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Temporal Variations of Vertical Mixing Across a Coastal Plain Estuary

Permanent Link: http://ufdc.ufl.edu/UFE0045216/00001

Material Information

Title: Temporal Variations of Vertical Mixing Across a Coastal Plain Estuary
Physical Description: 1 online resource (124 p.)
Language: english
Creator: Arnott, Kimberly Dawn
Publisher: University of Florida
Place of Publication: Gainesville, Fla.
Publication Date: 2013

Subjects

Subjects / Keywords: dissipation -- estuary -- mixing -- stratification -- turbulence
Civil and Coastal Engineering -- Dissertations, Academic -- UF
Genre: Coastal and Oceanographic Engineering thesis, Ph.D.
bibliography   ( marcgt )
theses   ( marcgt )
government publication (state, provincial, terriorial, dependent)   ( marcgt )
born-digital   ( sobekcm )
Electronic Thesis or Dissertation

Notes

Abstract: An experiment in the James River was carried out to investigate the temporal variability of TKE dissipation and vertical mixing across an estuary. Time series of dissipation exposed large values during greater floods, with larger values during spring than neap tide. In the channel, the largest values were near-bottom and surface, but were focused near-surface over the channel slope.While the bottom-generated dissipation in the channel was an anticipated finding, a novel discovery was displayed at the surface. Statistical analyses suggested that the surface dissipation was generated by vertical gradients in lateral velocities near-surface, which developed from lateral circulation. On a smaller time scale, a 12 hr spring tide survey displayed large vertical mixing results near-bottom during flood. Ebb revealed large mixing near-bottom and surface at two locations across the estuary. The near-surface mixing developed from the combined influences of a subsurface velocity jet within the pycnocline and lateral flows moving in opposing directions, similar to the near-surface TKE findings. These results suggested that not only does vertical mixing develop from bottom-generated turbulence, but it can also arise from vertical gradients in velocity near-surface. This result poses the need to reexamine well-accepted theory behind estuarine circulation modeling.  The relative influence of mixing asymmetries on the subtidal momentum balance was compared to that from lateral advection. During neap conditions, the flow induced by mixing asymmetry augmented the gravitational circulation at depth in the channel, similar to one-dimensional theory.During spring conditions, the residual flow was laterally sheared with landward flow over the south shoal and seaward flow throughout most of the channel and provided a distribution that compared favorably with cross-estuary section analytical model results. An examination of depth-averaged subtidal momentum balance terms contrasted the relative size between laterally advection and Coriolis during weakly stratified conditions over the channel slope. In the channel, asymmetric mixing competed with lateral advection. During stratified conditions, discrepancies amongst lateral advection and other terms suggested the other advection terms likely influenced the balance. Lastly, anon-dimensional number analysis provided evidence that lateral advection,Coriolis acceleration, and mixing asymmetries are, indeed, influential in the subtidal dynamics.
General Note: In the series University of Florida Digital Collections.
General Note: Includes vita.
Bibliography: Includes bibliographical references.
Source of Description: Description based on online resource; title from PDF title page.
Source of Description: This bibliographic record is available under the Creative Commons CC0 public domain dedication. The University of Florida Libraries, as creator of this bibliographic record, has waived all rights to it worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
Statement of Responsibility: by Kimberly Dawn Arnott.
Thesis: Thesis (Ph.D.)--University of Florida, 2013.
Local: Adviser: Valle-Levinson, Arnoldo.

Record Information

Source Institution: UFRGP
Rights Management: Applicable rights reserved.
Classification: lcc - LD1780 2013
System ID: UFE0045216:00001

Permanent Link: http://ufdc.ufl.edu/UFE0045216/00001

Material Information

Title: Temporal Variations of Vertical Mixing Across a Coastal Plain Estuary
Physical Description: 1 online resource (124 p.)
Language: english
Creator: Arnott, Kimberly Dawn
Publisher: University of Florida
Place of Publication: Gainesville, Fla.
Publication Date: 2013

Subjects

Subjects / Keywords: dissipation -- estuary -- mixing -- stratification -- turbulence
Civil and Coastal Engineering -- Dissertations, Academic -- UF
Genre: Coastal and Oceanographic Engineering thesis, Ph.D.
bibliography   ( marcgt )
theses   ( marcgt )
government publication (state, provincial, terriorial, dependent)   ( marcgt )
born-digital   ( sobekcm )
Electronic Thesis or Dissertation

Notes

Abstract: An experiment in the James River was carried out to investigate the temporal variability of TKE dissipation and vertical mixing across an estuary. Time series of dissipation exposed large values during greater floods, with larger values during spring than neap tide. In the channel, the largest values were near-bottom and surface, but were focused near-surface over the channel slope.While the bottom-generated dissipation in the channel was an anticipated finding, a novel discovery was displayed at the surface. Statistical analyses suggested that the surface dissipation was generated by vertical gradients in lateral velocities near-surface, which developed from lateral circulation. On a smaller time scale, a 12 hr spring tide survey displayed large vertical mixing results near-bottom during flood. Ebb revealed large mixing near-bottom and surface at two locations across the estuary. The near-surface mixing developed from the combined influences of a subsurface velocity jet within the pycnocline and lateral flows moving in opposing directions, similar to the near-surface TKE findings. These results suggested that not only does vertical mixing develop from bottom-generated turbulence, but it can also arise from vertical gradients in velocity near-surface. This result poses the need to reexamine well-accepted theory behind estuarine circulation modeling.  The relative influence of mixing asymmetries on the subtidal momentum balance was compared to that from lateral advection. During neap conditions, the flow induced by mixing asymmetry augmented the gravitational circulation at depth in the channel, similar to one-dimensional theory.During spring conditions, the residual flow was laterally sheared with landward flow over the south shoal and seaward flow throughout most of the channel and provided a distribution that compared favorably with cross-estuary section analytical model results. An examination of depth-averaged subtidal momentum balance terms contrasted the relative size between laterally advection and Coriolis during weakly stratified conditions over the channel slope. In the channel, asymmetric mixing competed with lateral advection. During stratified conditions, discrepancies amongst lateral advection and other terms suggested the other advection terms likely influenced the balance. Lastly, anon-dimensional number analysis provided evidence that lateral advection,Coriolis acceleration, and mixing asymmetries are, indeed, influential in the subtidal dynamics.
General Note: In the series University of Florida Digital Collections.
General Note: Includes vita.
Bibliography: Includes bibliographical references.
Source of Description: Description based on online resource; title from PDF title page.
Source of Description: This bibliographic record is available under the Creative Commons CC0 public domain dedication. The University of Florida Libraries, as creator of this bibliographic record, has waived all rights to it worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
Statement of Responsibility: by Kimberly Dawn Arnott.
Thesis: Thesis (Ph.D.)--University of Florida, 2013.
Local: Adviser: Valle-Levinson, Arnoldo.

Record Information

Source Institution: UFRGP
Rights Management: Applicable rights reserved.
Classification: lcc - LD1780 2013
System ID: UFE0045216:00001


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1 TEMPORAL VARIATIONS OF VERTICAL MIXING ACROSS A COASTAL PLAIN ESTUARY By KIMBERLY DAWN ARNOTT A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2013

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2 2013 Kimberly Dawn Arnott

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3 To my Mother and Father

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4 ACKNOWLEDGMENTS I would like to thank my advisor, Arnoldo Valle Levinson, for all of his guidance and support while pursuing both my M.S. and Ph.D. He has the wonderful ability to intrigue and inspire students, as I have seen with my own personal experience and with other s after me. He is the reason I love research and has a lot to do with why I came back to school. I also want to acknowledge his patience and availability, which are two things I am very grateful for. I would also like to thank Alex Souza for introducing me to the structure function and for providing helpful suggestions for my research at conferences. Additionally, I would like to ents, for sharing another technique to c alculate dissipation and for taking the time to hel p me. Input from these two greatly helped my progress in research. I would like to thank my committee, Dr. Donald Slinn, Dr. Lawrence Ukieley and Dr. Robert Thieke for their input during my qualifying exams and for taking the time to listen and give commen ts about my research. Thanks to Arnoldo, Bob Chant, Ming Li and everyone involved in collecting such a comprehensive data set. I could not have improved my oral Parra, who have given me constructive criticism a nd comments that have helped me improve along the way. Lastly, I would like to give thanks to Amy Waterhouse and Chloe Winant, who helped and supported me w ith my very first talk in Rome.

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5 TABLE OF CONTENTS page ACKNOWLEDGMENTS ................................ ................................ ................................ .. 4 LIST OF FIGURES ................................ ................................ ................................ .......... 7 LIST OF ABBREV IATIONS ................................ ................................ ............................. 9 ABSTRACT ................................ ................................ ................................ ................... 11 CHAPTER 1 INTRODUCTION ................................ ................................ ................................ .... 13 2 TEMPORAL VARIABILITY OF TKE DISSIPATION FROM CHANNEL TO CHANNEL SLOPE ACROSS A C OASTAL PLAIN ESTUARY ............................... 17 Synopsis ................................ ................................ ................................ ................. 17 Background ................................ ................................ ................................ ............. 18 Methodology ................................ ................................ ................................ ........... 19 Data Collection ................................ ................................ ................................ 20 Data Process ing ................................ ................................ ............................... 21 Results ................................ ................................ ................................ .................... 25 Hydrographic and Meteorological Variability ................................ .................... 26 Neap/ Spring Snapshots of TKE Dissipation ................................ .................... 27 Spectral Analysis ................................ ................................ .............................. 31 Empirical Orthogonal Function Analysis ................................ ........................... 32 Coherence Analysis ................................ ................................ ......................... 33 Discussion ................................ ................................ ................................ .............. 34 Summary ................................ ................................ ................................ ................ 38 3 VARIABILITY OF VERTICAL MIXING ACROSS A COASTAL PLAIN ESTUARY .. 48 Synopsis ................................ ................................ ................................ ................. 48 Background ................................ ................................ ................................ ............. 48 Methods ................................ ................................ ................................ .................. 50 Data Collection ................................ ................................ ................................ 50 Mixing Theory ................................ ................................ ................................ ... 51 Data Processing ................................ ................................ ............................... 54 Results ................................ ................................ ................................ .................... 55 Spring Tide: Late Flood ................................ ................................ .................... 56 Spring Tide: Late Ebb ................................ ................................ ....................... 57 Spring Tide: Lateral Circulation ................................ ................................ ........ 58 Spring Tide: Timescale Analysis ................................ ................................ ...... 59 Neap Tide: Late Ebb ................................ ................................ ........................ 61 Neap Tide: Maximum Flood ................................ ................................ ............. 62

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6 Neap Tide: Lateral Circulation ................................ ................................ .......... 63 Stratification Versus Shear Analysis ................................ ................................ 63 Discussion ................................ ................................ ................................ .............. 64 Summary ................................ ................................ ................................ ................ 67 4 INFLUENCE OF TIDAL MIXING ASYMMETRIES ON RESIDUAL EXCHANGE FLOW IN THE JAMES RIVER ESTUARY ................................ .............................. 81 Synopsis ................................ ................................ ................................ ................. 81 Background ................................ ................................ ................................ ............. 81 Background on Mixing Asymmetries ................................ ................................ ....... 82 Methods ................................ ................................ ................................ .................. 84 Data Collection ................................ ................................ ................................ 85 Data Processing ................................ ................................ ............................... 85 Results ................................ ................................ ................................ .................... 91 Tidal Variability of Vertical Mixing ................................ ................................ ..... 92 Stratification ................................ ................................ ................................ ...... 93 Residual Flows ................................ ................................ ................................ 93 Vertical Mixing ................................ ................................ ................................ .. 95 Mixing Asymmetry Induced Flow Observations and Model Comparison ......... 97 Advection and Mixing Asymmetry Comparison ................................ ................ 98 Depth averaged Subtidal Momentum Terms ................................ .................... 98 Non dimensional Analysis ................................ ................................ .............. 100 Discussion ................................ ................................ ................................ ............ 103 Summary ................................ ................................ ................................ .............. 105 5 CONCLUSIONS ................................ ................................ ................................ ... 116 Summary ................................ ................................ ................................ .............. 116 Near surface TKE Dissipation ................................ ................................ ........ 117 Near surface Vertical Mixing ................................ ................................ .......... 117 Tidal Asymmetries in V ertical Mixing and Subtidal Dynamics ........................ 118 Implications of Findings ................................ ................................ ........................ 118 LIST OF REFERENCES ................................ ................................ ............................. 120 BIOGRAPH ICAL SKETCH ................................ ................................ .......................... 124

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7 LIST OF FIGURES Figure page 2 1 Map and cross section of study site ................................ ................................ .. 3 9 2 2 Hydrographic and meterologis observations ................................ ..................... 40 2 3 Nea p tide snapshot : along and across channel velocity and velocity shears .... 41 2 4 Neap tide snapshot: potential energy anomaly, near bottom density anomaly, and TKE dissipation. ................................ ................................ ........................... 42 2 5 Spring tide snapshot: along and across channel velocity and velocity shears .. 43 2 6 Spring tide snapshot: potential energy anomaly, near bottom density anomaly, and TKE dissipation ................................ ................................ ............ 44 2 7 Spectra of velocity,velocity shears and TKE dissipation ................................ ..... 45 2 8 EOF results: spatial structure weighted amplitude, and spectrum of weighted amplitude. ................................ ................................ ................................ ........... 46 2 9 C oherency results between w eighted amplitude Mode 1 and hydrography and velocity shear in channel and channel slope ................................ ............... 47 3 1 James River plan view of study site and cross section ................................ ....... 68 3 2 Neap conditions Station 1 ................................ ................................ ................... 75 3 3 Neap conditions Station 2 ................................ ................................ ................... 76 3 4 Neap conditions Station 3 ................................ ................................ ................... 77 3 5 Neap conditions Station 4 ................................ ................................ ................... 78 3 6 D iff erential advection forcing and Coriolis forcing. ................................ .............. 79 3 7 Spring conditions Station 1 ................................ ................................ ................. 69 3 8 Spring conditions Station 2 ................................ ................................ ................. 70 3 9 Spring conditions Station 3 ................................ ................................ ................. 71 3 10 Spring conditions Station 4 ................................ ................................ ................. 72 3 11 Differential advection forcing and Coriolis forcing ................................ ............... 73 3 12 Four timescales characteristic of lateral circulation proces ses .......................... 74

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8 3 13 Richardson numbers, R i for Station 2 and 3 during neap and spring tide conditions ................................ ................................ ................................ .......... 80 4 1 James River plan view of study site and cross section ................................ .... 106 4 2 Neap and spring stress divergences at Stations 1 4 ................................ ........ 107 4 3 Tidally averaged density anomaly and buoyancy frequency. ........................... 108 4 4 Along and across channel residual exchange flow ................................ .......... 109 4 5 Tidally averaged vertical eddy viscosity and vertical shear. ............................. 110 4 6 T id ally averaged stress divergence, mean and fluctuating component of tidally averaged stress divergence ................................ ................................ ... 111 4 7 Residual along channel exchange flo w induced by mixing asymmetries ......... 112 4 8 Neap and spring fluctuating component of tidally averaged stress divergence and tidally averaged along channel advective acceleration .............................. 113 4 9 Subtidal momentum balanc e for neap and spring.. ................................ .......... 114

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9 LIST OF ABBREVIATIONS y Across channel x A long channel B Buoyancy flux of TKE N Buoyancy frequency C v 2 C onstant taken to be 2.1 in meteorology f Coriolis parameter h D epth of the water column m D epth mean water density Dissipation of TKE r Distance, analogous to turbulent eddy length scale F luctuating salinity R f Flux Richardson number g G ravity C Integration constant K inematic viscosity U i M ean flow m ef Mixing efficiency L o Ozmidov length scale P otential energy anomaly p P ressure P Production of TKE o R eference density o R eference water density Reynolds averaged across channel velocity

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10 Reynolds averaged along channel velocity Reynolds averaged vertical velocity Reynolds stress R i Richardson number rms Root mean square S aline expansivity 2 S quared velocity scale D(z,r) Structure function T emperature; T hermal expansivity d Thorpe displacements L t Thorpe length scale T Transport of TKE T urbulent fluctuating velocities u i T urbulent fluctuating velocity TKE Turbulent Kinetic Energy Pr t Turbulent Prandtl number w V ertical K Z Vertical eddy diffusivity A Z Vertical eddy viscosity W ater density

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11 Abstract of Dissertation Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy TEMPORAL VARIATIONS OF VERTICAL MIXING ACROSS A COASTAL PLAIN ESTUARY By Kimberly Dawn Arnott May 2013 Chair: Arnoldo Valle Levinson Major: Coastal and Oceanographic Engineering An experiment in the James River was carried out to investigate the temporal variability of TKE dissipation and vertical mixing across an estuary. Time series of dissipation exposed large values during greater floods, with larger values during spring than neap tide. In the channel, the largest value s were near bottom and surface, but were focused near surface over the channel slope. While the bottom generated dissipation in the channel was an anticipated finding, a novel discovery was displayed at the surface. Statistical analyses suggested that the surface dissipation was generate d by vertical gradients in lateral velocities near surface, which developed from lateral circulation. On a smaller time scale, a 12 hr spring tide survey displayed large vertical mixing results near bottom during flood Ebb revealed large mixing near botto m and surface at two locations across the estuary. The near surface mixing developed from the combined influences of a subsurface velocity je t within the pycnocline and lateral flows moving in opposing directions, similar to the near surface TKE findings These results suggested that not only does vertical mixing develop from bottom generated turbulence, but it can also arise from vertical gradients in velocity near surface. This result poses the need to reexamine well accepted theory behind estuarine circu lation

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12 modeling. T he relative influence of mixing asymmetries on the subtidal momentum balance was compared to that from lateral advection. During neap conditions, the flow induced by mixing asymmetry augmented the gravitational circulation at depth in th e channel, similar to one dimensional theory. During spring conditions, the residual flow was laterally sheared with landward flow over the south shoal and seaward flow throughout most of the channel and provided a distribution that compared favorably with cross estuary section analytical model results. An examination of depth averaged subtidal momentum balance terms contrasted the relative size b etween laterally advection and Coriolis during weakly stratified conditions over the channel slope In the channel, asymmetric mixing competed with lateral advection. D uring stratified conditions, discrepancies amongst lateral advection and other terms suggested the other advection terms likely influenced the balance. Lastly, a non dimensional number analysis provided evidence that lateral advection, Coriolis acceleration, and mixing as ymmetries are, indeed, influential in the subtidal dynamics.

