl., Abstract H72B-0852.

MacWilliams, M.L., 2002. Hydrodynamic Modeling and River Restoration, presented at California Water and Environmental Modeling Forum (formerly known as the Bay-Delta Modeling Forum), February 2002.

MacWilliams, M.L., R.L. Street, and P.K. Kitanidis, 1999. Modeling Shear Stresses in Incised and Multi-Stage Channels, EOS Trans. AGU, 80(46), Fall Meet. Suppl., p. F448.

MacWilliams, M.L. and P.K. Kitanidis, 1998. A Geostatistical Approach to the Inverse Problem for Transient Groundwater Flow, EOS Trans. AGU, 79(45), Fall Meet. Suppl., p. F291.

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Aaron J. Bever, Ph.D.

Dr. Bever has over ten years of experience using field observations and hydrodynamic, sediment transport, and wave models to better understand sediment transport in the coastal ocean and estuarine systems. His main focus has been on using state of the art three-dimensional numerical models validated against field observations to determine the dominant physical processes (e.g. waves, currents, high-density flows) causing sediment transport within a system, and then investigating the pathways the sediment takes in being transported from one location to another. Dr. Bever has also participated in numerous national and international data collection cruises, where he helped to collect some of the data necessary to initialize, validate, and calibrate his numerical modeling studies. His previous consulting experience includes numerical modeling of inlet hydrodynamics and sediment transport at the mouth of the Bevano River in Italy, and implementing the Regional Ocean Modeling System (ROMS) within the Caloosahatchee River as part of a project to evaluate the bioavailability and sources of nutrients and their linkages to nuisance drift algae. Recent work includes using coupled hydrodynamic, wave and sediment transport models to examine sediment dispersal following dredged material placements and the routing of sediment through the Sacramento-San Joaquin Delta and San Francisco Bay.

Dr. Bever also works on developing methods that use a standardized set of metrics to evaluate how skillful a model is, relative to a whole group of models, at reproducing a set of observations. Specifically, this work is for comparing how well different models reproduce physical variables (e.g. salinity and stratification), dissolved oxygen concentration, and the volume of water that is hypoxic within the Chesapeake Bay. This work is also helping to show that numerical models can give valuable insight for supporting management decisions and for improving observational sampling strategies and strategic instrument deployments.


Education

Ph.D., Virginia Institute of Marine Science, College of William & Mary, 2010

M.S., Virginia Institute of Marine Science, College of William & Mary, 2006

B.S., University of Washington, Oceanography with a minor in Earth and Space Systems, 2003


Professional History

Delta Modeling Associates, Inc., 2011 - present


Recent Publications

Bever, A.J., and C.K. Harris, in press. Storm and fair-weather driven sediment-transport within Poverty Bay, New Zealand, evaluated using coupled numerical models, Continental Shelf Research.

Bever, A.J., and M.L. MacWilliams, 2013. Simulating sediment transport processes in San Pablo Bay using coupled hydrodynamic, wave, and sediment transport models, Marine Geology, 345, 235-253.

Bever, A.J., M. A.M. Friedrichs, C.T. Friedrichs, M.E. Scully, and L.W.J. Lanerolle. 2013. Combining observations and numerical model results to improve estimates of hypoxic volume within the Chesapeake Bay, Journal of Geophysical Research, Oceans. 118(10). 4924-4944. (open access)

Bever, A.J., J.E. McNinch, and C.K. Harris, 2011. Hydrodynamics and sediment-transport in the nearshore of Poverty Bay, New Zealand: observations of nearshore sediment segregation and oceanic storms, Continental Shelf Research, 31(6), 507-526.

Bever, A.J., C.K. Harris, C.R. Sherwood, and R.P. Signell, 2009. Deposition and flux of sediment from the Po River, Italy: An idealized and wintertime numerical modeling study, Marine Geology, 260(1-4), 69-80.

Harris, C.K., C.R. Sherwood, R.P. Signell, A.J. Bever, and J.C. Warner, 2008. Sediment dispersal in the northwestern Adriatic Sea, Journal of Geophysical Research. 113 (C11S03).


Invited and Selected Talks

Bever, A.J., M.L. MacWilliams, F. Wu, C.S. Conner, P.F. Sing, and B. Goeden, 2013. South San Francisco Bay three-dimensional sediment transport modeling to examine dispersal of dredged material for beneficial reuse, State of the Estuary Conference, Oakland, CA, 29-20 October 2013.

Bever, A.J., and M.L. MacWilliams, 2012. Simulating sediment transport processes in San Francisco Bay using coupled hydrodynamic, wave, and sediment transport models, AGU Fall Meeting, San Francisco, CA, 3-7 December 2012.

Bever, A.J., and M.L. MacWilliams, 2012. Numerical simulations of first flush sediment dispersal throughout the Sacramento-San Joaquin Delta and San Francisco Bay, 7th Biennial Bay-Delta Science Conference, Sacramento, CA, 16-18 October 2012.

Bever, A.J. M.A.M. Friedrichs, and C.T. Friedrichs, 2011. Using Chesapeake Bay models to evaluate dissolved oxygen sampling strategies. Dissolved Oxygen Data Meeting. Annapolis, MD, 22 February 2011. Presented methods for using Chesapeake Bay models to evaluate dissolved oxygen sampling strategies.

Bever, A.J., 2010. Understanding hydrodynamics in Poverty Bay, New Zealand to better predict sediment-transport dynamics. Texas A&M University, College Station, TX. 14 June. Invited by Robert Hetland.

Bever, A.J., C.K. Harris, and J. Swenson, 2010. Dispersal basin geometry influences sediment deposition, shoreline progradation rates, and grain size segregation: A case study of Poverty Bay, New Zealand. AAPG Annual Convention and Exhibition, New Orleans, LA. 11-14 April.

Bever, A.J., 2010. How to implement the Regional Ocean Modeling System on a High Performance Computing Cluster, from downloading the source code to visualizing the output. CSDMS Integration Facility at INSTAAR, University of Colorado, Boulder, CO. 4 March. Invited by James Syvitski.

Bever, A.J., and C.K. Harris, 2006. Sediment Transport off the Po River: A Model-Data Comparison. Physics of Estuarine and Coastal Seas. Astoria, OR, 18-22 September.

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