thesis_refs_added.bib

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@book{nielsen_coastal_2009,
	Author = {Nielsen, Peter},
	Date-Added = {2014-08-07 00:10:22 +0000},
	Date-Modified = {2014-08-07 00:10:22 +0000},
	Isbn = {978-981-283-711-0, 978-981-283-713-4},
	Language = {en},
	Month = apr,
	Publisher = {{WORLD} {SCIENTIFIC}},
	Series = {Advanced Series on Ocean Engineering},
	Title = {Coastal and Estuarine Processes},
	Url = {http://www.worldscientific.com/worldscibooks/10.1142/7114},
	Urldate = {2014-08-07},
	Volume = {29},
	Year = {2009},
	Bdsk-Url-1 = {http://www.worldscientific.com/worldscibooks/10.1142/7114}}

@article{young_shear_1991,
	Abstract = {This review of shear dispersion emphasizes that the usual one‐dimensional diffusion equation, derived by Taylor [Proc. R. Soc. London Ser. A 2 1 9, 186 (1953)], is an asymptotic result that is valid only at large time. One route to earlier validity is a systematic wave‐number expansion based on the center manifold theorem. This procedure captures much of the early behavior but it does discard exponentially decaying transients. However, in some cases of practical importance, such as tracer release experiments in rivers, the observation of ``anomalous diffusion'' (i.e., tracer variance growing nonlinearly with time) is at odds with this asymptotic reduction. Alternative approximations and models, which account for exponential transients using a description that is nonlocal in time are reviewed. A secondary theme of this review is the application of shear dispersion to mixing of passive and active scalars in rivers and estuaries. An example is shear dispersion of salt in which the shear flow is created by salinity gradients. Other examples include fixed flux convection.},
	Author = {Young, W. R. and Jones, Scott},
	Date-Added = {2014-08-01 22:44:12 +0000},
	Date-Modified = {2014-08-01 22:44:12 +0000},
	Doi = {10.1063/1.858090},
	Issn = {0899-8213},
	Journal = {Physics of Fluids A: Fluid Dynamics (1989-1993)},
	Month = may,
	Number = {5},
	Pages = {1087--1101},
	Title = {Shear dispersion},
	Url = {http://scitation.aip.org/content/aip/journal/pofa/3/5/10.1063/1.858090},
	Urldate = {2014-07-30},
	Volume = {3},
	Year = {1991},
	Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/pofa/3/5/10.1063/1.858090},
	Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.858090}}

@book{young_brief_2004,
	Abstract = {Concise and focused-these are the two guiding principles of Young, Munson, and Okiishi's Third Edition of A Brief Introduction to Fluid Mechanics. The authors clearly present basic analysis techniques and address practical concerns and applications, such as pipe flow, open-channel flow, flow measurement, and drag and lift. Homework problems in every chapter-including open-ended problems, problems based on the {CD}-{ROM} videos, laboratory problems, and computer problems-emphasize the practical application of principles. More than 100 worked examples provide detailed solutions to a variety of problems. The Third Edition offers several new features and enhancements, including: A variety of new simple figures in the margins that will help you visualize the concepts described in the text.Chapter Summary and Study Guide sections at the end of each chapter that will help you assess your understanding of the material.Simplified presentation of the Reynolds transport theorem.New homework problems added to every chapter.Highlighted key works in each chapter.Experience fluid flow phenomena in action on a new {CD}-{ROM}! The Fluid Mechanics Phenomena {CD}-{ROM} packaged with this text presents: 75 short video segments that illustrate various aspects of fluid mechanics30 extended laboratory-type {problemsActual} experimental data for simple experiments in an Excel format168 review problems.},
	Address = {Hoboken, {NJ}?},
	Author = {Young, Donald F.},
	Date-Added = {2014-08-01 22:44:12 +0000},
	Date-Modified = {2014-08-01 22:44:12 +0000},
	Edition = {3 edition},
	Isbn = {9780471660774},
	Language = {English},
	Month = apr,
	Publisher = {Wiley},
	Title = {A Brief Introduction to Fluid Mechanics},
	Year = {2004}}