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13 CHAPTER 1 INTRODUCTION Understanding the spatiotemporal variability of turbulent mixing in coastal environments is the focus of several studies because of its direct influence on the transport of nutrients, sediments, and pollutants. The transport of these scalars can be described in numerical models, however vertical mixing is often parameterized with turbulence closures that need improvement in estuarin e environments because of their complexity. A better understanding of turbulent mixing will indeed lead to better implementations of closures in models. Turbulent kinetic energy (TKE) dissipation, is a value often used to estimate vertical mixing and ca n be measured readily. Given that stratification can suppress turbulent energy, the density structure of a water column is an important factor in the TKE balance. The degree of stratification can vary widely among estuaries, but for this investigation, the focus will be on a partially mixed water column. Estuaries with this stratification scheme are characterized by moderate to strong tidal forcing, weak to moderate river discharge and feature a we ak pycnocline (Valle Levinson, 2010). Simpson (1990) has fo und that stratification can be periodic in nature, resulting in a stratified water column during ebb and the destruction of stratification during flood. This tidal straining phenomenon arises from interactions between baroclinic (residual) and tidal flows with the water column structure During flood, when dense ocean water is inundating an estuary, residual flow enhances the tidal flow, resulting in large current velocities and the breakdown of stratification. Alternatively during ebb, currents flow out of the estuary and residual flow enhances stratification, weakens flows and suppresses turbulence. Less dense water is layered

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14 atop denser ocean water and differential advection in salinity creates stratification characterized by horizontal isopycnals (Nepf and Geyer, 1996). Rippeth et al. (2001), Stacey et al. (1999), and Peters (1997) have proposed that the vertical structure of turbulence in a coastal plain estuary is dominated by bottom generated turbulence. Rippeth et al. (2001) investigated the fortnightly variability of the vertical structure of and found that during neap tide conditions, maximum values were confined to the near bottom region by stratification and peaked during the largest tidal velocities. During spring tide conditions, large values of were observed to extend the water column during the well mixed flood phases and were again confined to the lower half of the water column during the more stratified ebb phases. Stacey et al. (1999) and Peters (1997) investigated the vertical structure of vertical eddy viscosity, A z and found that it was confined to near bottom during stratified conditions. The measurements of Rippeth et al. (2001), Stacey et al. (1999), and Peters (1997) were all obtained at one point in the channel of a coastal plain estuary. Presentl y, no studies examine the structure of and A z across an estuary. Geyer et al. ( 2000 ) investigated the dynamics of a partially mixed estuary and found that estuarine circulation was found to only depend on the magnitude of bottom turbulence. This finding lead to the proposition that estuarine circulation could be modeled without knowledge of the vertical eddy viscosity. The research in this manuscript aims to address any variability from accepted theory in c ontext of the findings of Geyer et al. (2000) and examine the implication of it. The subtidal momentum balance was determined by Pritchard (1956) to include baroclinic pressure gradient and friction, resulting in a vertically sheared two layer flow. Dense ocean water intrudes into the estuary in the lower layer, while less dense water

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15 exits the estuary in the upper layer. Recent studies have proposed that other terms in the subtidal momentum balance are significant and should be included. Lerczak and Geyer (2004) showed the influence of laterally induced along channel advection was actu ally larger than the along channel pressure gradient with a numerical model experiment. Likewise, Scully et al. (2009) showed that advective terms worked in concert with baroclinic pressure gradient to enhance the residual exchange flow. It has also been s hown by Jay (1991) that tidal asymmetries in vertical mixing developing from ebb/flood inequalities can enhance the gravitational exchange flow and also need to be considered when modeling the residual estuarine exchange flow. The objectives of this disse rtation are to determine the vertical structure of and A z and discuss the forcing mechanisms behind the observed variability. It also addresses the implications of these results on popular theory for estuarine circulation. Vertical mixing is investigated across the estuary to identify mixing asymmetries from ebb/flood inequalities. The observed residual flow induced by mixing asymmetries is compared with analytical and numerical model results. Lastly, an investigation into the along channel subtidal momen tum balance is used to examine the importance of terms The manuscript herein is organized into three papers, each one addressing a component of the above mentioned objectives. The first paper determi nes the lateral variability of TKE dissipation on a 30 day timescale and discerns the mechanisms influencing dissipation. The second paper investigates vertical mixing intratidally by comparing a tidal cycle during neap and spring conditions. The third and final paper addresses flood/ebb vertical mixing asymmetries and determines their contribution to

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16 the residual exchange flow and subtidal momentum balance. The comprehensive main message will then be presented in the conclusions section.

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17 CHAPTER 2 TEMPORAL VARIABILITY OF TKE DISSIPATION FROM CHANNEL TO CHANNEL SLOPE ACROSS A COASTAL PLAIN ESTUARY Synopsis A field experiment in the James River was carried out to investigate the intratidal and fortnightly lateral variability of turbulent kinetic energy (TKE) dissipation across an estuary. Acoustic Doppler Current Profilers (ADCPs) recorded velocity profiles i n the 10 m channel and over the 7.5 m channel slope throughout 40 days in April June 2010. To quantify stratification, Conductivity Temperature Depth (CTD) sensors were moored in a vertical profile at 3 depths over the channel slope. During neap tides, pot ential energy anomaly values revealed more mixed conditions on flood than on ebb. Time series estimates of TKE dissipation exposed large values that developed during greater floods and revealed larger values during spring than neap tide condition. An Empir ical Orthogonal Function analysis was used to expose the dominant spatial structure of dissipation, which varied from channel to channel slope. In the channel, the largest values were observed near bottom and surface, but were focused near surface over the channel slope. While the bottom generated dissipation observed in the channel was an anticipated finding, a novel discovery was displayed at the surface. Coherence analysis suggested that the surface dissipation was generated by vertical gradients in late ral velocities near the surface that developed from lateral circulation. Therefore, bottom generated dissipation does not dominate at every location across a partially mixed estuary and poses the need to reexamine well accepted theory behind estuarine circ ulation modeling.

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18 Background The local change of TKE energy is the result from the competition of shear production with dissipation and turbulent transport. In estuaries and shelf seas, the effect of density becomes important and can result on the destruction of turbulence for stable stratification or production due to convection during unstable stratification (Monismith, 2010). In coastal and estuarine studies, it has been observed that velocity shears generated from bottom boundary interactions an d wind stress compete with stratification to determine the density structure in the water column (Simpson et al., 1996; Rippeth et al., 2001; Souza et al., 2004). Stacey et al. (1999) and Peters (1997) have found the vertical structure of turbulence in a c oastal plain estuary tends to be dominated by bottom generated turbulence. Tidal velocities exhibit vertical shears through the influence of bottom stress. Turbulence production and dissipation are associated with those vertical shears. Rippeth et al., (20 01) determined that fortnightly modulation in forcing can influence the structure of turbulence dissipation. During neap tide conditions, the maximum values of dissipation were confined to near bottom and occurred during maximum tidal velocities. However, spring tide conditions showed the maximum values of dissipation during flood phases throughout most of the water column and were associated with the destruction of stratification. During ebb tidal phases, dissipation values were limited to the lower half o f the water column by stratification. Those measurements were obtained at one point in the channel of a coastal plain estuary. A dearth of observations exploring the lateral variability of turbulent dissipation across an estuary leads to the motivation beh ind this research. The objective of this research is to examine the temporal variations of the lateral structure of TKE dissipation. To address this objective, time series of high frequency (2 Hz) velocity

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19 profiles at two cross estuary transects in the Ja mes River, Virginia, USA, were used to determine dissipation via the structure function (Nikora and Goring, 1999; Wiles et al., 2006). Analysis of the data indicates that dissipation profiles vary fundamentally from channel to channel slope because of tra nsverse circulations and lateral variability in along estuary flows. This chapter is structured by first introducing a methodology section that describes the study site as well as outlines data collection and processing techniques. Next, a results section is subdivided by exploring a) hydrographic and meteorological influences on the estuary during the sampling period, b) snapshots into neap/spring TKE dissipation, and c) statistical analyses related to dissipation profiles. Subsequently, the results are pl aced in the context of lateral variability in the discussion section, followed by the conclusions. Methodology The study site is approximately 20 km landward of the mouth of the James River, near where the river co nnects to Chesapeake Bay ( Figure 2 1 a). Located on the northeastern coast of the United States, the James River is the southernmost tributary to the Chesapeake Bay. The bottom density anomaly differences at the study site vary between 6 and 18 kg/m 3 and receives annual mean discharge of 200 m 3 /s (Shen and Lin, 2006). The length of salt intrusion reaches approximately 50 to 70 km from the mouth, depending of the season. The estuary is forced by a semi diurnal tide and features spring and neap tidal elevation amplitudes of 0.45 m and 0.2 m, respec tively (Shen and Lin, 2006). The James River has a vertically sheared and laterally sheared residual circulation with landward flow near the bottom, in the channel, and seaward flow near the surface and from surface to bottom over shoals (Valle Levinson e t al,

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20 2000). Intermittent pulses of wind lasting 2 to 7 days often characterize the wind regi me of the Chesapeake Bay (Li et al., 2005). It exhibits seasonal variations with dominant southward winds in winter months (November to February) and northward win ds spanning for several days during the summer months. The James River is considered a moderately wide estuary (K>>2) with a Kelvin number (estuary width/internal radius of deformation) of K = 5, calculated using these observations. Valle Levinson (2008) d escribed the James River as having moderate friction, demonstrated by an Ekman number (friction/Coriolis) of E k = 0.15. The study site featured a significant horizontal density gradient during the experiment, highlighted by horizontal Richardson number of R iH = 0.003. This value is considered relatively large compared to values from a numerical modeling experiment in Burchard and Hetland (2010) and suggests enhanced residual exchange. A cross section of the study area reveals a ~10 m deep channel bisecting t wo 4 6 m flanking shoals ( Figure 2 1 b). Along the cross section, the bathymetry south of the channel features a gently sloping channel side that connects to the adjacent shoal. Data Collection In order to explore the temporal evolution of the lateral st ructure of turbulent kinetic energy dissipation, instruments recorded data for 40 days from April 28 th to June 9 th 2010, capturing two neap and two spring tides. Four Teledyne RD Instruments 1200 kHz ADCPs, sampling in high pinging mode 12, were moored at the bottom and positioned in two lateral lines separated by ~1 km. Each line featured an ADCP in the deepest section (~10 m) of the channel and along an adjacent channel slope (~7 m), spaced ~500 m apart ( Figure 3 1 a). The ADCPs collected bursts of veloci ty profiles every 30 min (2 bursts/hr) and were used to estimate TKE dissipation. The sampling

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21 frequency of each burst was 2 Hz (every ~0.57 seconds) and totaled 1024 profiles for a ~9.7 min duration. The first measurement was collected 0.37 m above the in strument and the bin size was 0.25 m. Near the ADCPs, CTD sensors were positioned at three depths (1.3, 4.3 m, and 7.4 m) in a vertical profile over the channel slope and another one near bottom in the channel (10 m). The CTD sensors took temperature and c onductivity measurements every 5 minutes. These data were used to calculate density anomaly values to explore water column stratification. All results shown herein are from line 1 as those for line 2 are essentially the same. Data Processing The production of turbulent energy in an estuary is generated by several mechanisms: mean shear in velocity and unstable stratification (denser water over less dense water). Turbulence is suppressed by stratification (converting mechanical energy into potential energy) and dissipated by viscous dissipation. The evolution of turbulent kinetic energy (TKE, Equation 2 1 below), is modified by the transport ( Equation 2 1 a), production ( Equation 2 1b ), buoyancy flu x ( Equation 2 1c ) and dissipation of energy ( Equation 2 1d ) (e.g. Monismith, 2010): ( 2 1) w here: ( 2 1a)

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22 ( 2 1b) ( 2 1c) ( 2 1d) The variables are: o reference water density; p pressure; u i turbulent fluctuating velocity; kinematic viscosity; U i mean flow; g gravity; water density. Li et al. (2010) found the transport mechanism ( Equation 2 1) transferred TKE from the bottom boundary layer to the pycnocline during particular tidal phases. This leaves the evolution of TKE as a balance among production, dissipation, buoyancy and transpo rt. Given that the purpose of this investigation was to study the vertical structure of TKE dissipation across an estuary and understanding that it can be modified by shear production, buoyancy and transport, these mechanisms will also be explored to ident ify agents contributing to dissipation. TKE dissipation was calculated using current measurements from ADCPs at two lateral locations across the estuary and implementing a structure function technique. Wiles et al. (2006) adapted this method from meteorolo gy to calculate TKE dissipation in the marine environment. The velocity profiles were Reynolds averaged in blocks of 1024 values at each depth to separate the observations into a mean flow (one value at every depth for each burst) and a turbulent fluctuati ng component. Wind pulses of 7 to 15 m/s occurred during the deployment and produced wave orbital velocities that would

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23 contaminate estimates of turbulence properties (Gargett and Wells, 2007; Gerbi et al., fy the significant wave periods and heights for each burst. The velocity for each beam was band stop filtered (before Reynolds averaging) around the peak wave period, for each 9 minute burst, to filter out velocities influenced by waves. Along each ADCP be am, the mean square difference, separated by a distance, r was calculated from the turbulent fluctuating velocities, to yield a second order structure function: ( 2 2) The distance r a prescribed value (typically 5 m in well mixed water columns), is analogous to a turbulent eddy length scale, whereas the function D(z,r) is analogous to a squared velocity scale, 2 Using Taylor cascade theory, TKE dissipation, is related to the r atio of velocity scale to turbulent length scale: ( 2 3) resulting in: ( 2 4) where C v 2 is considered a constant taken to be 2.1 in meteorology (Sauvageot, 1992) and also used in this study. The structure function ( Equation 2 2) was then fit to Equation 2 4 to solve for ( 2 5) is an offset used to account for uncertainties arising from noise from ADCP velocity measurements. To measure the accuracy of this fit, a goodness of fit test was implemented and fits that did not meet an 85% cut of f criterion were discarded. Using

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24 Equation 2 5, the TKE dissipation, can be solved for directly. Values of were obtained for each depth of all four beams. The values at each depth were compared and outlier values were rejected. The remaining values we re then averaged to yield a single estimate for each burst at all depths According to Wiles et al. (2006), restrictions exist on the applicability of this method in a stratified environment where the distance, r is limited by stratification. Using the estimates calculated from the fit of Equation 2 5, a new was then estimated using a distance, r, equal to twice the bin size (i.e. 0.5 m in this study). ( 2 6) Spikes were removed from the values estimated from Equation 2 6 and remaining values were averaged. Data from the bin closest to the bottom were discarded and those within 10 % of surface were removed to account for side lobe effects from the Doppler Shift. The time series of for each location were smoothed, with 2 neighbors, in two dimensions and interpolated onto a uniform time depth grid. To better understand the nature of the calculated dissipation values by relating them to water column stratification conditions, the dens ity values obtained from the CT measureme nts at the channel slope of line 2 were used to calculate the potential energy anomaly (Simpson et al., 1978): ( 2 7) The variables g h and m represent gravity acceleration (9.81 m/s 2 ), depth of the water column, water density, and depth mean water density respectively. The potential

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25 energy anomaly is a measurement of stratification and represents the amount of energy needed to instantaneously mix a water column. Therefore, relatively large potential energy anomaly values indicate a relatively more stratified water column. After the lateral structure of dissipation and the potential energy anomaly were explored, spectral analysis of along and across channel velocity shears and of TKE d issipation at the channel and channel slope were conducted to understand the spatial distribution of spectral energy. To explore the temporal and spatial variations in current velocities, the mean flow component (for each beam), obtained from Reynolds aver aging, was transformed into east west and north south components. These components were then rotated to yield along and across channel flow components. Both components at all ADCP locations were interpolated onto a uniform time grid. Velocity shears were then calculated by taking the vertical gradient, using centered differences, of the along channel and across channel velocities. The final steps in the data analysis decomposed the dissipation time series using an Empirical Orthogonal Function (EOF) analys is to identify dominant profiles of dissipation and their temporal variability. After the EOF decomposition, a coherence analysis was applied to identify various mechanisms influencing the dominant EOF mode of dissipation. Results The results of this study are organized into five subsections. The first subsection examines the hydrographic and meteorological influences on the system. Once these are established, the second subsection compares, qualitatively, the dissipation time series from channel to channel slope through snap shots during a neap and a spring tidal period. To discern the most energetic region of the water column, the spectral energy of velocity shears and TKE dissipation is shared in the third subsection. With the

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26 goal of identifying agents c ontributing to dissipation, an EOF approach was used to isolate the spatial structure and weighted amplitude of the dominant mode of variability of dissipation. Lastly, a coherence analysis was used to distinguish mechanisms contributing to heightened regi ons of dissipation Hydrographic and Meteorological Variability Given that winds >~7 m/s can produce velocity shears at the surface, hourly wind magnitudes obtained from the Dominion Tower NOAA station were plotted in Figure 2 2a. Hourly magnitudes ranged from ~0 to 15 m/s and showed the largest values near day 129, which corresponded to a period with the largest vertical shear in along channel velocity ( Figure 2 2d). The red boxes identify the smallest neap (May 3 rd to May 5 th ) and largest spring (May 23 rd to May 25 th ) tide conditions of the observation period. These segments will be discussed in the subsequent subsection. Because river discharge can influence the vertical density structure, river discharge values (from the United States Geologica l Survey) were plotted ( Figure 2 2b ) They displayed low frequency variability and featured values that decreased from 150 m 3 /s at the beginning of sampling to ~80 m 3 /s on day 133. Afterward, values nearly tripled to 300 m 3 /s just before the largest spring tide (~ day 142). Density anomaly values (density minus 1000 kg/m 3 ) at three depths (1.3 m, 4.3 m, and 7.4 m) ranged between ~6 kg/m 3 and 18 kg/m 3 These values were used to calculate the potential energy anomaly for the water column over the channel slope ( Fi gure 2 2c). Given that potential energy anomaly represents the amount of energy required to instantaneously mix a water column, larger values indicated greater stratification. Values of ranged from ~0 to 65 J/m 3 Fortnightly variations exhibited

