Mark T. Stacey

Measurements of Reynolds stress profiles in unstratified tidal flow

In this paper we present a method for measuring profiles of turbulence quantities using a broadband acoustic doppler current profiler (ADCP). The method follows previous work on the continental shelf and extends the analysis to develop estimates of the errors associated with the estimation methods. ADCP data was collected in an unstratified channel and the results of the analysis are compared to theory. This comparison shows that the method provides an estimate of the Reynolds stresses, which is unbiased by Doppler noise, and an estimate of the turbulent kinetic energy (TKE) which is biased by an amount proportional to the Doppler noise. The noise in each of these quantities as well as the bias in the TKE match well with the theoretical values produced by the error analysis. The quantification of profiles of Reynolds stresses simultaneous with the measurement of mean velocity profiles allows for extensive analysis of the turbulence of the flow. In this paper, we examine the relation between the turbulence and the mean flow through the calculation of u * , the friction velocity, and C d , the coefficient of drag. Finally, we calculate quantities of particular interest in turbulence modeling and analysis, the characteristic lengthscales, including a lengthscale which represents the stream-wise scale of the eddies which dominate the Reynolds stresses.

Structure and Flow-Induced Variability of the Subtidal Salinity Field in Northern San Francisco Bay

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 ...

Creation of residual flows in a partially stratified estuary

The creation of residual flows in estuaries is examined using acoustic Doppler current profiler data sets from northern San Francisco Bay. The data sets are analyzed using principal component analysis to examine the temporal variability of the flows which create the residual circulation. It is seen that in this periodically and partially stratified estuary the residual flows are created through a series of pulses with strong variability at the 24-hour timescale, through the interaction of shear, stratification and mixing. This interaction is captured through the use of a dimensionless number, the horizontal Richardson number (Rix), which is developed to examine the local balance between the stratifying and destratifying forces at the tidal timescale. It is seen that Rix is a valuable parameter in predicting the onset of the residual-creating events, with a threshold value of ≈3 on ebb tides. This critical value is argued to be a threshold, above which the stratification and shear flow create a feedback effect, each further intensifying the other. This feedback results in a highly variable exchange flow which creates the estuarine residual in intermittent pulses rather than as a steady flow. Although typically attributed to baroclinic forcing, an argument is made that these pulses of residual-creating exchange flow could be created by barotropic forcing in the presence of variable stratification which is asymmetric between flood and ebb tides. This result poses a great challenge for turbulence modeling, as the timing and magnitude of stratification and shear must be correctly simulated on the tidal timescale in order to reproduce the effects seen in the data sets presented.

Projected Evolution of California's San Francisco Bay-Delta-River System in a Century of Climate Change

BACKGROUND Accumulating evidence shows that the planet is warming as a response to human emissions of greenhouse gases. Strategies of adaptation to climate change will require quantitative projections of how altered regional patterns of temperature, precipitation and sea level could cascade to provoke local impacts such as modified water supplies, increasing risks of coastal flooding, and growing challenges to sustainability of native species. METHODOLOGY/PRINCIPAL FINDINGS We linked a series of models to investigate responses of Californias San Francisco Estuary-Watershed (SFEW) system to two contrasting scenarios of climate change. Model outputs for scenarios of fast and moderate warming are presented as 2010-2099 projections of nine indicators of changing climate, hydrology and habitat quality. Trends of these indicators measure rates of: increasing air and water temperatures, salinity and sea level; decreasing precipitation, runoff, snowmelt contribution to runoff, and suspended sediment concentrations; and increasing frequency of extreme environmental conditions such as water temperatures and sea level beyond the ranges of historical observations. CONCLUSIONS/SIGNIFICANCE Most of these environmental indicators change substantially over the 21(st) century, and many would present challenges to natural and managed systems. Adaptations to these changes will require flexible planning to cope with growing risks to humans and the challenges of meeting demands for fresh water and sustaining native biota. Programs of ecosystem rehabilitation and biodiversity conservation in coastal landscapes will be most likely to meet their objectives if they are designed from considerations that include: (1) an integrated perspective that river-estuary systems are influenced by effects of climate change operating on both watersheds and oceans; (2) varying sensitivity among environmental indicators to the uncertainty of future climates; (3) inevitability of biological community changes as responses to cumulative effects of climate change and other drivers of habitat transformations; and (4) anticipation and adaptation to the growing probability of ecosystem regime shifts.