@article{seymour_influence_1984,
	Author = {Seymour, Richard J. and Strange, R. Rea and Cayan, Daniel R. and Nathan, Robert A.},
	Date-Added = {2014-08-01 22:44:12 +0000},
	Date-Modified = {2014-08-01 22:44:12 +0000},
	Doi = {10.9753/icce.v19.},
	Issn = {2156-1028},
	Journal = {Coastal Engineering Proceedings},
	Number = {19},
	Title = {Influence of El Ni{\~n}os on California's wave climate},
	Url = {http://journals.tdl.org/icce/index.php/icce/article/view/3820},
	Volume = {1},
	Year = {1984},
	Bdsk-Url-1 = {http://journals.tdl.org/icce/index.php/icce/article/view/3820},
	Bdsk-Url-2 = {http://dx.doi.org/10.9753/icce.v19.}}

@article{schijf_theoretical_1953,
	Author = {Schijf, J. B and Sch{\"o}nfeld, J. C},
	Date-Added = {2014-08-01 22:44:12 +0000},
	Date-Modified = {2014-08-01 22:44:12 +0000},
	Journal = {Proceedingo of the Minnesota International Hydraulics Convention, Minneapolis, Minnesota},
	Language = {English},
	Pages = {321--333},
	Title = {Theoretical considerations on the motion of salt and fresh water},
	Year = {1953}}

@article{monismith_structure_2002,
	Abstract = {Abstract The structure of the salinity field in northern San Francisco Bay and how it is affected by freshwater flow are discussed. Two datasets are examined: the first is 23 years of daily salinity data taken by the U.S. Bureau of Reclamation along the axis of northern San Francisco Bay; the second is a set of salinity transects taken by the U.S. Geological Survey between 1988 and 1993. Central to this paper is a measure of salinity intrusion, X2: the distance from the Golden Gate Bridge to where the bottom salinity is 2 psu. Using X2 to scale distance, the authors find that for most flow conditions, the mean salinity distribution of the estuary is nearly self-similar with a salinity gradient in the center 70\% of the region between the Golden Gate and X2 that is proportional to X−12. Analysis of covariability of Q and X2 showed a characteristic timescale of adjustment of the salinity field of approximately 2 weeks. The steady-state response deduced from the X2 time series implies that X2 is proportional to riverflow to the 1/7 power. This relation, which differs from the standard 1/3 power dependence that is derived theoretically assuming constant exchange coefficients, shows that the upstream salt flux associated with gravitational circulation is more sensitive to the longitudinal salinity gradient than theory supposes. This is attributed to the strengthening of stratification caused by the stronger longitudinal salinity gradient that accompanies larger river flows.},
	Author = {Monismith, Stephen G. and Kimmerer, Wim and Burau, Jon R. and Stacey, Mark T.},
	Date-Added = {2014-08-01 22:44:12 +0000},
	Date-Modified = {2014-08-05 21:46:01 +0000},
	Doi = {10.1175/1520-0485(2002)032<3003:SAFIVO>2.0.CO;2},
	Issn = {0022-3670},
	Journal = {Journal of Physical Oceanography},
	Month = nov,
	Number = {11},
	Pages = {3003--3019},
	Title = {Structure and flow-Induced variability of the subtidal salinity field in northern San Francisco Bay},
	Url = {http://journals.ametsoc.org/doi/abs/10.1175/1520-0485(2002)032%3C3003:SAFIVO%3E2.0.CO%3B2},
	Urldate = {2014-07-29},
	Volume = {32},
	Year = {2002},
	Bdsk-Url-1 = {http://journals.ametsoc.org/doi/abs/10.1175/1520-0485(2002)032%3C3003:SAFIVO%3E2.0.CO%3B2},
	Bdsk-Url-2 = {http://dx.doi.org/10.1175/1520-0485(2002)032%3C3003:SAFIVO%3E2.0.CO;2}}