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27 greater stratification during neap than in spring, an expected result from weaker tidal velocities (e.g. Haas, 1977). Higher frequency variability was also observed but stratification, overall, was dominated at fortnightly timescales. The production of turbulent k inetic energy is generated through vertical shears in velocity, which are displayed for the along and across channel components in the channel ( Figur es 2 2d and 2 2e). During the smallest neap tide (days 122 to 125), large negative along channel vertical shears ( 0.1 s 1 ) were observed over large positive values (0.1 s 1 ). This pattern indicated a subsurface velocity jet that developed in the pycnocline, where shear values were near zero. The across channel flows also indicated an opposing shearing distrib ution that emerged during ebb where positive shear values (0.1 s 1 ) were found over negative shears ( 0.1 s 1 ) at about 5 m above the ADCP transducers. The across channel shear distribution developed at the interface of opposing velocities corresponding wi th a lateral circulation that was enhanced from days 123 to 133. The greatest along channel shear was observed during the largest wind pulse (day 129), when wind stress enhanced the subsurface velocity. The time series of velocity shears highlighted the in fluence of low frequency forcing on the magnitude of the shears in the upper portion of the water column. Given that turbulent dissipation depends on shear production, stratification, and viscous effects, the time series of TKE dissipation were then compar ed to these mechanisms. Neap/ Spring Snapshots of TKE Dissipation Along and across channel velocity and velocity shears, stratification, and TKE dissipation were compared for the smallest neap and largest spring tide. During neap (days 123 to 125), the a long channel velocity in the channel ( Figure 2 3a) and channel slope ( Figure 2 3b) featured the largest flood velocities (0.6 m/s) between 5 and 6 m

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28 above the ADCP transducers and the largest ebb velocities ( 0.6 m/s) at the surface. The vertical shear in along channel velocity revealed large positive shears (0.2 s 1 ) near bottom during flood tides that were transported upward with time and damped before reaching 5 m above the ADCP transducers ( Figure 2 3c). During ebb, positive vertical shears (0.05 s 1 ) were observed over negative shears ( 0.1 s 1 ) between 4 and 6 m above the transducers. This opposing vertical shear distribution from flood to ebb highlighted the location of the pycnocline and corresponded with a subsurface velocity maximum that briefly d eveloped after maximum ebb. The subsurface maximum developed because the stratification in the pycnocline suppressed the vertical transport of momentum. While velocities around the pycnocline began to decrease with the reversal of the tide, the flow above and below the pycnocline became briefly uncoupled from the flow within the pycnocline and allowed for the jet to develop. The subsurface maximum remained until vertical shears in long channel velocity overcame the stratifying effects of the pycnocline. The along channel vertical shear in velocity over the channel slope featured similar near bottom positive shears (0.2 s 1 ) during flood but do not feature the opposing vertical shear distribution ( Figure 2 3d). The across channel velocities showed a similar d istribution for channel ( Figure 2 3e) and channel slope ( Figure 2 3f). During flood, a clockwise lateral circulation (with the perspective looking landward) was observed and showed southward (right side of Figure 2 1b) bottom flows (4 m and below) at 0.15 m/s overlain by northward (left) return flow at 0.1 m/s. The circulation was reversed during ebb and showed northward bottom velocities ( 0.1 m/s) below southward near surface velocities (0.1 m/s). The lateral circulation was highlighted in the vertical sh ears of across channel velocity in both the channel ( Figure

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29 2 3g) and channel slope ( Figure 2 3h). Large positive shears (>0.1 s 1 ) observed over negative ( 0.1 s 1 ) shears represented the interface of opposing lateral flows. The vertical shear distributio n reversed in sign during flood. The potential energy anomaly (black) was plotted with the surface velocity over the channel slope and showed values that ranged from 40 J/m 3 to >55 J/m 3 ( Figure 2 4a). Days 123.6 and 124 revealed that stratification incre ased toward the end of ebb and decreased during flood. A diurnal inequality between the magnitudes of successive flood and ebb tidal velocities was observed and is common with semidiurnal tides. The near bottom density anomaly values for the channel and ch annel slope displayed a lag in time between locations when the density increased during floods and decreased during ebbs ( Figure 2 4b). The delay suggested an advection front from channel to shoal on flood, influenced by differential advection of the longi tudinal density gradient (Lerczak and Geyer, 2004). Scully et al. (2009) found that the thermal wind balance is broken during flood, allowing for strong lateral flows to develop. Whereas during ebb, the baroclinic forcing is in opposition to the bottom Ekm an transport, resulting in a reduced lateral circulation relative to flood, as observed in the l ateral flow observations. The TKE dissipation, is shown for the channel and channel slope, respectively ( Figure 2 5c & d ) In the channel, the largest (10 5.5 m 2 /s 3 ) was observed near bottom and near surface. Two pulses (days 123.2 and 124.2) were observed to extend over the water column during flood, when the corresponding stratification was weaker than ebb. Over the channel slope, pulses of large occurre d during flood and the greatest values emerged near surface during days 123 and 125 and near bottom on day 124. During the greatest ebb at both locations, moderate dissipation was observed near surface.

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30 The greatest spring tide condition (days 143.5 to 14 5.5) displayed along channel velocities for the channel ( Figure 2 5a) and channel slope ( Figure 2 5b) that ranged from 0.7 m/s to 0.6 m/s and featured the largest values at the surface, in contrast to the sub surface neap floods. The along channel vertica l shears in velocity in the channel exhibited a similar shear distribution as during neap ( Figure 2 5c). Positive shears (0.05 s 1 ) were observed near bottom during flood and were transported to the surface with time. During ebb, positive shears overlaid n egative shears and corresponded with a subsurface velocity maximum. The channel slope also featured positive near bottom vertical shears during flood and negative near bottom vertical shears during ebb that were observed to transport upward with time ( Figu re 2 5d). The lateral velocities for the channel ( Figure 2 5e) and channel slope ( Figure 2 5f) displayed a circulation comparable to neap, featuring clockwise lateral circulation during flood that reversed during ebb. The across channel vertical shears for the channel ( Figure 2 5g) and channel slope ( Figure 2 5h) displayed ~ 0.15 s 1 values near the location where surface northward lateral flows encountered southward bottom velocities. The values in spring tide were much smaller than neap, ranging only fr om 4 J/m 3 to 14 J/m 3 ( Figure 2 6a). The water column was more stratified during flood than in ebb, opposite to that expected from tidal straining. Scully and Friedrichs (2007) found that the classic pattern of tidal straining was observed at the deepest portion of the cross section (the channel). However, the shallower portions of the cross section exhibited the opposite pattern (i.e. more stratified during flood), which they attributed to lateral processes. Scully and Geyer (2012) took a closer look at the lateral processes influencing a more stratified water column during flood and described a front that was

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31 advected shoal ward during flood tide. This resulted in the la teral advection of stratification and demonstrated more stratification during flood than ebb. Similar to neap tide, a lag was observed between tidal variations in density anomaly from channel to channel slope ( Figure 2 6b). In the channel, large (10 5.25 m 2 /s 3 ) developed near bottom during flood and was transported upward (Figs 1 6c). Over the channel slope, developed at the surface during the beginning of flood and near the bottom after maximum flood ( Figure 2 6d). Similar to the channel during flood, was generated at the surface over the channel slope. To obtain a representative distribution of energy for the entire sampling period, a spectral analysis was performed on and velocity shears and presented in the following section. Spectral Analysis A spectral analysis was implemented on the vertical shears of along and across channel velocities and to investigate the depth distribution of the spectral energy and potentially identify forcing agents. In both the channel ( Figures 3 7a and 1 7c) and c hannel slope ( Figures 3 7b and 1 7d), the along and across channel velocity shear spectra ranged from 10 1 to 10 1.5 ( m / s ) 2 /cpd and revealed the largest energy at the semi diurnal frequency. Over the channel slope, the energy at 2 cpd developed from bottom friction and occupied most of the water column. Yet, in the channel, the spectral energy was confined to the lower half of the water column by stratification. Low frequency energy was observed at two depths in the channel, separated by a region of low ene rgy. This was likely due to enhanced shearing around the pycnocline that was observed during neap and enhanced during the large wind event. Over the channel slope, moderate energy was observed in the upper portion of the water column. The across channel sh ears at both locations also displayed the largest energy at the semi

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32 diurnal frequency. However the channel spectra demonstrated that energy was confined to between 4 m and 7 m above the ADCP while the channel slope featured energy throughout the upper hal f of the water column. The largest energy in along channel velocity at both lateral locations occurred near bottom at 2 cpd and resulted from bottom friction. The greatest energy in the across channel velocity shears developed near surface at 2 cpd and res ulted from shears induced by lateral circulation. Spectra of at the channel ( Figure 2 7 e) and channel slope ( Figure 2 7f) displayed the greatest energy (>10 9 (m 2 s 3 ) 2 /cpd) at the diurnal frequency and reduced energy (>10 9.5 ( m 2 s 3 ) 2 /cpd ) at the semidiurnal frequency. The diurnal pulse in the channel occupied the entire water column and was greatest near surface and bottom, yet over the channel slope the largest diurnal energy was found near surface. The diurnal dominance arose from pulse s of dissipation that developed during the greater floods, as demonstrated in the neap/spring tide conditions with unequal successive flood tide maximums. Increased near bottom energy was observed in the channel at the semidiurnal and quarter diurnal tidal frequencies and highlighted the influence of bottom friction. Now that it has been determined that the greatest energy in dissipation occurred at the diurnal frequency rather than the semidiurnal frequency, an empirical orthogonal function analysis was pe rformed to decompose the signal into dominant modes to later determine what mechanisms are influencing this temporal pattern. Empirical Orthogonal Function Analysis An EOF analysis was performed on the time series of to decompose the signal into dominant modes and investigate the spatial structure of these modes. Of particular interest was the result that had a near surface maximum ( Figures 3 4, 1 6 and 1 8) so this analysis provided information on the relevance of such observation. The temporal

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33 variab ility weighted amplitude of most dominant EOF mode ( Figure 2 8a), the spectrum associated with the weighted amplitude ( Figure 2 8b), and the spatial structure ( Figure 2 8c) of the most dominant mode, accounting for 46% of the total variance is diplayed T he weighted amplitude ranged between 0.5 x 10 5 to 3 x 10 5 and showed variations at different periods. To determine the frequency of these variations, the spectrum of the weighted amplitude was calculated and revealed the largest energy (10 7.8 cpd 1 ) at the diurnal frequency while two more peaks emerged at low (<1 cpd) and semidiurnal frequencies. The diurnal dominance suggested that the pulses of dissipation developed during the largest flood in the tidal cycle. The spatial structure showed larger dissip ation values in the channel than over the channel slope. The channel featured a profile with increased values near the bottom and surface, and the largest values near bottom (0.12 m 2 /s 3 ). The channel slope contained a profile that was relatively uniform ( 0.08 m 2 /s 3 ) from 0 to 0.7 and increased to 0.09 m 2 /s 3 near the surface. The spatial structure exemplified typical near bottom results and highlighted dissipation that developed from frictional influences. Nevertheless, an interesting result emerged near the surface at both locations as comparable or larger dissipation values appeared there. Now that the dominant frequencies and vertical structures have been identified, a coherence analysis was used to ascertain which mechanisms were contributing to those principal frequencies. Coherence Analysis To determine which component of velocity was shaping the dominant diurnal pulses of dissipation, the coherences of the along and across channel velocity shears with the dominant mode were calculated for the channel and channel slope locations. At the diurnal frequency, coherence of ~0.6 to 0.8 was observed near bottom in the

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34 channel in the along and across channel velocity shears ( Figures 3 9a and b). Given that this region is governed by a semidiurnal tidal cycle, this coherence indicated dissipation generated from bottom friction at the largest flood stage of the tidal cycle. Near surface, the across channel vertical shears displayed marginal coherence (0.4 to 0.6), a result of shears generated at the inter face of the lateral gyre. Over the channel slope, stronger coherence (0.8) in the across channel shear was observed near surface and also emphasized the shears generated from lateral circulation ( Figure 2 9d). This finding suggested that, in the channel, n ear bottom associated with the dominant mode was being generated in the weakly stratified bottom boundary region, implying minimal diapycnal fluxes (vertical mixing). This was an expected result from large velocity shears from the greatest flood stage of the tidal cycle interacting with the bottom. Marginally weaker developed near surface and was generated from vertical gradients in velocity at the interface of lateral circulation. Over the channel slope, the largest was located near surface and also developed from the lateral circulation associated with the greater floods. Density measurements over the channel slope exposed greater stratification in the upper water column, as anticipated, implying the conditions for increased vertical mixing in this r egion. Discussion The objective of this study was to examine how the vertical structure of TKE dissipation varied across an estuary at intratidal and fortnightly timescales. A neap tide condition revealed smaller velocities and greater stratification than that observed during spring tide. The largest along channel velocity shears were confined to near bottom region by the pycnocline and developed from large tidal flows interacting with the bottom. This influence was observed in the channel dissipation valu es, where large

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35 near bottom values were displayed during maximum flood velocities. A clockwise lateral circulation developed during flood and featured southward near bottom flows beneath northward near surface flows. Lateral flows on the flood developed fr om lateral baroclinic pressure gradients that augmented the lateral circulation associated with bottom Ekman transport. The lateral circulation reversed with the tide and was markedly weaker. This suggested that lateral baroclinicity competed with bottom E kman transport, resulting in a weaker counter clockwise circulation. At the interface between the opposing lateral flows, the lateral velocity was nearly zero and resulted in large vertical shears in lateral velocities. Influences from the lateral velocity shear distribution were observed in the dissipation values, where large values were depicted near surface during the greater floods at both the channel and channel slope. The spring tide condition exhibited larger dissipation values than neap and featured the greatest in the channel near bottom and surface during flood. Over the channel slope, weaker pulses of dissipation were observed at the beginning of flood and existed only near surface at end of flood. Along channel shears extended to the surface an d highlighted the influence of bottom friction in the presence of weak stratification. The spectra of TKE dissipation at the channel and channel slope revealed the greatest energy at the diurnal frequency, in addition to significant energy at the semidiurn al frequency. Contrary to these observations, Souza et al. (2004) showed that bottom friction exhibited a quarter diurnal frequency, which arose from the largest flood and ebb velocities interacting with the bottom (four times/day). The observations of th is study showed diurnal dominance of dissipation energy and suggested that dissipation developed from a mechanism uncoupled with bottom friction. Semidiurnal inequalities

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36 were observed in the neap and spring tide condition sections, demonstrated by unequal successive flood tides. Form factors were calculated for each day from water level observations and varied from F = 0.04 (Strongly semidiurnal) to F = 0.43 (mixed semidiurnal/diurnal). The interaction between the semidiurnal and diurnal tide created inequ alities between successive tides. Therefore, enhanced lateral circulation during the greater flood generated the largest pulses of dissipation in the time series, leading to the diurnal dominance in the dissipation spectra for the channel and channel slope To determine the dominant mode of dissipation, an EOF analysis was used and revealed the largest values near bottom and surface of the spatial structure of in the channel. The profile of dissipation over the channel slope displayed largest values near surface. A coherency analysis was used to discern the mechanisms influencing the near bottom and surface dissipation. In the channel, large coherence emerged near bottom between the dominant mode and the vertical shears in along and across channel veloci ty and highlighted the influence of bottom friction on near bottom flows during the greater floods. The coherence between the dominant mode and vertical shears in across channel velocities at both locations revealed coherence near surface, indicating that the surface dissipation was, indeed, generated by vertical shears from across channel flows. Collignon and Stacey (2013) recently found a region of maximum TKE shear production in the upper half of the water column and peak depth averaged TKE dissipation d uring the late ebb in South San Francisco Bay. They attributed the near surface turbulence to lateral circulation and developed an analytical analysis to investigate four mechanisms from lateral circulation that can influence water column

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37 stability. Their findings suggested that during late ebb, that straining of the lateral density gradient and velocities gradients in the lateral circulation were found to be significant. The data in the current investigation does not allow for all of the mechanisms present ed by Collignon and Stacey (2013) to be calculated; however their findings compliment the main message of this research. The results of this investigation, along with Collignon and Stacey (2013), suggested that near bottom turbulence does not dominate at e very location across the estuary. This has implications on previous theory regarding the dynamics of a partially mixed estuary. Geyer et al. (2000) suggested that estuarine circulation depended merely on the intensity of bottom generated turbulence and pro posed that the residual flow could be modeled without any knowledge of the vertical eddy viscosity. However the results of this paper showed near surface generated turbulence (uncoupled from bottom friction) was significant and can dominant in some locatio ns across the estuary, thereby proposing necessity to use an accurate vertical eddy viscosity in the prediction of estuarine circulation. Additionally, Scully et al. (2009) showed with a numerical experiment that advective acceleration terms contribute to the subtidal momentum balance at leading order. However, Scully et al. (2009) proposed that fortnightly variations in advective accelerations associated with lateral circulation are canceled by spring/neap variations in interfacial shear stress. This, ther efore, suggested why the traditional subtidal balance scaled somewhat accurately. The results of the current observations provided evidence that vertical shears from lateral circulation influenced near surface dissipation, which suggested that interfacial friction is analogous to vertical

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38 mixing from lateral shears. Although this is speculative, the link between lateral shears and vertical mixing will be addressed in future Summary Previous studies found that turbulence was dominated by bottom friction in the channel of a partially mixed estuary. In this study, results have shown that not only was near bottom dissipation important in the channel, but also near surface dissipation gen erated by vertical gradients in across channel velocities. The vertical structure of dissipation varied across the estuary, finding the largest values near surface over the channel slope. The main result of this investigation is that lateral circulation du ring the greater flood phase can produce vertical shears in across channel flows that favor the appearance of maximum dissipation at the surface, depending on the position across the estuary. Therefore, these results provoke the necessity to revisit the mo deling of estuarine circulation

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39 Figure 2 1 a) M ap of study site and b) cross section looking seaward showing bathymetry. Red circles denote ADCPs placed in channel, yellow denote ADCPs placed over channel slope.