The Scaling and Structure of the Estuarine Bottom Boundary Layer

Abstract A two-week dataset from a partially and periodically stratified estuary quantifies variability in the turbulence across the tidal and spring–neap time scales. These observations have been fit with a two-parameter model of the Reynolds stress profile, which produces estimates of the time variation of the bottom boundary layer height and the friction velocity. Conditions at the top of the bottom boundary layer indicate that the dynamics governing the development of the estuarine bottom boundary layer are different on ebb tides than on flood tides. The asymmetry in the flow is explained by consideration of the strain-induced buoyancy flux, which is stabilizing on ebb tides and destabilizing on flood tides. Based on these observations, a scaling approach to estimating estuarine bottom boundary layer parameters (height and friction velocity) is presented, which includes a modified Monin–Obukhov length scale to account for the horizontal buoyancy flux created by the sheared advection. Comparison with t...

Biological communities in San Francisco Bay track large-scale climate forcing over the North Pacific.

Long-term observations show that fish and plankton populations in the ocean fluctuate in synchrony with large-scale climate patterns, but similar evidence is lacking for estuaries because of shorter observational records. Marine fish and invertebrates have been sampled in San Francisco Bay since 1980 and exhibit large, unexplained population changes including record-high abundances of common species after 1999. Our analysis shows that populations of demersal fish, crabs and shrimp covary with the Pacific Decadal Oscillation (PDO) and North Pacific Gyre Oscillation (NPGO), both of which reversed signs in 1999. A time series model forced by the atmospheric driver of NPGO accounts for two-thirds of the variability in the first principal component of species abundances, and generalized linear models forced by PDO and NPGO account for most of the annual variability of individual species. We infer that synchronous shifts in climate patterns and community variability in San Francisco Bay are related to changes in oceanic wind forcing that modify coastal currents, upwelling intensity, surface temperature, and their influence on recruitment of marine species that utilize estuaries as nursery habitat. Ecological forecasts of estuarine responses to climate change must therefore consider how altered patterns of atmospheric forcing across ocean basins influence coastal oceanography as well as watershed hydrology.

Turbulent characteristics of a shallow wall-bounded plane jet: experimental implications for river mouth hydrodynamics

Jets arising from rivers, streams and tidal flows entering still waters differ from most experimental studies of jets both in aspect ratio and in the presence of a solid bottom boundary and an upper free surface. Despite these differences, the applicability of experimental jet studies to these systems remains largely untested by either field or realistically scaled experimental studies. Here we present experimental results for a wall-bounded plane jet scaled to jets created by flow discharging into floodplain lakes. A characteristic feature of both our prototype and experimental jets is the presence of large-scale meandering turbulent structures that span the width of the jets. In our experimental jets, we observe self-similarity in the distribution of mean streamwise velocities by a distance of six channel widths downstream of the jet outlet. After a distance of nine channel widths the velocity decay and the spreading rates largely agree with prior experimental results for plane jets. The magnitudes and distributions of the cross-stream velocity and lateral shear stresses approach self-preserving conditions in the upper half of the flow, but decrease in magnitude, and deviate from self-preserving distributions with proximity to the bed. The presence of the meandering structure has little influence on the mean structure of the jet, but dominates the jet turbulence. A comparison of turbulence analysed at time scales both greater than and less than the period of the meandering structure indicates that these structures increase turbulence intensities by 3–5 times, and produce lateral shear stresses and momentum diffusivities that are one and two orders of magnitude greater, respectively, than turbulence generated by bed friction alone.