@article{lerczak_mechanisms_2006,
	Abstract = {Abstract The subtidal salt balance and the mechanisms driving the downgradient salt flux in the Hudson River estuary are investigated using measurements from a cross-channel mooring array of current meters, temperature and conductivity sensors, and cross-channel and along-estuary shipboard surveys obtained during the spring of 2002. Steady (subtidal) vertical shear dispersion, resulting from the estuarine exchange flow, was the dominant mechanism driving the downgradient salt flux, and varied by over an order of magnitude over the spring--neap cycle, with maximum values during neap tides and minimum values during spring tides. Corresponding longitudinal dispersion rates were as big as 2500 m2 s−1 during neap tides. The salinity intrusion was not in a steady balance during the study period. During spring tides, the oceanward advective salt flux resulting from the net outflow balanced the time rate of change of salt content landward of the study site, and salt was flushed out of the estuary. During neap tides, the landward steady shear dispersion salt flux exceeded the oceanward advective salt flux, and salt entered the estuary. Factor-of-4 variations in the salt content occurred at the spring--neap time scale and at the time scale of variations in the net outflow. On average, the salt flux resulting from tidal correlations between currents and salinity (tidal oscillatory salt flux) was an order of magnitude smaller than that resulting from steady shear dispersion. During neap tides, this flux was minimal (or slightly countergradient) and was due to correlations between tidal currents and vertical excursions of the halocline. During spring tides, the tidal oscillatory salt flux was driven primarily by oscillatory shear dispersion, with an associated longitudinal dispersion rate of about 130 m2 s−1.},
	Author = {Lerczak, James A. and Geyer, W. Rockwell and Chant, Robert J.},
	Date-Added = {2014-08-01 22:44:12 +0000},
	Date-Modified = {2014-08-05 21:45:31 +0000},
	Doi = {10.1175/JPO2959.1},
	Issn = {0022-3670},
	Journal = {Journal of Physical Oceanography},
	Keywords = {Antarctica, dynamics, Ice shelves},
	Month = dec,
	Number = {12},
	Pages = {2296--2311},
	Title = {Mechanisms driving the time-dependent salt flux in a partially stratified estuary},
	Url = {http://journals.ametsoc.org/doi/abs/10.1175/JPO2959.1},
	Urldate = {2014-07-30},
	Volume = {36},
	Year = {2006},
	Bdsk-Url-1 = {http://journals.ametsoc.org/doi/abs/10.1175/JPO2959.1},
	Bdsk-Url-2 = {http://dx.doi.org/10.1175/JPO2959.1}}

@article{hunkins_salt_1981,
	Abstract = {Abstract The seaward transport of salt by river discharge through an estuary is balanced under steady conditions by landward dispersion effected by various physical mixing processes. Observations of current and salinity in the lower Hudson estuary provide a basis for assessing the relative importance of these different dispersion processes. Wind effects were estimated from two moored current meter records of 1- and 2-months length. There was a significant but weak correlation between wind and currents. Three cross-sectional surveys each lasting 25 h provide estimates of salt dispersion by other processes. Current and salinity data from the surveys were decomposed into various temporal and spatial means and departures from these means. Covariances between the various quantities are interpreted in terms of physical dispersion processes. The largest contributor to salt dispersion in the Hudson is the steady shear of gravitational circulation. Steady shear dispersion varies by a factor of 5 between spring high-flow and summer low-flow conditions. Dispersion by tidally varying shear was much lower in magnitude. Correlation between sectionally averaged current and salinity yields a paradoxical negative dispersion which can be explained in terms of two documented estuary characteristics, the tendency of bottom tidal currents to lead upper layer currents in phase and the increased longitudinal salinity gradient near the surface.},
	Author = {Hunkins, Kenneth},
	Date-Added = {2014-08-01 22:44:12 +0000},
	Date-Modified = {2014-08-01 22:44:12 +0000},
	Doi = {10.1175/1520-0485(1981)011<0729:SDITHE>2.0.CO;2},
	Issn = {0022-3670},
	Journal = {Journal of Physical Oceanography},
	Month = may,
	Number = {5},
	Pages = {729--738},
	Title = {Salt Dispersion in the Hudson Estuary},
	Url = {http://journals.ametsoc.org/doi/abs/10.1175/1520-0485(1981)011%3C0729:SDITHE%3E2.0.CO%3B2},
	Urldate = {2014-07-30},
	Volume = {11},
	Year = {1981},
	Bdsk-Url-1 = {http://journals.ametsoc.org/doi/abs/10.1175/1520-0485(1981)011%3C0729:SDITHE%3E2.0.CO%3B2},
	Bdsk-Url-2 = {http://dx.doi.org/10.1175/1520-0485(1981)011%3C0729:SDITHE%3E2.0.CO;2}}