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40 Figure 2 2. a) Wind magnitude from Dominion Tower NOAA station and subtidal wind magnitude (blue), b) river discharge obtained from Richmond VA USGS station, c) potential energy anomaly over channel slope, d) vertical shear in along channel velocity in channel (s 1 ), e) vertical shear in a cross channel velocity in channel (s 1 ). The red boxes identify the smallest neap tide (days 123 to 125 and largest spring tide (days 143.5 to 145.5) snapshots.

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41 Figure 2 3. Neap tide snapshot: along channel velocity u (m/s): a) in channel, b) over chann el slope; along channel shear (s 1 ): c) in channel and d) over channel slope; across channel velocity v (m/s): e) in channel and f) over channel slope; across channel shear (s 1 ): g) in channel and h) over channel slope.

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42 Figure 2 4. Neap tide snapshot: a) surface velocity (black) and potential energy anomaly (blue) over channel slope, b) near a (kg/m 3 ) over channel (blue 10 m) and channel slope (red 7.4 m) c) TKE dissipation log 10 2 /s 3 )] in channel, d) TKE dissipation log 10 [ 2 /s 3 )] over channel slope.

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43 Figure 2 5 Spring tide snapshot: along channel velocity u (m/s): a) in channel, b) over channel slope; along channel shear (s 1 ): c) in channel and d) over channel slope; across channel velocity v (m/s): e) in channel and f) over channel slope; across channel shear (s 1 ): g) in channel and h) over channel slope.

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44 Figure 2 6. Spring tide snapshot: a) surface velocity (black) and potential energy anomaly (blue) over channel slope, b) near a (kg/m 3 ) over channel (blue 10 m) and channel slope (red 7.4 m) c) TKE dissipation log 10 2 /s 3 )] in channel, d) TKE dissipation log 10 2 /s 3 )] over channel slope.

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45 Figure 2 7. Spectra of a) along channel velocity shear log 10 [s 2 /cpd] in channel, b) along channel velocity shear log 10 [s 2 /cpd] over channel slope, c) across channel velocity shear log 10 [s 2 /cpd] in channel, d) across channel velocity shear log 10 [s 2 /cpd] over channel slope, e) TKE dissipation log 10 2 /s 3 )] in channel, f) TKE dissipation log 10 2 /s 3 )] over channel slope

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46 Figure 2 8. EOF results: Mode 1 0.46 variance : a) spatial structure: black channel and blue channel slope, b) weighted amplitude, c ) spectrum of weighted ampl itude.

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47 Figure 2 9. C oherence results between weighted amplitude Mode 1 and: a) along channel velocity shear in channel; b) across channel velocity shear in channel; c) along channel velocity shear over channel slope; and d) across channel velocity shear over channel slope. Black line denotes 95% confidence limit.

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48 CHAPTER 3 VARIABILITY OF VERTICAL MIXING ACROSS A COASTAL PLAIN ESTUARY Synopsis The structure of vertical mixing across an estuary was determined during a field campaign launched in the James River, where current velocity and hydrographic profiles were collected at four lateral locations during a neap and spring tidal cycle in 2010. Neap tide results revealed that vertical mixing was largest near bottom, arising from frictional influences during maximum velocities and were greatest in the channel during flood. Spring tide mixing results were larger than those observed during neap tide and were confined to the lower half of the water column during flood However, ebb phases displayed large vertical mixing near bottom and surface at two locations across the estuary. The vertical mixing at the surface developed from the combined influences of a subsurface along estuary velocity jet within the pycnocline and with lateral flows moving in opposing directions. These results suggested that not only does vertical m ixing develop from bottom generated turbulence, but it can also arise from vertical gradients in velocity near the surface. Background Estuaries promote the exchange of nutrients, sediment, and pollutants between rivers and oceans. The vertical distributio n of mixing is a key process in estuaries because of its influence on the exchange flow, stratification, residence time, and scalar transport (Geyer et al., 2008). Vertical mixing can be generated in regions of increased velocity gradients, most often foun d where flow interacts with the bottom or from sustained winds at the surface. While velocity vertical shears promote mixing, vertical stratification of water density acts to inhibit it. When compared to stratified and well

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49 mixed estuaries, partially mixed systems feature the most energetic exchange flow because of inherent mixing that sets up horizontal density gradients, which drive the flow. Therefore it is essential to understand the mechanisms behind vertical mixing at various temporal and spatial scal es. Peters (1997) explored the spring/neap and intratidal variability of vertical mixing in the Hudson River. During neap conditions, the largest vertical mixing was observed at maximum flood and was confined to the portion beneath the pycnocline. However during spring tides, the largest vertical mixing extended throughout the water column by the end of ebb. The measurements supporting those results were collected over the deepest section (the channel) across the estuary. The objective of this investigatio n is to build upon those findings by examining the spatiotemporal distribution of vertical mixing across a coastal plain estuary. This objective is pursued with profiles of velocity and turbulent kinetic energy dissipation measured at 4 stations distribut ed across the James River estuary. Chapter 3 begins with a background of the James River in the Methods section. Next, the data collection and processing techniques are outlined. The Results section follows with a description of observations and is divide d into Neap and Spring Conditions subsections. Within each of these subsections, observations exploring vertical mixing are provided at every lateral location across the estuary. In the final Results subsection, the competition between stratification and shear is explored through Richardson numbers. The mixing results are put into context of lateral variability in the Discussion section, after which the main message is presented in Conclusions

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50 Meth ods The Chesapeake Bay is the largest estuary in the United States and is located on the northeastern coast, bordered by Virginia and Maryland. The James River is the southern waterway to the bay and provided an annual mean discharge value of 198 m 3 /s in 2 010 according to United States Geological Survey. It is classified as a coastal plain estuary featuring a partially mixed water column (Shen and Lin, 2006), with a top to bottom density anomaly range of 6 to 18 kg/m 3 in this study. The tides in the James R iver are predominantly semidiurnal (Form factor F=0.213) and exhibit a 0.45 m spring tidal amplitude and 0.2 m neap tidal amplitude. The typical residual circulation is vertically and laterally sheared, featuring landward flow near the bottom in the channe l, and seaward flow near the surface and from surface to bottom over shoals (Valle Levinson et al., 2000). The Chesapeake Bay has intermittent pulses of w ind lasting 2 to 7 days (Li et al., 2005). The seasonal pattern yields dominant southward wind during winter months (November to February) and northward winds during summer months. Measurements were collected along a 2 km transect approximately 20 km landward of the mouth ( Figure 3 1a). A cross section looking seaward reveals that the bathymetry consists of a 10 m deep channel bi secting two 4 6 m shoals ( Figure 3 1 b). Along the cross section, the bathymetry south of the channel features a gently sloping incline that connects the adjacent shoal to the channel. Now that the scene for this experiment has pre sented, the elements of data collection are reviewed next. Data Collection With the purpose of determining the temporal variability in the lateral structure of vertical mixing, a field campaign was undertaken to capture a neap and spring tide in

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51 May of 201 0. On May 5 th (neap) and May 27 th (spring) 2010, profiles of velocity and hydrography were collected across a 2 km transect for a tidal cycle (~12.4 hours). Velocity measurements were obtained using a 1200 kHz RDI Acoustic Doppler Current Profiler (ADCP), pointing downward on a 1.2 m catamaran that was towed alongside of a boat at typical speeds of 1.5 m/s to 2 m/s. The ADCP sampled at 2 Hz collecting velocity measurements with a 0.25 m resolution ranging from 0.5 m to 10 m depth. In addition to the ADCP, a Self Contained Autonomous Microstructure Profiler (SCAMP) by P recision Measurement Engineering (P ME ) was deployed at four lateral locations across the estuary. The instrument descended at 1 cm/s and collected temperature and conductivity measurements at 100 Hz. The four hydrographic stations, denoted by red circles ( Figure 3 1b ) were selected to represent two shoals, the deepest section of the channel, and a gently sloping inclination that connected the south shoal to the channel. Hydrographic measureme nts were collected hourly as the ADCP sampled continuously. The fundamental theory behind the calculation of vertical mixing from the above mentioned measurements is outlined next. Mixing Theory The objective of this study is to determine variations in vertical mixing from channel to shoal across an estuary and determine whether fortnightly variability modulates the distribution. Starting from the momentum balance in the along estuary direction x : (3 1) where x is along channel, y is across channel, z is vertical, t is time, is Reynolds averaged along channel velocity, is Reynolds averaged across channel velocity,

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52 is Reynolds averaged vertical velocity, f is the Coriolis paramete r, o is a reference density, and P pressure. The first term on the left hand side (l.h.s.) of Equation 3 1 represents local changes in velocity, while the second, third, and fourth terms represent advective accelerations. The remaining term on the l.h.s is the Coriolis acceleration. On the right hand side (r.h.s.), the first term denotes the pressure gradient term, while the remaining term is the Reynolds stress divergence term. The Reynolds stresses represent temporal averages of the covariance betwee n along estuary, and vertical, fluctuating velocity components, via Reynolds decomposition The Reynolds stresses can be parameterized using a vertical eddy viscosity, A Z and the vertic al gradient in velocity: (3 2) The vertical eddy diffusivity of a tracer (e.g. salt), K z can be calculated using efficiency, m ef times the ratio of turbulent kinetic energy (TKE) dissipation, to squ ared buoyancy frequency, N 2 : (3 3) (3 4) The numerator of Equation 4 3 can be estimated using an Ozmidov length scale L o approach, as outlined by Thorpe (1977). In this method, ( Equation 3 5) is calculated using Thorpe length scales L t computed from Thorpe displacements, d ( Equation 3 6). (3 5)

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53 (3 6) The constant, C in Equation 3 5 was found by Peters et al., (1988) to be 0.91 and represents the relationship between the Ozmidov and Thorpe length scales The Thorpe displacements, d were calculated using the sorting algorithm included in the SCAMP processing software. Density profiles measured by SCAMP are statically unstable at scales <0.1 m and the algorithm sorts the profile to be monotonically increa sing. Sorting allows calculation of the distance between the location of unstable density measurements from the original profile to the location in the sorted profile. Equation 3 6 shows that L T is calculated by finding the root mean square of d in each bin of the vertical profile. The L T represents the vertical distance over which heavier water is actually observed over lighter water and indicates the length scale of a turbulent eddy. Previous studies (Peters, 1997) have assumed a constant m ef of 0.20 under the assumption that the flux Richardson number, R f does not e xceed a critical value of 0.15: (3 7) Given the periodic nature of stratification in partially mixed estuaries, this is unlikely a valid assumption. To estimate a spatiotemporal (1993 ) parameterization was used to estimate a turbulent Prandtl number, Pr t as a function of the Richardson number, R i : (3 8 )

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54 (3 9 ) When using Equation 3 8, constraints were taken into consideration regardi ng the limiting value of Ri Baumert and Peters (2009) demonstrated that turbulence does not exist when R i > 0.5 because TKE is converted to wave energy. Following the method of Ilicak et al. (2008), Pr t = 10 for all R i values larger than this threshold. Pr t also represents the ratio of R f to R i and A z to K z : (3 10) which is used to estimat e the mixing efficiency. Lastly, K z and Pr t can be used in Equation 3 10 to estimate a vertical eddy viscosity. Now that the background for mixing theory has been reviewed, the specifics of data processing are presented next. Data Processing The raw ADCP velocity data were averaged over 10 seconds to yield a spatial resolution of 10 to 20 m and calibrated to remove compass errors (Joyce, 1989). The continuous data s et was separated by the start and stop time of each transect and interpolated onto a rectangular grid. The grid for each transect was 45 by 77 cells with a resolution of 0.25 m in the vertical and 25 m in the horizontal. Velocity components were rotated fr om East West and North South to along and across estuary directions. Velocity profiles were extracted for each transect at the 0.12, 0.55, 1.37, and 1.94 km distances from the transect origin to build velocity time series for each station, to make them co incide with the location of SCAMP profiles. Vertical gradients in velocity were calculated by vertically differentiating the along and across channel velocity time series at each station. The raw SCAMP profiles were separated by station. In order to estim ate

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55 the TKE dissipation, buoyancy frequency values, N were calculated with the SCAMP processing software and were averaged into 30 cm bins. Values of L T were determined by calculating the root mean square of the Thorpe displacements (also calculated via S CAMP processing software), of each 30 cm bin. Both the N and d profiles were de spiked by removing outlier values above the 95 th and below the 5 th percentile. To find the temporal evolution of mixing at each station, the vertical eddy viscosity values wer e interpolated onto the velocity shear grid. These values were multiplied together and differentiated in the vertical to yield the stress divergence. When plotting the along and across channel velocity shears, buoyancy frequency, Thorpe length scales, TKE dissipation, vertical eddy viscosity and along and across channel stress divergence at each station, a two dimensional filter was applied to smooth these distributions. Now that data processing has been detailed, the vertical mixing results for the neap and spring tide are presented in the following section. Results The objective of this research is to determine the fortnightly variability of vertical mixing acr oss an estuary. Results for spring and neap tides are presented separately during noteworthy pe riods where time series of u i N L T A Z and are reviewed for each station across the estuary to determine the mechanism influencing vertical mixing. To explore the forces shaping lateral circulation, time series of differential advection and Coriolis forcing of lateral flows are compared Next, a timescale anal ysis is used to identify the mechanism associated with lateral circulation that is influencing m i xing. Lastly, time series of Richardson numbers

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56 are shown in the channel and south flank during a neap and spring survey with the purpose of explaining the ne ar surface mixing observed during the spring observations Spring Tide: Late Flood Enhanced vertical mixing during the flood phase occurred after peak velocities, between the hours of 14 and 16 GMT on May 27 th 2010. The largest along and across estuary stress divergence values (10 4 m/s 2 ) were displayed near bottom over Stations 1 and 2, representing the north flank ( Figure 3 2 i & j) and channel ( Figure 3 3 i & j). Weaker vertical mixing (10 6 m/s 2 ) was featured near bottom over Stations 3 and 4, denoting the channel slope ( Figure 3 4 i & j) and south flank ( Figure 3 5 i & j ). The along estuary flood velocities u during this period ranged between ~ 0.1 m/s and 0.35 m/s a cross the transect ( Figures 3 2 through 3 5 a). The vertical gradient of the u velocities revealed the largest near bottom shears (~ 0.1 s 1 ) over Stations 1 and 2 and corresponded with the regions of peak vertical mixing that developed from bot tom friction ( Figures 3 2 & 3 c). A counterclockwise lateral circulation (looking seaw ard) developed during flood and featured 0.12 m/s southward velocities below near surface 0.1 m/s no rthward velocities ( Figures 3 2 through 3 5 b). The vertical gradient of v displayed large (0.1 s 1 ) shears near bottom and resulted from lateral flows int eracting with t he bottom ( Figures 3 2 through 3 5 d). The stratification across the transect during this time was relatively weak compared to the ebb stage. Smaller buoyancy frequency N values ~0.006 s 1 were observed in a mixed region in the lower water column, while larger values (0.06 s 1 ) emerged near surface and delineated a broad pycnocline ( Figures 3 2 through 3 5 e). The largest density overturns were observed near bottom in the channel and were demonstrated by 0.6 m Thorpe length scales L T The remainder of the transect exhibited smaller L T values of 0.3 m near bottom. The largest TKE

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57 dissipation values (10 7.5 m 2 /s 3 ) were observed below 5 m depth in the channel and over the c hannel slope ( Figures 3 3 & 4 g). Over the flanks, weaker (10 8 m 2 /s 3 ) values were observed throughout the shallower water column ( Figures 3 2 & 5 g). The largest vertical eddy viscosity A Z values complimented the vertical shears in u and stress divergence values by displaying the largest values (10 3 m 2 /s) near bottom at the north flank and channel ( Figures 3 2 & 3 h). These observations revealed the greatest flood stage vertical mixing near bottom over the north flank as well as the channel and were influenced by bottom friction. Spring Tide: Late Ebb An unanti cipated vertical mixing structure emerged at several locations across the estuary after maximum ebb velocities, during the hours of 19 to 21 GMT. The largest stress divergence values (10 4 m/s 2 ) were observed near surface in the channel and over the so uth flank ( Figures 3 3 & 3 5 i & j). A subsurface u maximum developed in the channel and over the south flank ( Figures 3 3 & 5 a). Negative ~ 0.08 s 1 over positive ~0.08 s 1 shears outlined the jet like subsu rface u maximum ( Figures 3 3 & 5 c), which correspo nded with the location of the pycnocline and featured 0.1 s 1 N values ( Figures 3 3 & 5 e). A clockwise lateral circulation developed during ebb and featured an interface between opposing v flows that occurred at similar depths as the u jet in the pycnocli ne in the channel and over the south flank ( Figures 3 3 & 5 b). This resulted in a vertical shear v distribution marked by near surface negative shears, representing increasing southward flow toward the surface above positive shears signifying increasing northward flo w with depth ( Figures 3 3 & 5 d). Density overturns were featured near surface of the channel as well as the south flank and featured 0.4 m L T values ( Figures 3 3 & 5 f). The largest (10 7 m 2 /s 3 ) and A z values (10 3 m 2 /s) were also