On the effects of topography on wind and the generation of currents in a large multi-basin lake

AbstractThe wind field over a lake surface is the key element in driving the exchange of momentum and energy at the free surface. It is rarely uniform, having a considerable degree of spatial variability, both on a synoptic and a local scale. Topographic features are one of the most common contributors to this variability. The aerodynamic effects of topography on the windfield, and its influence on the circulation patterns and interbasin exchange rates in a large multi-basin lake are documented. The complex landscape that surrounds this lake is dominated by the presence of a mountain peak rising over 900 m above the lake level. The circulation patterns in those basins of the lake located in the leeward side of the mountain reflect the spatial patterns of the wind field generated by the surrounding topography. The spatial variations in the wind field are shown to significantly alter the residence times of each basin and the exchange rates between basins, isolating one from the other two basins of the lake. The inter-basin exchange rates determined with wind field variability are consistent with annual contaminant loadings estimated for each of the three basins, which suggests a close link between chemical and hydrodynamic behavior.

The Influence of Oceanic Swell on Flows Over an Estuarine Intertidal Mudflat in San Francisco Bay

In this study, we examine the role that remotely forced ocean waves play in the hydrodynamics of an intertidal, estuarine mudflat. The observations indicate that long-period (10–20 s) ocean waves are a potentially important source of near-bed energy and shear stress in this environment. Over a two-week period in February 2001, we deployed an autonomous SonTek Hydra system on a mudflat in Central San Francisco Bay, and measured velocity and sediment concentration approximately 10 cm from the bed using an acoustic Doppler velocimeter (ADV) and an optical backscatter sensor (OBS). The experiment continued through wet (high tide) and dry (low tide) periods over an entire spring–neap cycle, and thus included the variation of near-bed velocity over a range of timescales. Results show that during large ebb tides, tidally forced flows dominate the near-bed dynamics during calm conditions. Wind waves dominate whenever the wind direction exposes the mudflat to wind coming off the bay (from the south and southwest), as occurs during winter storms. During periods when tidal forcing is limited and wind waves are small, remotely forced ocean swells become an important energy source. These motions appear in the burst samples at frequencies between 0.1 and 0.04 Hz and their energy correlates well ðq > 0:8Þ with ocean swell measured from a buoy offshore of San Francisco. Spectral analysis of data shows that the average energy of ocean waves per tide varied between 2 and 15% of total energy load. Moreover, extreme values in the distribution of ocean waves bring episodic bursts of greater energy onto the estuarine mudflat, which may influence local suspension of sediments. 2003 Elsevier Ltd. All rights reserved.

Intradaily Variability of Water Quality in a Shallow Tidal Lagoon: Mechanisms and Implications

Although surface water quality and its underlying processes vary over time scales ranging from seconds to decades, they have historically been studied at the lower (weekly to interannual) frequencies. The aim of this study was to investigate intradaily variability of three water quality parameters in a small freshwater tidal lagoon (Mildred Island, California). High frequency time series of specific conductivity, water temperature, and chlorophylla at two locations within the habitat were analyzed in conjunction with supporting hydrodynamic, meteorological, biological, and spatial mapping data. All three constituents exhibited large amplitude intradaily (e.g., semidiurnal tidal and diurnal) oscillations, and periodicity varied across constituents, space, and time. Like other tidal embayments, this habitat is influenced by several processes with distinct periodicities including physical controls, such as tides, solar radiation, and wind, and biological controls, such as photosynthesis, growth, and grazing. A scaling approach was developed to estimate individual process contributions to the observed variability. Scaling results were generally consistent with observations and together with detailed examination of time series and time derivatives, revealed specific mechanisms underlying the observed periodicities, including interactions between the tidal variability, heating, wind, and biology. The implications for monitoring were illustrated through subsampling of the data set. This exercise demonstrated how quantities needed by scientists and managers (e.g., mean or extreme concentrations) may be misrepresented by low frequency data and how short-duration high frequency measurements can aid in the design and interpretation of temporally coarser sampling programs. The dispersive export of chlorophylla from the habitat exhibited a fortnightly variability corresponding to the modulation of semidiurnal tidal currents with the diurnal cycle of phytoplankton variability, demonstrating how high frequency interactions can govern long-term trends. Process identification, as through the scaling analysis here, can help us anticipate changes in system behavior and adapt our own interactions with the system.