@article{hetland_idealized_2004,
	Abstract = {Abstract Classic models of estuarine circulation are reexamined using a three-dimensional, primitive equation numerical ocean model. The model is configured using an idealized estuary/shelf domain with rectangular cross section, constant vertical mixing, and steady riverine discharge. Tidal dispersion is neglected, so the analysis does apply to well-mixed estuaries and lagoons. Estuarine scales for the length of steady-state salt intrusion, vertical stratification, and estuarine exchange flow estimated from steady-state model results are found to have the same functional relationships to vertical mixing and riverine discharge as the classic analytic solutions. For example, for steady-state conditions, the stratification is found to be virtually independent of the strength of vertical mixing. The estuarine structure was controlled by the interior estuarine circulation, and not by limited exchange at the mouth. Thus, the numerical solutions were not ``overmixed,'' although the solutions showed a dependence on freshwater flux functionally similar to the overmixed solution. Estuarine adjustment time scales are also estimated from the simulations, and they are related to the steady-state estuarine scales. Two classes of nonsteady solutions are examined: the response to a step change in riverine discharge and estuarine response to changes in vertical mixing. Spring/neap tidal variations are examined by modulating the (spatially constant) vertical mixing with a fortnightly period. Unlike the steady solutions, there is a clear dependence of stratification on mixing rate in the time-dependent solutions. The simulations involving changes in riverine discharge show asymmetries between response to increasing and decreasing river flow that are attributed to quadratic bottom drag.},
	Author = {Hetland, Robert D. and Geyer, W. Rockwell},
	Date-Added = {2014-08-01 22:44:12 +0000},
	Date-Modified = {2014-08-01 22:44:12 +0000},
	Doi = {10.1175/JPO2646.1},
	Issn = {0022-3670},
	Journal = {Journal of Physical Oceanography},
	Month = dec,
	Number = {12},
	Pages = {2677--2691},
	Title = {An Idealized Study of the Structure of Long, Partially Mixed Estuaries*},
	Url = {http://journals.ametsoc.org/doi/full/10.1175/JPO2646.1},
	Urldate = {2014-07-30},
	Volume = {34},
	Year = {2004},
	Bdsk-Url-1 = {http://journals.ametsoc.org/doi/full/10.1175/JPO2646.1},
	Bdsk-Url-2 = {http://dx.doi.org/10.1175/JPO2646.1}}

@article{hayes_steelhead_2008,
	Abstract = {Abstract We monitored growth and life history pathways of juvenile steelhead Oncorhynchus mykiss and compared growth rates between the upper watershed and estuary in Scott Creek, a typical California coastal stream. Growth in the upper watershed was approximately linear from May to December for age-0 fish. For passive integrated transponder ({PIT}) tagged, age-1+ fish, growth transitioned to a cyclic pattern, peaking at 0.2\% per day during February-April, when maximum flows and temperatures of 7-12$\,^{\circ}$C occurred. Growth of {PIT}-tagged fish then slowed during August-September (0.01\% per day), when temperatures were 14-18$\,^{\circ}$C and flows were low. During each spring, smolts (mean fork length [{FL}] $\pm$ {SE} = 98.0 $\pm$ 1.2 mm) and fry migrated to the estuary; some fish remained there during summer-fall as low flows and waves resulted in seasonal sandbar formation, which created a warm lagoon and restricted access to the ocean. Growth in the estuary-lagoon was much higher (0.2-0.8\% per day at 15-24$\,^{\circ}$C). Our data suggest the existence of three juvenile life history pathways: Upper-watershed rearing, estuary-lagoon rearing, and combined upper-watershed and estuary-lagoon rearing. We present a model based upon the above data that reports size at age for each juvenile life history type. The majority of fish reaching typical steelhead ocean entry sizes (∼150-250 mm {FL}; age 0.8-3.0) were estuary-lagoon reared, which indicates a disproportionate contribution of this habitat type to survival of Scott Creek steelhead. In contrast, steelhead from higher latitudes rear in tributaries during summer, taking several years to attain ocean entry size.},
	Author = {Hayes, Sean A. and Bond, Morgan H. and Hanson, Chad V. and Freund, Ellen V. and Smith, Jerry J. and Anderson, Eric C. and Ammann, Arnold J. and MacFarlane, R. Bruce},
	Date-Added = {2014-08-01 22:44:12 +0000},
	Date-Modified = {2014-08-05 21:43:49 +0000},
	Doi = {10.1577/T07-043.1},
	Issn = {0002-8487},
	Journal = {Transactions of the American Fisheries Society},
	Number = {1},
	Pages = {114--128},
	Shorttitle = {Steelhead Growth in a Small Central California Watershed},
	Title = {Steelhead growth in a small Central California watershed: Upstream and estuarine rearing patterns},
	Url = {http://dx.doi.org/10.1577/T07-043.1},
	Urldate = {2014-07-21},
	Volume = {137},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1577/T07-043.1}}