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58 observed near surface over the channel and south flank. The surface vertical mixing observed in late ebb developed from the combined influence of velocity shears associated with a subsurface along estuary velocity maximum and lateral circulat ion. Spring Tide: Lateral Circulation Some of the most influential m echanisms that can generate lateral flows are Coriolis effects, differential advection of the longitudinal density gradient, and centrifugal acceleration. The vertical gradient of the cro ss stream momentum equation (in a curvilinear coordinate system) describes the forcing mechanisms of secondary flows (Chant, 2010): (3 11) where u n and u s is streamwise and cross stream flow, R is the Rossby number, f is the Coriolis parameter, and is stress. The first term is the local acceleration of the lateral flow; the second is the straining of lateral flow by velocity shear in streamwise flow; the third is the streamwise advection of streamwise gradients in lateral flows; the fourth represents f orcing from centrifugal acceleration; the fifth is from forcing from Coriolis acceleration; the sixth is forcing from cross stream density gradients (differential advection) and the seventh term is friction. For this investigation, two of the major forcing mechanisms of secondary flows will be compared: differential advection and Coriolis. Contours of secondary flow forcing from differential advection from the longitudinal density gradient, and Coriolis, are displayed for between the channel and chann el slope ( Figures 3 6 a & b) and between the channel slope and

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59 south flank ( Figures 3 6 c & s). Lateral flow forcing from differential advection and Coriolis during spring tide exposed markedly smaller values than during neap and showed similar distributio ns between Stations 2 and 3 and Stations 3 and 4. During flood, (hrs <12 to 16 GMT ) differential advection displayed ~ 1e 5 s 2 values that acted in concert with Coriolis values (< 0.5e 5 s 2 ) in the lower half of the water column and opposed ~0.5e10 5 s 2 in the upper half. Between hrs 14 to 18 GMT differential advection forcing values switched signs (<0.5e 5 s 2 ) after the end of flood and was likely an influence of decreased stratification. At the end of ebb, 2e 5 s 2 values developed throughout the wa ter column between Stations 3 and 4, while < 1e 5 s 2 values emerged below 3 m between Stations 2 and 3. Coriolis forcing reflected opposing values that were largest (2e 5 s 2 ) near bottom at both locations. The enhanced lateral circulation during flood wa s a result of forcing from differential advection and Coriolis acting in concert near bottom. To ascertain which lateral circulation forcing was influencing the near surface mixing, a timescale analysis was used next to examine the stability of the water c olumn. Spring Tide: Timescale Analysis Collignon and Stacey (2013) developed theoretical framework that assessed the relative influence of four lateral flow mechanisms on the stability of the water column. The analysis involved taking the time derivative of the Richardson number, R i and relating it to vorticity, x The resulting expression describes the temporal evolution of R i in terms of density straining, shear straining, Coriolis, and unsteadiness: (3 12)

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60 where S 2 is the amplitude of the squared vertical shear of u and v (i.e. the denominator of the R i ) ; x is longitudinal vorticity, represented as the negative vertical gradient of v ; and R is the remainder term not involving x The terms within the square brackets represent the contribution to R i from density straining (first term), shear st raining (second term), Coriolis (third term) and unsteadiness (fourth term); all associated with lateral circulation. The above mentioned analysis can be used to quantify the relative important of the four terms on the stability of the water column so that which mechanisms are destabilizing the water column can be determined. Collignon and Stacey (2013) used an approach that quantified timescales of the four characteristic processes to compare with one another: (3 14) (3 15) (3 16) (3 17) where is the timescale associated with density straining, u is shear straining, f is Coriolis, and t is unsteadiness. A positive timescale value represents a process that stabilizes the water column (increases R i ) and a negative value acts to induce mixing by decreasing R i The relative importance is evaluated by comparing the timescale in hours with half of the semidiurnal tidal period. Therefore, values larger than 6.2 hrs have a

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61 weaker influence than smaller values. Given that during late ebb, near surface vertical mixing was observed to be influenced by lateral circulation, this approach was used to determine the lateral circulation process that was generating near surface mixing over the channel and south flank. The above mentioned timescales were calculated near surface (where vertical mixing was observed) for between channel and channel slope ( Figure 3 7 a) and channel slope and south flank ( Figure 3 7 b). Just after maximum ebb (hrs 18 to 19) between Stations 2 an d 3, the timescales revealed that density straining and shear straining acted in concert to de stratify the water column and exhibited th e marginal dominance of shear straining. Between Stations 3 and 4, surface mixing ensued after h r 21. Timescales reveal ed again that density and shear straining acted together to d e stratify the water column, but showed density straining to have a slightly larger role. This analysis confirms that, indeed, the surface mixing observed at these two locations were influenced b y density straining (i.e. differential advection of a stratified water column) and velocity shear straining associated with the vertical gradient of along channel velocity. It has been shown that large vertical mixing was observed near bottom during late f lood as an influence of bottom friction. During late ebb, the largest mixing developed near surface and was influenced by lateral circulation and a u velocity jet in the pycnocline. These observations will be compared next to a neap survey, when smaller ti dal velocities were observed and the water column was more stratified. Neap Tide: Late Ebb During the neap tide survey on May 5 th 2010, relatively weak <10 5 m/s 2 vertical mixing values compared to spring tide were observed across the transect during the late ebb hours of 14 to 16 GMT ( Figures 3 8 through 3 11 i & j ). Similar to the spring

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62 observations, a subsurface u maximum developed in the pycnocline after peak ebb velocities in the channel and ov er the channel slope ( Figures 3 9 & 10 a). At comparable depths to the velocity jet, the interface of a clockwise lateral circulation was highlighted through 0.10 s 1 over 0.08 s 1 vertical shears in v The large vertical shears did not result in vertical mixing because of the increased strat ification, demonstrated by N values that ranged from ~0.15 s 1 in the pycnocline to 0.05 s 1 near bottom ( Figures 3 8 through 3 11 e). The largest values (10 7.5 m 2 /s 3 ) developed near botto m over the north flank ( Figure 3 8 g), while weaker values of 10 8.25 m 2 /s 3 emerged near surface and bottom at the channel and chann el slope ( Figure 3 10 & 11 g). A z values were smaller during neap and exhibited 10 5 m 2 /s beneath the pyc nocline in the channel ( Figure 3 9 h). Given the increased stratification d uring th e late ebb of the neap observations vertical mixing was suppressed along the cross section. Neap Tide: Maximum Flood The largest vertical mixing values in the neap observations emerged during maximum flood velocities, from the hours of 18 to 20 GMT. The largest along and across estuary stress divergence values (10 5 m/s 2 ) were displayed below the pyc nocline in the channel ( Figure 3 9 i & j) while weaker values of 10 5 .5 m/s 2 developed over the north and channel slope ( Figures 3 8 & 3 10 i & j). Across t he transect, near bottom > 0.15 s 1 vertical shears in u developed an d influenced lower water column vertical mixing. Similar to the spring results, a counterclockwise lateral circulation devel oped during the flood ( Figures 3 8 through 3 11 b). The greates t stratification throughout the tidal cycle developed during flood over the channel slop e and south flank ( Figures 3 10 & 3 11 e) and featured 0.15 s 1 N values in the pycnocline. The largest instabilities (0.3 m) were displayed near bottom of the channel, where the largest

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63 vertic al mixing was observed ( Figure 3 9 f). Smaller 0.2 m to 0.25 m instabilities transpired over the channel slope and south flank ( Figures 3 10 & 3 11 f) The largest (10 7.5 m 2 /s 3 ) and A Z values (10 4 m 2 / s) were observed below the pycn ocline in the channel ( Figures 3 9 g & h), while smaller ~10 5 m 2 /s values were observed over the channel sl ope and north flank ( Figures 3 8 & 3 10 g & h). The greatest vertical mixing occurred during peak flood velocities ne ar bottom in the channel, where velocities were the largest. Neap Tide: Lateral Circulation Between Stations 2 and 3, differential advection ( Figure 3 12 a) and Coriolis forcing ( Figure 3 12 b) at in concert near bottom and surface during ebb (hrs < 12 to 1 5). For the depths b etween, these two forcings counter balance d one another. During the flood stage (hrs ~16 to 22), differential advection featured values of 1e10 5 s 2 and opposed Coriolis forcing values of <10 5 s 2 Contours between Stations 3 and 4 f eatured similar distributions, but exhibited differences near bottom during ebb, when differential advection ( Figure 3 12 c) acted against Coriolis forcing ( Figure 3 12 d) T hese contours revealed that, during flood, differen tial advection forced flow near bottom to the south, while Coriolis mildly acted to hinder it. Differential advection acted to force flow toward the north during ebb and was balanced by Coriolis throughout most of the water column, with near bottom and surface exceptions. To explore why near surface mixing developed during the spring observations and not during ebb, Richardson numbers were used next to examine the stability of the water column. Stratification Versus Shear Analysis The Richardson number R i represents the ratio of the sq uared buoyancy frequency to the squared total of the vertical shears of along and across channel

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64 velocity ( Equation 4 9 ). This non dimensional number indicates whether stratification inhibits turbulence and values < 0.25 indicate conditions where mixing can develop. However values above 0.25 suggest that stratification suppresses vertical mixing. R i values in the channel during spring ( Figure 3 13 a ) and neap ( Figure 3 13 c ) and over the south flank during spring ( Fi gure 3 13 b ) and neap ( Figure 3 13 d) suggested why near surface vertical mixing only emerged during the spring tide. The black dotted line denoted the threshold between mixing and suppression (R i = 0.25). Therefore all values smaller (darker blue) suggest ed regions where conditions could support vertical mixing and all values larger (tending to red) were regions where conditions suggested suppression. During neap tide, Richardson numbers implied vertical mixing near bottom. However during spring tide, the Richardson numbers not only suggested vertical mixing near bottom, but also indicated mixing above the pycnocline during ebb. This observation proposed that near surface, velocity shears overcame the stratifying effects of the pycnocline and allowed for ve rtical mixing to develop close to the surface. Discussion The purpose of this investigation was to quantify v ertical mixing throughout a spring and neap tidal cycle across an estuary. Neap tides observations revealed greatest vertical mixing near bottom ac ross the transect during the largest flood velocities, and displayed maximum values in the cha nnel. As expected, the spring survey exposed larger vertical mixing values than the neap observations Similar to neap, the largest vertical mixing was observed near bottom during late flood, with the largest values in the channel and the smallest values over the channel slope. During ebb, the channel and south flank (Stations 2 and 4) showed large vertic al mixing near bottom and at the surface, separated by a region of suppression from the pycnocline

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65 that restricted the upward transfer of momentum. Just after maximum ebb, a subsurface velocity maximum developed within the pycnocline at these two locations While the flow around the pycnocline began to reduce, the stratification in the pycnocline allowed for the momentum within the region to become briefly trapped and uncoupled from the surrounding area Once the vertical shear in along estuary velocity ove rcame the stratifying effects of the pycnocline, mixing developed and resulted in the decay of stratification and the velocity jet. Lateral surface flows (~0.1 m/s) produced across estuary velocity shears that enhanced vertical mixing at the surface. The lateral circulation influencing the surface mixing varied from neap to spring tide conditions. During neap, differential advection of the longitudinal density gradient dominated over Coriolis in forcing lateral flows. This resulted in a differential advect ion front that was forced from the channel to the south flank, thereby causing the greatest stratification to occur during flood rather than late ebb over the channel slope and south flank. During ebb, these mechanisms opposed one another and acted in conc ert after maximum flood. However during the spring observations these mechanisms acted in con cert during the beginning of flood after which the differential advection forcing transitioned to compete with Coriolis forcing during late flood This finding d iffered from neap tide results because a time lag emerges between when these mechanisms balance one another. This discrepancy suggested that decreased stratification during spring tide resulted in weaker lateral density gradients which took longer to indu ced lateral flows This triggered these mechanisms to act in con cert during the beginning of flood

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66 It was observed that near surface vertical mixing during spring tide was being influenced by lateral circulations. To determine what mechanism associated w ith lateral circulation was inducing surface mixing after maximum ebb, the timescales of density straining, shear straining, Coriolis and unsteadiness where compared near surface Results confirmed that density and shear straining were acting in concert to destratify the surface after maximum ebb velocities and showed that density straining had a marginally larger impact over the south flank, while shear straining had a slightly larger influence in the channel An investigation into the Richardson numbers i n the channel and south flank for a spring and neap tidal cycle provided the explanation for vertical surface mixing during spring conditions rather than neap conditions. Richardson numbers represent a competition between stratification and velocity shear. During both neap and spring tidal conditions, low R i (< 0.25) were observed near bottom in a mixed layer, where larger vertical shears in velocity emerged from flow interacting with the bottom and N values were smallest. Neap/spring tide disparities in R i above the mixed layer emerged, particularly during ebb (hrs 1 3 16 in neap and hrs 17 to 21 in spring). R i > 0.25 encompassed most of the region above the mixed region during neap, when markedly larger N values were observed. Spring tide values also displa y ed values R i > 0.25 during flood above the near bott om mixed region. However, a mixed area at the surface developed after max ebb (hr 18.5) and corresponded with a section where large vertical shears in along and across channel velocities establi shed fro m the combined influence of a subsurface velocity maximum in the pycnocline and opposing velocities from lateral circulation. Above the mixed area during neap, increased stratification and lower

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67 velocities than those observed during spring promoted the sup pression of vertical mixing. During spring, increased velocities and lower stratification allow ed for surface mixing to ensue at the end of ebb. The key to why surface mixing developed during the spring observations and was suppressed during neap was strat ification. Even though the subsurface velocity jet and lateral circulation developed during both neap and spring observations after maximum ebb, the overall weaker stratification during spring tide allowed for velocity shear to overcome stratification and induce mixing. Collignon and Stacey (2013) recently published findings from a channel shoal interface in South San Francisco Bay. Results indicated increased shear production at the surface and increased depth averaged TKE dissipation late in the ebb phase of the tidal cycle. This study suggested that the surface turbulence was being generated by lateral circulation. Moreover, the previously introduced timescale approach was employed and revealed that density and shear straining were drivers for destratifyi ng the water column and reinforce the main message of the present investigation. Summary This investigation confirmed that near bottom vertical mixing was greatest during maximum flood velocities across the estuary and was consistent with Peters (1997) fin dings. A revealing finding developed later in the ebb phase of the tidal cycle, when large near bottom and surface vertical mixing arose at several locations across the estuary. While near bottom mixing was generated by bottom stresses, as expected, surfac e mixing developed from the combined influence of along estuary vertical shear from a velocity jet in the pycnocline and large vertical shear from lateral flows moving in opposite directions. This new finding proposes that near bottom vertical mixing may d ominate during flood, however ebb near surface mixing can dominate depending on

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68 the location across the estuary and develop from mechanisms uncoupled from bottom friction. Therefore, vertical mixing shows different structure across the estuary. Investiga tions in other estuaries should provide generalities on this finding. Figure 3 1. a) James River plan view of study site with transect denoted by black line and b) cross section looking seaward of study site highlighting each hydrographic station named Stations 1 through 4 from left to right.

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69 Figure 3 2 Spring conditions, Station 1 time series: a) along estuary velocity, u (m/s); b) across estuary velocity, v (m/s); c) along estuary velocity shear, (s 1 ); d) across estu ary velocity shear, (s 1 ); e) buoyancy frequency, N (s 1 ); f) Thorpe length scales, L T (m); Log 10 : g) TKE dissipation (m 2 /s 3 ); h) vertical eddy viscosity, A Z (m 2 /s); i) along estuary stress divergence (m/s 2 ); j) across estuary stress dive rgence (m/s 2 ).

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70 Figure 3 3 Spring conditions, Station 2 time series: a) along estuary velocity, u (m/s); b) across estuary velocity, v (m/s); c) along estuary velocity shear, (s 1 ); d) across estuary velocity shear, (s 1 ); e) buoyancy frequency, N (s 1 ); f) Thorpe length scales, L T (m); Log 10 : g) TKE dissipation (m 2 /s 3 ); h) vertical eddy viscosity, A Z (m 2 /s); i) along estuary stress divergence (m/s 2 ); j) across estuary stress dive rgence (m/s 2 ).

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71 Figure 3 4 Spring conditions, Station 3 time series: a) along estuary velocity, u (m/s); b) across estuary velocity, v (m/s); c) along estuary velocity shear, (s 1 ); d) across estuary velocity shear, (s 1 ); e) buoyancy freq uency, N (s 1 ); f) Thorpe length scales, L T (m); Log 10 : g) TKE dissipation (m 2 /s 3 ); h) vertical eddy viscosity, A Z (m 2 /s); i) along estuary stress divergence (m/s 2 ); j) across estuary stress dive rgence (m/s 2 ).

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72 Figure 3 5 Spring conditions, Station 4 time series: a) along estuary velocity, u (m/s); b) across estuary velocity, v (m/s); c) along estuary velocity shear, (s 1 ); d) across estuary velocity shear, (s 1 ); e) buoyancy frequency, N (s 1 ); f) Thorpe length scales, L T (m); Log 10 : g) TKE dissipation (m 2 /s 3 ); h) vertical eddy viscosity, A Z (m 2 /s); i) along estuary stress divergence (m/s 2 ); j) across estuary stress dive rgence (m/s 2 ).

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73 Figure 3 6 Between Stations 2 and 3: a) differential advection forcing and b) Coriolis forcing; between Stations 3 and 4 c) differential advection forcing and d) Coriolis forcing.

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74 Figure 3 7 Four timescales characteristic of lateral circulation processes: a) between Stations 2 and 3 and b) between Stations 3 and 4. Blue: density straining, yellow: shear straining, and green: Coriolis. Red line marks zero threshold and black dashed lines mark the 6.2 hr threshold, where values larger play a smaller role in water column stability. (a) (b)

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75 Figure 3 8. Neap conditions, Station 1 time series: a) along estuary velocity, u (m/s); b) across estuary velocity, v (m/s); c) along estuary velocity shear, (s 1 ); d) across estuary velocity shear, (s 1 ); e) buoyancy frequency, N (s 1 ); f) Thorpe length scales, L T (m); Log 10 : g) TKE dissipation (m 2 /s 3 ); h) vertical eddy viscosity, A Z (m 2 /s); i) along estuary stress divergence (m/s 2 ); j) across estuary stress dive rgence (m/s 2 ).

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76 Figure 3 9. Neap conditions, Station 2 time series: a) along estuary velocity, u (m/s); b) across estuary velocity, v (m/s); c) along estuary velocity shear, (s 1 ); d) across estuary velocity shear, (s 1 ); e) buoyancy frequency, N (s 1 ); f) Tho rpe length scales, L T (m); Log 10 : g) TKE dissipation (m 2 /s 3 ); h) vertical eddy viscosity, A Z (m 2 /s); i) along estuary stress divergence (m/s 2 ); j) across estuary stress dive rgence (m/s 2 ).

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77 Figure 3 10. Neap conditions, Station 3 time series: a) along estuary velocity, u (m/s); b) across estuary velocity, v (m/s); c) along estuary velocity shear, (s 1 ); d) across estuary velocity shear, (s 1 ); e) buoyancy frequency, N (s 1 ); f) Thorpe length scales, L T (m); Lo g 10 : g) TKE dissipation (m 2 /s 3 ); h) vertical eddy viscosity, A Z (m 2 /s); i) along estuary stress divergence (m/s 2 ); j) across estuary stress dive rgence (m/s 2 ).

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78 Figure 3 11. Neap conditions, Station 4 time series: a) along estuary velocity, u (m/s); b) across estuary velocity, v (m/s); c) along estuary velocity shear, (s 1 ); d) across estuary velocity shear, (s 1 ); e) buoyancy frequency, N (s 1 ); f) Thorpe length scales, L T (m); Log 10 : g) TKE dissipati on (m 2 /s 3 ); h) vertical eddy viscosity, A Z (m 2 /s); i) along estuary stress divergence (m/s 2 ); j) across estuary stress dive rgence (m/s 2 ).

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79 Figure 3 12. Between Stations 2 and 3: a) differential advection forcing and b) Coriolis forcing; between Stations 3 and 4 c) differential advection forcing and d) Coriolis forcing.

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80 Figure 3 13 Richardson numbers, R i for Station 2 during a) neap and c) spring tide conditions and for Station 4 during b) neap and d) spring tide con ditions.

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81 CHAPTER 4 INFLUENCE OF TIDAL MIXING A SY M METRIES ON RESIDUAL EXCHANGE FLOW IN THE JAMES RIVER ESTUARY Synopsis Measurements of hydrography and velocity from the James River were collected during a neap and spring tidal cycle to compare observed residual flows induced by tidal mixing asymmetries with model results. Furthermore, the relative influence of mixing asym metries on the subtidal momentum balance was compared to that from lateral advection. During neap conditions, the flow induced by mixing asymmetry augmented the gravitational circulation at depth in the channel, similar to one dimensional theory. During sp ring conditions, the residual flow was laterally sheared with landward flow over the south shoal and seaward flow throughout most of the channel and provided a distribution that compared favorably with cross estuary section analytical model resu lts An exa mination of depth averaged subtidal momentum balance terms contrasted the relative size b etween laterally induced along estuary advection and Coriolis acceleration during weakly stratified conditions over the channel slope In t he channel, asymmetric mixin g competed with laterally induced advection. Yet d uring stratified conditions, a large disparity between laterally induced along channel advection and the other terms suggested the longitudinal and vertical advection likely influenced the subtidal balance. Lastly a non dimensional number analysis provided evidence that lateral advection, Coriolis acceleration, and mixing asymmetries are, indeed, influential in the subtidal dynamics. Background In 1956, Pritchard outlined the dynamical framework for the sub tidal momentum balance in a coastal plain estuary. The results of his study proposed the residual

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82 circulation in the James River was gravitationally driven by pressure gradient and balanced by stress divergence. This resulted in a two layer residual exchan ge flow characterized by inflow of dense ocean water in the lower layer and outflow of less dense river water in the upper layer. More recently, Lerczak and Geyer (2004) proposed with numerical model results that laterally induced along channel advection w as larger than along channel pressure gradient during stratified conditions, thereby influencing the subtidal dynamical balance. Scully et al. (2009) found similar results using a numerical model and demonstrated that advective terms driven by lateral flow s augmented the baroclinic pressure gradient, thus enhancing residual circulation. On the other hand, it has been shown by Jay (1991) that tidal asymmetries in mixing can enhance the gravitational exchange flow and also need to be considered in the subtida l momentum balance. The objective of this study is to explore the roles of laterally induced nonlinear advection and asymmetries in tidal mixing in the along channel subtidal momentum balance using observations from the James River. Background on Mixing As ymmetries T idal asymmetries in mixing represent the covariance between tidal fluctuations of eddy viscosity and tidal variations of vertical shear. They develop from the interaction of tidal velocities that vary in direction with the tide and along channel density gradient that acts in the same direction (Jay, 2010). Typically during flood, dense ocean water intrudes the estuary, enhancing tidal flows and resulting in the breakdown of stratification through vertical mixing. Oppositely during ebb, ou tflowing currents enhance stratification, thereby suppressing mixing. The asymmetry in mixing between flood and ebb leads to tidal mixing asymmetries. The tidally averaged stress divergence

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83 representing vertical mixing, is comprised of a tidal mean (denoted by an overbar) and a tidal fluctuating component (by primes in Equation 4 1): (4 1) where A z is the vertical eddy viscosity (m 2 /s), u is the along channel velocity (m/s), and z is the vertical coordinate (m). The first term on the right hand side of the equation is related to the mean circulation, whereas the second term is linked to the tidal circulation (Jay, 2010). Several recent studies have explored the flow induced by tida l asymmetries in mixing. Stacey et al. (2008) used a numerical water column model to explore the residual flow generated by mixing asymmetries associated with tidal asymmetries in density stratification. Results showed that the mixing asymmetry induced flo w followed the same vertical structure as gravitationally induced flow and featured similar magnitudes. In 2010, Cheng et al. also explored the residual currents induced by asymmetric tidal mixing in weakly stratified narrow estuaries and found that it was strongly dependent on the timing of large vertical mixing. Stronger vertical mixing during flood produced a residual flow structure that favored the gravitational exchange flow. While strong vertical mixing during ebb induced a residual flow that competed with gravitational circulation. Chapter 4 is organized as follows: the Methods section describes the study site and outlines data collection and processing. Results begins describing the study site by introducing tidal variations in mixing across the tran sect to present the asymmetric temporal distribution of mixing as it varies from flood to ebb and from neap to spring tidal conditions. Next, the tidally averaged hydrography, velocities and mixing components are displayed to introduce vertical mixing. The flow induced by the mixing

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84 asymmetries is then compared with analytical model results The mixing asymmetries and laterally induced along channel advection are compared and their relative influence is evaluated with depth averaged subtidal momentum balanc e terms. Lastly, the comparative significance of subtidal terms is evaluated with a non dimensional number analysis. The Discussion section places the observations in context of the subtidal momentum balance and compares observed residual flow induced by m ixing asymmetries with analytical and numerical model results. Lastly, the main message is presented in Conclusions Methods This investigation takes place in the James River, the southernmost tributary of the Chesapeake Bay ( Figure 4 1a). The James River is partially mixed, fe aturing a top to bottom density anomaly difference of 6 to 18 kg/m 3 at the study site. The main tidal harmonic constituent is semi diurnal with a Form factor F=0.213. Neap tidal amplitudes reach 0.2 m, while spring tidal amplitudes more than double to 0.45 m (Shen and Lin, 2006). The James River has a vertically sheared and laterally sheared residual circulation with landward flow near the bottom, in the channel, and seaward flow near the surface and from surface to bottom over shoal s (Valle Levinson et al 2000). The area receives a mean annual discharge of 200 m 3 /s (Shen and Lin, 2006). The wind regime of the Chesapeake Bay is characterized by intermittent pulses of wind lasting 2 to 7 days and has seasonal variations with dominan t southward winds in winter months (November to February) and northward winds during the summer months (Li et al., 2005). Measurements were collected along a 2 km transect approximately 20 km landward of the mouth. A cross section of the study area (lookin g seaward) displays a ~10 m deep channel in between t wo 4 6 m flanking shoals ( Figure 4 1 b).

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85 Data Collection Measurements of current velocity and microstructure profiles were collected during a neap and spring tidal cycle in May 2010 with the purpose of q uantifying asymmetries in tidal mixing. A1200 kHz RDI Acoustic Doppler Current Profiler (ADCP) collected profiles of velocity, while a PME Self Contained Autonomous Microstructure Profiler (SCAMP, 100 Hz resolution) collected profiles of electrical conduct ivity and temperature gradient for a tidal cycle (~12.4 hrs). The ADCP was pointing downward on a 1.2 m catamaran that was towed off the side of a boat a speeds of 1.5 m/s to 2 m/s. The ADCP sampled at 2 Hz collecting velocity measurements with a 0.25 m ve rtical resolution ranging from 0.5 m to 10 m depth. The SCAMP was deployed at 4 locations across the estuary as d epicted by red circles ( Figure 4 1 b ) which were selected to represent two shoals, the deepest section of the channel, and a gently sloping inc lination that connected the south shoal to the channel. The instrument descended at 1 cm/s and collected measurements at 100 Hz. Data Processing Turbulent Kinetic Energy (TKE) dissipation can be quantified using the Ozmidov length scale, L o described b y Thorpe (1977). The is calculated using Thorpe length scales, L t computed from Thorpe displacements, d ( Equation 4 4): (4 2) (4 3) (4 4) where g is gravity; o is reference density and is density. N denotes buoyancy frequency ( Equation 4 3) and is a measure of stratification. It represents the frequency a

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86 parcel of fluid will oscillate in a stratified water column. The constant, C in Equation 4 4 was found by Peters et al. (1988) to be 0.91 and represents the relationship between the Ozmi dov and Thorpe length scales The Thorpe displacements, d were calculated using the sorting algorithm included in the SCAMP processing software. Density profiles measured by SCAMP are statically unstable at scales <0.1 m and the algorith m sorts the profile to be monotonically increasing. Sorting allows calculation of the distance between the location of unstable density measurements from the original profile to the location in the sorted profile. Equation 4 4 shows that L T is calculated b y finding the root mean square of d in each bin of the vertical profile. The L T represents the vertical distance over which heavier water is actually observed over lighter water and indicates the length scale of a turbulent eddy. The vertical eddy diffusi vity of a tracer (e.g. salt), K Z can be calculated using efficiency, m ef times the ratio of turbulent kinetic energy (TKE) dissipation, to squared buoyancy frequency, N 2 (4 5) A constant m ef of 0.20 has been implemented in previous studies (Peters, 1997) under the assumption that the flux Richardson number, R f does not exceed a critical value of 0.15. This is unlikely a valid assumption because of periodicity of stratification in partially mixed estuaries. To estimate a ) parameterization was implemented to calculate a turb ulent Prandtl number, Pr t as a function of the Richardson number, R i :

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87 (4 6) (4 7) Baumert and Peters (2009) showed that for R i > 0.5, TKE is converted to wave energy and turbulence does not exist. Following the method of Ilicak et al. (2008), Pr t = 10 for all R i values larger than this threshold. Pr t represents the ratio of the flux Richardson number, R f to R i : (4 8 ) When is used to estimate the mixing efficiency, a function of R f : (4 9) Given that a depth and time dependent mixing efficiency can be quantified, the vertical eddy diffusivity values are used to calculate the vertical eddy viscosity using the relationship that the Pr t is equal to ratio of the vertical eddy viscosity, A Z to K Z : (4 10 ) Now that the theory behind quantifying A Z has been described, the detailed data processing steps are outlined next. The raw ADCP velocity data were calibrated to remove compass errors (Joyce, 1989) and averaged over 10 seconds to produce a spatial resolution of 10 to 20 m. The continuous data set was separated by the start and stop time of each transect and interpolated onto a rectangular grid. The grid for each transect was 45 by 77 cells with a resolution of 0.25 m in the vertical and 25 m in the horizontal. Velocity components were rotated from East West and North South to along and across estuary directions. Velocit y profiles were extracted for each transect at the 0.12, 0.55, 1.37, and 1.94 km

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88 distances from the transect origin to build velocity time series for each station, to make them coincide with the location of SCAMP profiles. Vertical gradients in velocity we re calculated by vertically differentiating the along and across channel velocity time series at each station. The raw SCAMP profiles were divided into stations. Buoyancy frequency values, N were calculated with the SCAMP processing software and were ave raged into 30 cm bins. Values of L T were determined by calculating the root mean square of the Thorpe displacements (also calculated via SCAMP processing software), of each 30 cm bin. Both the N and d profiles were de spiked by removing outlier values abov e the 95 th and below the 5 th percentile to eliminate outliers. The vertical eddy viscosity values were interpolated onto the velocity shear grid. These values were multiplied together and differentiated in the vertical to yield the stress divergence. When plotting the along and across channel velocity shears, buoyancy frequency, Thorpe length scales, TKE dissipation, vertical eddy viscosity and along and across channel stress divergence, a two dimensional filter was applied to smooth these distributions. To compute the tidally averaged stress divergence, a least squares fit was applied to the stress divergence to yield the mean values (left hand side of Equation 4 1). The mean contribution of the total mean stress divergence (first term of right hand side of Equation 4 1) was calculated by applying a least squares fit to the vertical eddy viscosity and vertical shear in along channel velocity separately. The mean values were then multiplied and differentiated to achieve the mean contribution. The amplitude s and phases obtained from the least squares fit of the vertical eddy viscosity and velocity shear were used to reconstruct the signal (without the mean component) to obtain the

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89 tidal fluctuations. These values were then multiplied, averaged, and verticall y differentiated to obtain the mean of the tidal fluctuations (last term of Equation 4 1). A method was developed by Burchard and Hetland (2010) that decomposed the residual flow into contributions from tidal straining, gravitational circulation, wind str aining and depth mean residual flow from freshwater runoff. The technique was derived from tidally averaged momentum equations and was extended to a parabolic cross section in Burchard et al. (2011) to explore lateral variability. In these models, tidal mi xing asymmetries were represented inside the tidal straining mechanism. They found that in weakly stratified estuaries, the residual exchange flow was dominated by tidal straining. However, during stronger stratification, advective and gravitationally indu ced flow increased considerably while the tidal straining contribution collapsed and became negative. Burchard et al. (2012) used an idealized modeling study to investigate the role of tidal straining, expressed as the covariance between vertical eddy visc osity and vertical shear, on the residual exchange flow. They found that in well mixed estuaries, the total tidal straining is dominated by the interaction of tidal asymmetry in lateral advection of along channel shear and vertical eddy viscosity. The clas sical longitudinal tidal straining (Simpson et al., 1990) accounts for the minor part of the total tidal straining, thereby expressing the effects of lateral circulation on tidal straining and the residual flow. Cheng et al. (2013 ) developed another analy tical model that that is an extension of previous analytical models (Ianniello, 1977; McCarthy, 1993, Cheng et al., 2011) and includes across estuary sections. It solves tidally averaged momentum and continuity equations for each component of residual curr ents such as: river discharge, along

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90 estuary density gradients, nonlinear advection, asymmetric tidal mixing, and wind. The flow induced by tidal mixing asy mmetries from Cheng et al. (2013 ) will be used to compare with these observations, keeping in mind t hat these results were obtained using an idealized numerical experiment simulating a weakly stratified estuary with strong tidal forcing. To calculate the mixing asymmetry induced flow from observations, the balance for tidal mixing asymmetries from Cheng et al. was modified to reflect fixed z rather than sigma coordinates to estimate the residual flow composition. While sigma coordinates are beneficial in estimating the residual flow induced by Stokes return flow, the goal of this research is to compare th e residual flow from tidal asymmetries. Therefore, f ixed coordinates were used. Assuming an along estuary momentum balance between the total tidally averaged stress divergence (mean and fluctuating) and the barotropic pressure gradient: (4 11 ) The first term on the far right hand side (r.h.s) represents the vertical gradient of the tidally averaged vertical eddy viscosity and tidally averaged vertical shear of along channel. The second term on the r.h.s represents the vertical gradient of the ti dally averaged covariance of the tidal fluctuations of vertically eddy viscosity and vertical shear of along channel velocity. Given that the total stress divergence (second term in Equation 4 12) is a known quantity, it can substitute the pressure gradie nt and the equation is solved for :

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91 (4 12) The results of the neap and spring tide observations using methods detailed above are presented next with the objective of determining the relative influence of mixing asymmetries and lateral advection in the subtidal dynamics. Results The results are presented as a side by side fortnightly comparison of tidal and subtidal parameters. First, the tidal evolution of vertical mixing at each location is presented to categorize the distribution of mixing Ne xt, the tidally averaged density anomaly and buoyancy frequency are described to outline the fortnightly variability of tidally averaged stratification. The along and across estuary residual flow patterns are described next and will be used as a baseline to compare with the residual flow induced by asymmetric mixing. Next, the tidally averaged vertical eddy viscosity and along channel shear contours are shown to introduce the framework for vertical mixing. The total, mean and fluctuating stress divergence distributions are then compared The fluctuating stress divergence values were then used to estimate the mixing induced residual flow, which is compared to analytical model results. The along channel advection from lateral flows and mixing asymmetries are displayed to determine their role in the subtidal momentum balance. The results are tied together with an evaluation of depth averaged terms in the subtidal momentum balance and the comparative influences are evaluated using multiple non dimensional number s

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92 Tidal Variability of Vertical Mixing The fortnightly comparison of stress d ivergence is presented in Figure 4 2 to determine the phase of the tide that exhibited the greatest mixing. The intratidal variability determines if the asymmetry is typical (larger mixing during flood) or atypical (larger mixing during ebb). The along channel velocity distribution during neap conditions demonstrated that sampling began during ebb (positive) and concluded at the end of flood (negative) ( Figure 4 2 a). Along ch annel stress divergences are presented for the north flank (Fig ure 4 2 c), the channel ( Figure 4 2 e), the channel slope ( Figure 4 2 g), and the south flank ( Figure 4 2 i). Observations d epicted 10 5 m/s 2 stress divergence values near bottom during flood a nd established a typical mixing asymmetry. During spring tides, the along channel velocity distribution showed that sampling began during flood ( Figure 4 2 b). The stress diverge nce distribution revealed a more complicated mixing asymmetry than that observ ed during the neap survey The north flank revealed large vertical mixing throughout the cycle, with peak values (10 4 m/s 2 ) observed during maximum flood velocities ( Figure 4 2 d). L arger values were observed at depth during flood than ebb in the channel, proposing a typical mixing asymmetry ( Figure 4 2 f). However, comparable values were also observed near surface during late ebb and suggested an atypical mixing asymmetry at the surface. The channel slope displayed typical mixing asymmetry, demonstrated b y 10 5 m/s 2 near bottom values during flood ( Figure 4 2 h). Y et the south flank displayed atypical mixing asymmetry, and featured 10 4 m /s 2 values at the surface ( Figure 4 2j). Tidally average d density anomaly and buoyancy frequency contours are presented next to examine the spatial distribution of subtidal stratification.