@article{elder_dispersion_1959,
	Author = {Elder, J. W.},
	Date-Added = {2014-08-01 22:44:12 +0000},
	Date-Modified = {2014-08-01 22:44:12 +0000},
	Doi = {10.1017/S0022112059000374},
	Journal = {Journal of Fluid Mechanics},
	Number = {04},
	Pages = {544--560},
	Title = {The dispersion of marked fluid in turbulent shear flow},
	Volume = {5},
	Year = {1959},
	Bdsk-Url-1 = {http://dx.doi.org/10.1017/S0022112059000374}}

@article{bond_marine_2008,
	Abstract = {To investigate the role that estuaries play in the survival of steelhead, Oncorhynchus mykiss, we compared juvenile size at ocean entry with back-calculated measures of size at ocean entry for returning adults in Scott Creek, a representative California coastal stream. During the annual spring emigration, the largest smolts ({\textgreater}150 mm fork length ({FL})) move directly to sea, while some smaller smolts remain in the estuary until sandbar formation creates a closed freshwater lagoon. High growth rates in the estuary throughout the summer result in a near doubling of fork length from the time of estuary entry (mean {FL} of spring migrants = 102.2 mm; mean {FL} of fall lagoon resident = 195.9 mm). Analysis of the scale morphology of returning adult steelhead indicates that there is strong size-dependent mortality at sea, with estuary-reared steelhead showing a large survival advantage, comprising between 87\% and 95.5\% (based on tag returns and scale analysis, respectively) of the returning adult population despite be..., Afin d'estimer le r{\^o}le jou{\'e} par les estuaires dans la survie de la truite arc-en-ciel anadrome, Oncorhynchus mykiss, nous avons compar{\'e} la taille des jeunes au moment de leur arriv{\'e}e en mer avec les mesures obtenues par r{\'e}trocalcul de la taille des adultes qui reviennent de l'oc{\'e}an au moment de leur propre entr{\'e}e en mer dans Scott Creek, un cours d'eau c{\^o}tier typique de Californie. Durant l'{\'e}migration annuelle du printemps, les saumoneaux les plus grands ({\textgreater}150 mm de longueur {\`a} la fourche ({FL})) se rendent directement en mer, alors que certains des saumoneaux plus petits demeurent dans l'estuaire jusqu'{\`a} ce que la formation de barres cr{\'e}e une lagune ferm{\'e}e d'eau douce. De forts taux de croissance dans la lagune au cours de l'{\'e}t{\'e} produisent un doublement de la longueur {\`a} la fourche par rapport au moment de l'arriv{\'e}e dans l'estuaire ({FL} moyenne des migrateurs du printemps = 102,2 mm; {FL} moyenne des r{\'e}sidents de la lagune {\`a} l'automne = 195,9 mm). L'analyse de la morphologie des {\'e}cailles des truites arc-en-ciel...},
	Author = {Bond, Morgan H. and Hayes, Sean A. and Hanson, Chad V. and MacFarlane, R. Bruce},
	Date-Added = {2014-08-01 22:44:12 +0000},
	Date-Modified = {2014-08-01 22:44:12 +0000},
	Doi = {10.1139/F08-131},
	Issn = {0706-652X},
	Journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	Month = sep,
	Number = {10},
	Pages = {2242--2252},
	Title = {Marine survival of steelhead (Oncorhynchus mykiss) enhanced by a seasonally closed estuary},
	Url = {http://www.nrcresearchpress.com/doi/abs/10.1139/F08-131},
	Urldate = {2014-07-21},
	Volume = {65},
	Year = {2008},
	Bdsk-Url-1 = {http://www.nrcresearchpress.com/doi/abs/10.1139/F08-131},
	Bdsk-Url-2 = {http://dx.doi.org/10.1139/F08-131}}