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93 Stratification Cross sections ( looking seaward ) of tidally averaged density anomaly contours are presented for neap ( Figure 4 3a) and spring ( Figure 4 3c) tidal conditions. During neap tide the density anomaly ranged from <8 to 14 kg/m 3 and featured the largest values at depth in the c hannel and smallest values near surface. The isopycnals from the surface to 5 m depth were ti lted from left to right, which indicated a negative density gradient that would generate lateral flow to the south (right). The spring survey density observations revealed more mixed conditions, with values that ranged from 8 kg/m 3 at the surface to 11 kg/ m 3 over the south shoal. To put this in context of stratification, buoyancy frequency values were investigated. The tidally averaged buoyancy frequency contours during neap tide exposed the weakest stratification (0. 0 2 s 1 ) at depth across the transect ( F igure 4 3 c ). The pycnocline was observed at 2 m depth, ranged from 0.09 to 0.12 s 1 and revealed the greatest stratification over the flanks. The spring survey displayed buoyancy frequency observations depicting weak stratification at depth from chan nel to the south shoal and near surface over the north shoal ( Figure 4 3 d). The weakest stratification (<0.2 s 1 ) was observed in the channel, while the greatest stratification was observed near surface from the channel slope to the sou th flank and near botto m of the north flank. Now that the stratification of the system during neap and spring tidal conditions have been discussed, the along and across channel residual flow distributions will be examined next. Residual Flows The along channel residual exchange flow during neap tide featured a combined laterally and horizontally sheared distribution ( Figure 4 4 a). Landward flo w ( 0.11 m/s)

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94 was observed near bottom and over the north flank and seaward fl ow (0.05 m/s) was observed near surface from the south flan k to the middle of the channel. During spring, the residual exchange flow was larger and featured a similar distribution, although the seaward flow extended only to the channel slope and approached 0.15 m/s. Larger exchange flows are typically observed dur ing neap, assuming the pressure gradient is balanced by friction because of the suppression of mixing, as indicated by the Hansen and Rattray (1965) scaling for residual flow: (4 13 ) where C o is an integration constant and H is water depth. Given that the eddy viscosity is in the denominator, a smaller value would yield larger results. Since A Z values are characteristically larger during spring than neap tide the exchange flow should be weaker, which was not observed. This f inding suggested that another term must have influence the along channel subtidal momentum balance. Given that intratidal lateral velocities exposed a secondary circulation that reversed with the tide, the tidally averaged lateral flow distribution was dis played next to investigate the residual influences. The tidally averaged across estuary velocities during neap tide displayed a three layer distribution, demonstrated by larger northward 0.06 m/s flow in the lower channel and smaller ~ 0.02 m/s flow near surface over the channel slope and south flank between 0.04 m/s southward flow ( Figure 4 4 b). The spring survey displayed a two layered vertically sheared distribution characterized by 0.05 m/s northward flow in the lower channel and ~0.05 m/s southward flow everywhere else ( Figure 4 4 d).

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95 Vertical Mixing The spatial structure of the tidally averaged vertical eddy viscosity A z during neap tide showed the largest values (10 4. 5 m 2 /s) in the lower half of the channel ( Figure 4 5 a). This compared favorably with the largest vertical mixing tha t occurred near bottom ( Figure 4 2 ) During spring tide, the distribution displayed the largest values (10 3 .5 m 2 /s) near surface over the channel and near bottom of the north flank and north wall of the channe l ( Figure 4 5 c). Large 10 4.25 m 2 /s values were also displayed near surface over the south flank. These distributions reveal ed that eddy viscosity values were larger during spring than neap, as expected. The tidally averaged vertical shear in along channe l velocity during neap demonstrated small positive shears (~0.005 s 1 ) near bottom across the transect and represented the mean flow interacting with the bottom ( Figure 4 5 b). Between 2 and 4 m depth from the channel to the south flank, large negative she ars ( 0.06 s 1 ) were observed beneath positive shears and represented a distribution that developed from a jet that briefly formed in the pycnocline after maximum ebb. The spatial structure varied during spring and displayed large positive shears near bott om and the largest values (~0.005 s 1 ) between 2 and 4 m from the north flank to the channel ( Figure 4 5 d). Large neg ative shears were observed near surface over the south flank. Given that stress diver gence describes the divergence o f the covariance of t hese two parameters the stress divergences will be explored next. The total stress divergence for neap ( Figure 4 6 a) and spring ( Figure 4 6 b) conditions varied by one order of magnitude. The neap vertical mixing ranged from 3e 6 to 1e 6 m/s 2 and demonstrated a two layer distribution across most of the transect. The structured featured negative values near surface and positive values beneath and

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96 highlighted the confinement of vertical mixing to the lower half of the water column. During the sp ring survey, the values were larger (1e 5 to 1e 10 5 m/s 2 ) and exposed a three layer distribution in the channel, two layer over the channel slope, and uniform distribution over the south flank The largest positive values were observed o ver the north flan k, extended to the surface of the channel and depicted large near surface vertical mixing. Weaker positive values were observed near bottom and indicated frictional influences. The divergence of the covariance of the mean eddy viscosity and mean vertical shear is presented for neap ( Figure 4 6 c) and spring ( Figure 4 6 d) tidal conditions and represents one component of Figures 3 6 a and 3 6 b. During neap the values ranged from 5e 7 to ~9e 7 m/s 2 and reflected a three layer distribution in the channel. During spri ng, values ranged from 1e 5 to 1e 5 m/s 2 and also displayed a three layer structure in the channel (similar to total stress divergence) and a nearly uniform positive structure over the south flank. The mixing asymmetries are presented in Figures 3 6 e (neap) and 3 6 f (spring) and demonstrated the final component of the total stress divergence. During neap tide, values ranged from 1e 7 to 1e 6 m/s 2 and reflected a two layered distribution demonstrated by negative values near surface and p ositive values beneath The values ranged from 1e 5 to 5e 6 m/s 2 during the spring survey Pos itive values were observed near surface and bottom, while negative values emerged between. Over the channel slope and south flank, a two layer distribution revea led negative values in the upper layer and positive values beneath. The flow induced by the fluctuating component of the stress divergence will be compared to analytical model results next.

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97 Mixing Asymmetry Induced Flow Observations and Model Comparison T he spatial distribution of the residual flow induced by asymmetries in mixing, i.e. Figure 4 6 e for the neap tidal conditions, is shown in Figure 4 7 a. The flow ranged from 0.03 to 0 .01 m/s and was laterally sheared, featuring landward flow over the nor th shoal and half of the north channel wall and seaward flow everywhere else. This residual flow opposed the observed residual exchange flow from the middle of the north wall of the channel to the north flank and near the surface from the channel to the so uth flank. This influence was clearly identified in the observed residual flow distribution over t he north flank, where values were near zero. Asymmetries in mixing in the channel enhanced the residual exchange flow in the lower half of the channel. During spring, the flow induced by asymmetries in mixi ng ranged from ~ 0.01m/s to 0.06 m/s and was predominantly landward with several regions of weak seaward flow near surface over the channel slope and flank ( Figure 4 7 b). The largest velocities were observed over the channel slope and reflected the greatest near bottom disparity in vertical mixing that was observed during spring ( Figure 4 2 h). The results of Cheng revealed a laterally sheared distribution with seaward flow i n the channel and landward flow over the shoals. This distribution opposed the total residual flow at depth in the channel and over the shoals. While the neap tidal mixing asymmetry induced flow was laterally sheared near the north shoal, the flow enhanced the exchange flow in the channel of the observations, while the analytical model results competed with it. The asymmetric mixing induced flow during spring was similar to analytical model results over the south flank, featuring landward flow throughout th e water column. Also, the distribution featured mainly outflow in the channel. However, marginal d ifferences between analytical model results

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98 and observed asymmetric mixing induced flow during spring emerged over the north flank and channel slope. Now that the flow induced by asymmetries in mixing has been discussed, the asymmetri c mixing and along channel advection from lateral flows are compared next. Advection and Mixing Asymmetry Comparison The tidal fluctuating mixing asymmetries that have been previously described are compared with along channel advection influenced by lateral flows, in Figure 4 8. The neap tide displayed advection values that ranged betwe en 2 e 5 to 2e 5 m/s 2 ( Figure 4 8 b). The advective accelerations are two orders of magni tude larger than mixing asymmetries and depicted a laterally sheared structure beneath the surface of the channel and negative values at the surface over the north flank and channel. These terms appeared to enhance one another at the surface over the chann el and compete with one another near bottom over the channel slope, but never canceling each other out. During spring, the advection values are comparable to the mixin g a symmetries and ranged from 1e 5 to 1e 5 m/s 2 ( Figure 4 8 d). From the surface to 4 m depth, these values compete with each other, suggesting these two terms cancel each other out in the upper layer of the water column. Beneath, these terms seem to marginally enhance one another. The depth averaged terms from the momentum balance were compared next to obtain a clearer representation of the rela tive significance of each term. Depth averaged Subtidal Momentum Terms The depth averaged mean, and mean fluctuating, components of the tidally averaged stress divergence were compared with Coriolis,

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99 and laterally induced along channel advection, to establish the relative contributions to the momentum budget. The neap tide results displayed very small values for the vertical mixing terms and Coriolis acceleration and depicted advection values that were an order of magnitude larger at the north wall of the channel ( Figure 4 9 a). Given that the laterally induced along channel advection was markedly larger than the other terms, the along channel advection was calculated using ADCPs moored in two longitudinal locations in the channel. The longitudina l advection was balanced both Coriolis and laterally induced advection. This suggested that vertically inf luenced along channel advection, was significant the momentum balance in the channel These findings suggested the importance of advection terms the subtidal along channel momentum balance. Similar to these findings, Basdurak and Valle Levinson (2012) found that non linear advective terms were important in subtidal dynamics by exhibiting values the same order of magnitude as pressure gradient and friction. Further, results revealed that longitudinal advection often competed wi th laterally induced advection, as observed in the channel of this study. The spring tide observations showed values of the same order of magnitude for all terms ( Figure 4 9 b). In the channel, the advection and mean fluctuating stress divergence compete d with one another and seemingly nearly cancel. The balance varied o ver t he channel slope where Coriolis and laterally induced advection compete d To further explore the relative contributions of the terms in the subtidal momentum balance, a collection of n on dimensional numbers were examined

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100 Non dimensional Analysis Six non dimensional numbers were used to assess the relative importance of various subtidal momentum balance terms with one another. The Simpson number, S i was calculated to explore variat ion s in the longitudinal buoyancy gradient: (4 14) where g is the gravity, U is the the root mean square of near bottom velocities (at bin 2), H is the mean water depth, is the longitudinal near bottom density gradient. The The Ekman number, E k was used to explore ratio of tidally averaged vertical mixing to Coriolis acceleration: (4 15 ) A new Ekman number was proposed, comparing the mixing asymmetries to Coriolis a cceleration and will be termed the fluctuating Ekman number, E kf :

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101 (4 16 ) The Rossby number, R o was used to compare tidally averaged, laterally induced advection to Coriolis acceleration: (4 17 ) To explore the influence of laterally induced advection with vertical mixing, the estuarine Reynolds number, R e was used. (4 18 ) A second non dimension number was proposed, which demonstrated the relationship between laterally induced advection and mixin g asymmetries and was coined the fluctuating estuarine Reynolds number, R ef (4 18) The above mentioned non dimensional numbers were calculated using subtidal, depth averaged values and are presented across the transect during the spring and neap tide. During the neap survey, R o values were < 1 in the center of the channel and over the south flank and suggested that Coriolis acceleration dominated over laterally induced along channel advection in the subtidal balance ( Figure 4 10 a). However, values > 1 were present for the remainder of the tr ansect and confirmed that advection controlled in these areas, as previously discussed in the above section. T he subtidal E k

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102 and E k f numbers were < 1 everywhere except the channel slope, between 1 km and 1.4 km ( Figure 4 10a). The suggested that subtidal C oriolis acceleration dominated over subtidal vertical mixing over most of the transect. However, for 0.4 km over the channel slope, the total vertical mixing and mixing asymmetries were larger than Coriolis influences in the subtidal balance. The R e and R e f revealed that tota l subtidal mixing dominated over lateral advection in the middle of the channel, while both total mixing and mixing asymmetries dominated over the channel slope. These findings reinforce d the dominance of laterally induced advection a cross most of the transect, but highlight ed the influence of mixing asymmetries over the channel slope during neap tide. Even though mixing asymmetries are weak across most of the transect, they become influential over the channel slope, which demonstrated their importance in the subtidal balance. The spring survey again revealed R o values < 1 in the channel and south flank, but also at the junction between the channel and channel slope, around 1 km ( Figure 4 10 b). The subtidal E k suggested the dominance of Coriolis over vertical mixing over the south flank, similar to neap, but also over the channel slope. The E k f values were important over the channel slope, varying from neap, and indicated that mixing asymmetries were less influential in the subtidal dynamics of this region. The R e revealed that total mixing dominated over laterally induced advection over the north flank, channel, and south flank. The R e f emphasized the dominance of mixing asymmetries over the flanks and center of the chan nel. The spring tide survey showed that mixing asymmetries are important over the flanks and in the center of the channel and revealed results that varied from the neap observations.

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103 Discussion The objectives of this investigation were to determine the in fluence of mixing asymmetries on the residual flow and to examine the significance of mixing asymmetries and longitudinal advection from lateral flows. Previous numerical and analytical results have proposed that flow induced by mixing asymmetries will eit her enhance or compete with the density driven exchange flow depending on the temporal evolution of the stratification in the system. Stacey et al. (2008) and Cheng et al. (2010) presented 1 D models that supported a vertically sheared two layer asymmetry induced residual flow that enhanced the typical gravitational circulation (landward flow near bottom, seaward flow at surface) when greater mixing occurred during flood rather than ebb. Likewise, Cheng et al. (2010) investigated the case where greater mixi ng occurred on the ebb rather than the flood phase and found a two layer structure that competed with the gravitational circulation. Cheng et al. (2013 ) expanded upon this, developing a 3D analytical solution that determined a three layer horizontally shea red distribution featuring landward flow over shoals and seaward flow in the channel. The neap observations for mixing asymmetry induced flow revealed a spatial structu re similar to Cheng et al. (2013 and featured a laterally sheared distributi on near the north shoal. However the direction of the induced flow was reversed. Given that during neap, the largest mixing was observed near bottom during flood, these results are somewhat consistent with Stacey et al. (2008) and Cheng et al. dings because the near bottom flows enhanced gravitational circulation. The spring tide mixing asymmetry induced flow provided a more complex structure, which was somewhat vertically and horizontally sheared with two regions of very weak landward flow near surface and seaward flow everywhere else These observations

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104 compliment ed Cheng et al. (2013 by featuring a similar distribution over the south flank and throughout most of the channel. Similarities likely emerged between analytical model results during spring rather than neap because the analytical model was simulated using a weakly stratified estuary with strong tidal forcing, analogous to spring tide conditions. When comparing mixing a sym m etries with th e along channel advection induced by lateral flows, disparities emerged between neap and spring tides During neap tide, the fluctuating stress divergence is between one and two orders of magni tude smaller than advection. The distributions seem to enhance each other throughout much of the cross section. However during spring, these terms are comparable. In fact, from the surface to 4 m depth, the distribution seemingly canceled each other out. A depth averaged approach to the subtidal momentum balances reve aled a large inequality between laterally induced advection and the other terms during neap conditions. This suggested that the vertical and along channel advective terms are significant in the subtidal balance during stratified conditions The depth avera ged momentum balance comparison during spring conditions demonstrated that the relative influence of laterally induced along channel advection decreased during less stratified conditions. In the channel, mixing asymmetries and advection balance, while Cori olis competed with laterally induced advection over the channel slope. These results suggested that advection, Coriolis and asymmetric mixing are important in the subtidal momentum balance. A non dimensional analysis emphasized the relative importance of mixing asymmetries in the subtidal dynamics. During neap observations, when the water

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105 column was more stratified and the tidal velocities were smaller mixing asymmetries dominated over laterally induced advection and Coriolis acceleration over the channe l slope. At a similar distance across, the residual flow induced by asymmetric mixing showed the largest values, which enhanced the residual exchange flow. Spring observations exposed the dominance of mixing asymmetries over laterally induced advection and Coriolis acceleration at the south flank and center of the channel. However, in these areas, advection was much weaker that Coriolis, as shown through small Rossby numbers. In comparison to the mixing asymmetry induced residual flow, very weak seaward flo w emerged when R ef and R o were < 1, while the rest of the cross section displayed landward flow. Summary During stratified conditions, the flow induced by mixing asymmetries was laterally sheared and in concert with gravitational acceleration near bottom in the channel similar to previous theory. However, during spring when the water column was less stratified, the asymmetric mixing induced residu al flow displayed mainly inflow. Exceptions emerged at two areas where asymmetric mixing and Coriolis were larger than laterally induced advection and resulted in very weak seaward flow These results were similar to analytical model results in that they showed mainly landward flow in the channel. An invest igation into the subtidal dynamics revealed that asymmetric mixing was influencing the spring/neap disparity of laterally induced advection. Moreover, the relative influence of laterally induced advection, Coriolis acceleration, and asymmetric mixing in th e subtidal dynamics proposed that the balance consists of more than merely pressure gradient and friction.

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106 Figure 4 1. a) James River plan view of study site with transect denoted by black line and b) cross section looking seaward of study site highlighting each hydrographic station named Stations 1 through 4 from left to right.

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107 Figure 4 2 Neap conditions: a) Station 2 along channel velocity, u (m/s); along channel stress divergence, (m/s 2 ) c) Station 1, e) Station 2, g) Station 3 and i) Sta tion 4; Spring conditions: b ) Station 2 along channel velocity, u (m/s); along channel st ress divergence, (m/s 2 ) d) Station 1, f ) Station 2, h) Station 3 and j) Station 4.

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108 Figure 4 3. Tidally averaged density anomaly (kg/m 3 ) during a) neap and c) spring tide; tidally averaged buoyancy frequency N (s 1 ) during b) neap and d) spring tide.

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109 Figure 4 4. Along channel residual exchange flow u m (m/s) during a) neap and c) spring tide; across channel residual flow v m (m/s) durin g b) n eap and d) spring tide.

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110 Figure 4 5. Tidally averaged vertical eddy viscosity Log 10 [ A z (m 2 /s) ] during a) neap and c) spring tide; tidally averaged vertical shear in along channel velocity (s 1 ) during b) neap and d) spring tide.

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111 Figure 4 6. Neap tide: a) tidally averaged stress divergence (m/s 2 ), c) mean component of tidally averaged stress divergence (m/s 2 ), e) fluctuating component of tidally averaged stress divergence (m/s 2 ); spring tide: b) tidally averaged stress divergence (m/s 2 ), d) me an component of tida lly averaged stress divergence (m/s 2 ), f) fluctuating component of tidally averaged stress divergence (m/s 2 ); white lines indicate zero contours.

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112 Figure 4 7. Residual along channel exchange flow induced by mixing asymmetries u t (m/s ) for a) neap and b) spring tide.

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113 Figure 4 8. Neap tide a) fluctuating component of tidally averaged stress divergence (m/s 2 ) and b) tidally averaged along channel advective acceleration v du/dy (m/s 2 ); spring tide c) fluctuating component of tidally a veraged stress divergence (m/s 2 ) and d) tidally averaged along channel advective acceleration v du/dy (m/s 2 )

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114 Figure 4 9. Subtidal momentum balance for a) neap and b) spring. Black dashed line denotes zero. c) bathymetry. Yellow lateral advection; blue Coriolis; magenta along channel advection; red mean component stress divergence; green mean fluctuating component stress divergence.

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115 Figure 4 10 Non dimensional analysis for (a) neap and (b) spring tide conditions. The Ekman number, E k the fluctuating Ekman number, E kf the Rossby number, R o the estuarine Reynolds number, R e and fluctuating estuarine Reynolds number, R ef are present across the transect.

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116 CHAPTER 5 CONCLUSIONS T he lateral variability of the vertical structure of tur bulence dissipation at a cross section of the James River was examined Chapter 2 explored the vertical structure of TKE dissipation at two locations across the estuary and provided observations over several fortnightly cycles. Chapter 2 discerned mechanis ms influencing the greatest mode of dissipation. Chapter 3 examined vertical mixing across the estuary during two semidiurnal tidal cy cles (1 neap and 1 spring). The results of Chapter 3 used a more fine scale appr oach of examining turbulence tha n Chapter 2 but found simi la r mechanisms influencing near surface vertical mixing. Chapter 4 put the results of C hapter 2 in context of a tidally averaged stress divergence. Chapter 3 explored flood/ebb asymmetries in vertical mixing across the transect and determi ned their influence in subtidal dynamics. Summary The unifying theme in this work is that bottom generated turbulence does not dominate at all locations across the estuary and at all phases of the tide. Results from this research showed that near surface turbulence can develop during the greater floods in the channel and over the channel slope. Additional, near surface turbulence can develop during the greater ebb in the channel location and featured similar forcing mechanisms as flood dominated surface turbulence. Furthermore, vertical mixing results reve aled the development of surface mixing during spring in the channel and over the south flank. These results have implications in the scaling of the stress divergence term in modeling estuarine processes, which is often quantified using the quadratic bottom drag law. These consequences become evident when comparing flow

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117 induced by mixing asymmetries with flow predicted by models, which commonly feature an eddy viscosity profile that exhibits the largest values just above the bottom. The three crucial finding s of this research are outlined below. Near surface TKE Dissipation Previous studies found that turbulence was dominated by bottom friction in the channel of a partially mixed estuary. In this study, results have shown that not only was near bottom dissipa tion important in the channel, but also near surface dissipation generated by vertical gradients in across channel velocities. The vertical structure of dissipation varied across the estuary, finding the largest values near surface over the channel slope. The main result of this investigation is that lateral circulation during the greater flood phase can produce vertical shears in across channel flows that favor the appearance of maximum dissipation at the surface, depending on the position across the estua ry. Therefore, these results provoke the necessity to revisit the modeling of estuarine circulation Near surface Vertical Mixing This investigation confirmed that near bottom vertical mixing was greatest during maximum flood across the estuary and was cons istent with Peters (1997) findings. A revealing finding developed later in the ebb phase of the tidal cycle, when large near bottom and surface vertical mixing arose at several locations across the estuary. While near bottom mixing was generated by bottom stresses, as expected, surface mixing developed from the combined influence of along estuary vertical shear from a velocity jet in the pycnocline and large vertical shear from lateral flows moving in opposite directions. This new finding proposes that near bottom vertical mixing may dominate during flood, however ebb near surface mixing can dominate depending on the location

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118 across the estuary and develop from mechanisms uncoupled from bottom friction. Therefore, vertical mixing shows different structure a cross the estuary. Investigations in other estuaries should provide generalities on this finding. Tidal Asymmetries in Vertical Mixing and Subtidal Dynamics When typical mixing asymmetry was observed across the transect, the flow induced by mixing asymmet ries was laterally sheared and in concert with gravitational acceleration near bottom in the channel. These results were somewhat comparable with previous studies. However, the complex vertical mixing distribution during spring provided results that did n ot compare with analytical or numerical results. The subtidal along channel momentum balance showed that nonlinear advection and Coriolis are of the same order of magnitude or larger than the mean and fluctuating components of stress divergence. Moreover, the relative importance of nonlinear advection increased under st ratified conditions and suggested that the subtidal balance consists of more than just pressure gradient and friction. Implications of Findings The results of this research provide evidence t hat bottom generated turbulence does not dominate the profile at all locations across a partially mixed estuary. The lateral variability of this finding draws the necessity to reexamine residual estuarine modeling, which commonly uses a bottom drag formul ation for friction and requires no knowledge of vertical eddy viscosity. Significant asymmetries were observed between flood and ebb at varying locations in the water column (not only near bottom) and resulted in discrepancies between the observed residual flow induced by these asymmetries and those predicted by numerical and analytical models. This outcome therefore leads to the requirement to reconsider how vertical eddy viscosity is

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119 parameterized in estuaries and the subtidal momentum balance often assum ed to predict estuarine circulation.

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120 LIST OF REFERENCES Basdurak, N. B., A. Valle Levinson, 2012: Influence of advective accelerations on estuarine exchange at a Chesapeake Bay tributary. Journal of Physical Oceanography 42 1617 1634. Baumert, H. Z. and H. Peters, 2009: Turbulence closure: turbulence, waves and the wave turbulence transition Part 1: Vanishing mean shear. Ocean Sciences 5 47 58. Burchard, H. and R. D. Hetland, 2010: Quantifying the contributions of tidal straining and gravitational acceleration to residual circulation in periodically stratified tidal estuaries. Journal of Physical Oceanography 40 1243 1262. Burch ard, H., H. Schuttelaars, 2012: Analysis of tidal str aining as driver for estuarine circulation in well mixed estuaries. Journal of Physical Oceanography, 42 261 271. Burchard, H., P. D. Craig, J. R. Gemmrich, H. van Haren, P. Mathieu, H. E. Markus Meier, W. A. M. Nimmo Smith, H. Prandke, T. P. Rippeth, E. D. Skyllingstad, W. D. Smyth, D. J. S. Welsh, H. W. Wijesekera, 2008: Observational and numerical modeling methods for quantifying coastal ocean turbulence and mixing. Progress In Oceanography 76 Issue 4, 399 442. Burchard, H., R. D. Hetland, E. Schulz, H. M. Schuttelaars, 2011: Drivers of residual estuarine circulation in tidally energetic estuaries: straight and irrotational channels with parabolic cross section. J. Phys. Oceanography, 41 548 570. Chant, R. J., 2010: Estuarine secondary circulation In A. Valle Levinson (Ed.), Contemporary issues in estuarine physics (145 182). New York: Cambridge University Press. Cheng, P., A. Valle Levinson, H. E. de Swart, 2010: Residual currents induced by asymmetric tidal mixing in weakly stratified narrow estuaries. Journal of Physical Oceanography 40 2135 2147. Cheng, P., A. Valle Levinson, H. E. de Swart, 2011: A numerical study of residual circulation induced by asymmetri c tidal mixing in weakly stratified narrow estuaries. Journal of Geophysical Research 116 C01017, doi:10.1029/2010JC006137. Cheng, P. M. Li, A. Valle Levinson, 2012: Decomposition of Residual Estuarine Currents. Submitted to Continental Shelf Research Collignon, A., M. Stacey, 2013: Turbulence dynamics at the shoal channel interface in a partially stratified estuary. Journal of Physical Oceanography Doi:10.1175/JPO D 1 3 0115.1, in press.

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121 Craig, P. D., M. L. Banner, 1994: Modeling waves enhanced turbule nce in the ocean surface layer. Journal of Physical Oceanography. 24 2546 2559. Gargett, A. E., J. R. Wells, 2007: Langmuir turbulence in shallow water. Part 1. Observations. Journal of Fluid Mechanics 576 27 61. Gerbi, G. P., J. H. Trowbridge, E. A. Te rray, A. J. Plueddemann, T. Kukulka, 2009: Observations of trubulence in the ocean surface boundary layer: Energetics and transport. Journal of Physical Oceanography 39 1077 1096. Geyer, R. W. M. E. Scully, D. K. Ralston, 2008: Quantifying vertical mix ing in estuaries. Environmental Fluid Mechanics 8 495 509. Gey er, W. G., J. H. Trowbridge, M. M. Bowen, 2000: The dynamics of a partially mixed estuary. Journal of Physical Oceanography 30 2035 2048. Haas, L.W.,1977: The effect of the spring neap tidal cycle on the vertical salinity structure of the James, York and Rappahannock Rivers, Virginia, U.S.A. Estuarine and Coastal Marine Science 5(4), 485 496. Hansen, D. V., M. Rattray, 19 65: Gravitational circulation in str aits and estuaries. Journal of Marine Research 23 104 122. Ilicak, M., T. M. Ozgokmen, H. Peters, H. Z. Baumert, and M. Iskandarani., 2008: Performance of two equation turbulence closures in three dimensional simulations of the Red Sea overflow. Ocean Mo delling 24 12 3 139. Jay, D. A., 2010: Estuarine Variability. In A. Valle Levinson (Ed.), Contemporary issues in estuarine physics (6 3 99). New York: Cambridge University Press. Jay, D. A., Smith, D., 1990: Circulation, density distribution and neap sprin g transitions in the Columbia River Estuary. Progress in Oceanography 25 81 112. Jay, D. A.,1991: Internal asymmetry and anharmonicity in estuarine flows. In B. B. Parker (Ed.), Progress in Tidal Hydrodynamics (521 566), John Wiley & Sons, New York. Joyc e, T.M., 1989: board ADCPs. Journal of Atmospheric and Oceanic Technology 6 169 172. Lerczak, J. A., W. R. Geyer, 2004: Model l ing the lateral circulation in straight, stratified estuaries. Journal of Physical Oceanography 34 1410 1428. Li, M., L. Zhong, W. C. Boicourt, 2005: Simulations of Chesapeake Bay estuary: Sensitivity to turbulence mixing parameterizations and comparison with observations. Journal of Geophysical Research 110 C12004, doi:10.1029/2004JC002585

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122 Li, M. S. Radhakrishna n, U. Piomelli and W. R. Geyer., 2010 : Large Eddy Simulation of the tidal cycle variations of an estuarine boundary layer. Journal of Geophysical Research, 115 C08003, doi:10.1029/2009JC005702. Monismith, S. G., 2010: Mixing in estuaries. In A. Valle Levinson (Ed.), Contemporary issues in estuarine physics (145 182). New York: Cambridge University Press. Nikora V.I. and D. G. Goring, 1999: On the relationship between Kolmogorov's and generalized structure functions in the inertial subrang e of developed turbulence. Journal of Physics A: Gen. Math. 1999, 32 4963 4969. Osborn, T.R., 1980: Estimates of the local rate of vertical diffusion from dissipation measurements. Journal of Physical Oceanography 10 83 89. Peters, H., 1997: Observatio ns of stratified turbulent mixing in an estuary: neap to spring variations during high river flow. Estuarine, Coastal and Shelf Science 45 69 88. Peters, H., M. C. Gregg, J. M. Toole, 1988: On the parameterization of equatorial turbulence. Journal of Geo physical Research 93 1199 1218. Pritchard, D. W, 1956: The dynamic structure of a coastal plain estuary. Journal of Marine Research 15 33 42. Rippeth, T.P., N R. Fisher, and J. H. Simpson, 2001: The cycle of turbulent dissipation in the presence of tidal straining. Journal of Physical Oceanography, 31 2458 2470. Sauvageot, H.,1992: Radar Meteorology 334, Artech House, Norwood, Massachusetts. Scully, M. E., C. T. Friedrichs, 2007: The importance of tidal and lateral asymmetries in stratification to residual circulation in partially mixed estuaries. Journal of Physical Oceanography 37 1496 1511. Scully, M. E., W. R. Geyer, J. A. Lerczak, 2009: The influence of lateral advection on the residual estuarine circulation: a numerical modeling study of the Hudson River Estuary. Journal of Physical Oceanography 39 107 124. Scully, M.E., W. R. Geyer 2012: The role of advection, straining, and mixing on the tidal variability of estuarine stratification Journal of Physical Oceanography 42 855 868. Shen, J., J. Lin, 2006: Modeling study of the influences of tide and stratification on age of water in the tidal James River. Estuarine, Coastal and Shelf Science 68 101 112. Simpson, J. H., J Brown, J. M atthews, G. Allen, 1990: Tidal straining, density currents,

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123 and stirring in the control of estuarine stratification. Estuaries 13 125 132. Simpson, J. H., W. R. Crawford, T. P. Rippeth, A. R Campbell, and J. V. S. Cheok, 1996: The vertical structure of turbulent dissipation in shelf seas. Journal of Physical Oceanography 26 1579 1590. Simpson, J.H., C. M. Allen, and N. Morris, 1978: Fronts on the Continental Shelf. Journal of Geophysical Research 83(C9): doi: 10.1029/0JGREA0000830000C9004607000001. Souza, A. J., L. G. Alvarez, and T. D. Dickey (2004) Tidally induced turbulence and suspended sediment. Geophysical Research Letters 31 L20309, doi:10.1029/2004GL021186. Stacey, M. T., J. P. Fram, F. K. Chow, 2008: Role of tidally periodic density strati fication in the creation of estuarine subtidal circulation. Journal of Geophysical Research 113 C08016, doi:10.1029/2007JC004581. Stac e y, M. T., S. G. Monismit h, J. R. Burau, 1999: Observations of turbulence in a partially stratified estuary. Journal of Physical Oceanography 29 1950 1970. Thorpe, S. A.,1977: Turbulence and mixing in a Scottish loch. Philosophical Transactions of the Royal Society A 286 125 181. Tjernstrom, M., 1993: Turbulence length scales in a stably stratified free shear flow analy zed from slant aircraft profiles. Journal of Applied Meteorology 32 948 963. Valle Levinson, A., 2008: Density driven exchange flow in terms of the Kelvin and Ekman numbers, Journal of Geophysical Research 113 C04001, doi:10.1029/2007JC004144. Valle Levinson A., 2010: Definition and classification of estuaries. In A. Valle Levinson (Ed.), Contemporary issues in estuarine physics (1 11). New York: Cambridge University Press. Val le Levinson, A., K. C. Wong, K. M. M. Lwiza, 2000: Fortnightly Varia bility in the transverse dynamics of a coastal plain estuary, Journal of Geophysical Research 105 3413 3424. Wiles, P.J., T. P. Rippeth, J. H. Simpson, P. J. Hendricks 2006 A novel technique for measuring the rate of turbulent dissipation in the marine environment. Geophysical Research Letters 33 L21608, doi:10.1029/2006GL027050

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124 BIOGRAPHICAL SKETCH Kimberly Arnott was raised in south Florida, primarily in Stuart. She spent her summers and weekends enjoying the beach, snorkeling, and scuba div ing. She began her college career at University of Central Florida and studied industrial e ngineering After realizing this discipline was not a perfect fit for her, she transferred to Univer sity of North Florida to study civil e ngineering. After graduatin g with her B.S., she applied to University of Florida and mad e the natural progression into coastal e ngineering. Her advisor, Arnoldo Valle Levinson pushed her to condu thesis, which she is undoubtedly grateful for. After graduati ng, Kimberly briefly worked as a Coastal Engineer until realizing that her ambition to do research in an academic environment. Thanks to her supportive and inspiring advisor, Kimberly returned back to UF to pursue a Ph.D. and a career in academia. She rec eived her Ph.D. in the spring of 2013 and started a post doctoral research position at Texas A&M Corpus Christi.