Lynch Daniel R.

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Lynch
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Daniel R.
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Article

Model simulations of the Bay of Fundy Gyre : 1. Climatological results

2008-10-29 , Aretxabaleta, Alfredo L. , McGillicuddy, Dennis J. , Smith, Keston W. , Lynch, Daniel R.

The characteristics of a persistent gyre in the mouth of the Bay of Fundy are studied using model simulations. A set of climatological runs are conducted to evaluate the relative importance of the different forcing mechanisms affecting the gyre. The main mechanisms are tidal rectification and density-driven circulation. Stronger circulation of the gyre occurs during the later part of the stratified season (July–August and September–October). The density-driven flow around the gyre is set up by weak tidal mixing in the deep basin in the central Bay of Fundy and strong tidal mixing on the shallow flanks around Grand Manan Island and western Nova Scotia. Spring river discharge has an important influence on near-surface circulation but only a small effect when averaged over the entire water column. Retention of particles in the gyre is controlled by the residual tidal circulation, increased frontal retention during stratified periods, wind stress, and interactions with the adjacent circulation of the Gulf of Maine. Residence times longer than 30 days are predicted for particles released in the proximity of the gyre.

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Preprint

Modeling turbulent dispersion on the North Flank of Georges Bank using Lagrangian Particle Methods

2004-09-29 , Proehl, Jeffrey A. , Lynch, Daniel R. , McGillicuddy, Dennis J. , Ledwell, James R.

Circulation and transport at the North Flank of Georges Bank are studied using a data-assimilative 3-D model of frontal dynamics under stratified, tidally energetic conditions over steep topography. The circulation model was used in real-time during a cross-frontal transport study. Skill is evaluated retrospectively, relative to CTD, ADCP, drifter, and fluorescent dye observations. Hydrographic skill is shown to be retained for periods of weeks, requiring only initialization from routine surveys and proper atmospheric heating subsequently. Transport skill was limited by the wind stress input; real-time forecast winds taken from an operational meteorological model produced cross-isobath Ekman transport which was not observed locally. Retrospective use of observed local wind stress removed this cross-frontal bias. The contribution of tidal-time motion to the dispersion of a passive tracer is assessed using an ensemble of passive particles. The particle release simulates an at-sea dye injection in the pycnocline, which is followed for four days. Non-advective vertical tracer transport is represented as a random walk process sensitive to the local eddy diffusivity and its gradient, as computed from the turbulence closure. Non-advective horizontal tracer transport is zero for these ensembles. Computations of ensemble variance growth support estimates of (Lagrangian) horizontal dispersion. Off-bank, ensembles are essentially non-diffusive. As an ensemble engages the mixing front, its vertical diffusivity rises by 3 orders of magnitude, and horizontal spreading occurs in the complex front. The resultant horizontal dispersion is estimated from the ensemble variance growth, in along-bank and cross-bank directions. It is partitioned, roughly, between that contributed by 3-D advection alone, and that initiated by vertical diffusion. Engagement in the mixing front occurred in the forecast ensemble as a result of Ekman drift produced by an erroneous wind prediction. In the hindcast, observed wind left the ensemble non-diffusive and compact, advecting parallel to the mixing front and experiencing some advective shear dispersion. Lagrangian dispersion is event-specific and both simulations here represent credible events with dramatically different ecological outcomes. The skill metrics used are less sensitive, indicating that metrics tailored to surface-layer phenomena would be more appropriate in a data-assimilative context. The hindcast is closer to truth, based on first principles (better information). The level 2.5 closure used is realistic in the ocean interior; the near-surface processes need further refinement, especially as both surface- and bottom-generated turbulence affect these events strongly.

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Article

Model simulations of the Bay of Fundy Gyre : 2. Hindcasts for 2005–2007 reveal interannual variability in retentiveness

2009-09-03 , Aretxabaleta, Alfredo L. , McGillicuddy, Dennis J. , Smith, Keston W. , Manning, James P. , Lynch, Daniel R.

A persistent gyre at the mouth of the Bay of Fundy results from a combination of tidal rectification and buoyancy forcing. Here we assess recent interannual variability in the strength of the gyre using data assimilative model simulations. Realistic hindcast representations of the gyre are considered during cruises in 2005, 2006, and 2007. Assimilation of shipboard and moored acoustic Doppler current profiler velocities is used to improve the skill of the simulations, as quantified by comparison with nonassimilated drifter trajectories. Our hindcasts suggest a weakening of the gyre system during May 2005. Retention of simulated passive particles in the gyre during that period was highly reduced. A recovery of the dense water pool in the deep part of the basin by June 2006 resulted in a return to particle retention characteristics similar to climatology. Retention estimates reached a maximum during May 2007 (subsurface) and June–July 2007 (near surface). Interannual variability in the strength of the gyre was primarily modulated by the stratification of the dense water pool inside the Grand Manan Basin. These changes in stratification were associated with mixing conditions the preceding fall–winter and/or advectively driven modification of water mass properties.

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Preprint

Mechanisms regulating large-scale seasonal fluctuations in Alexandrium fundyense populations in the Gulf of Maine : results from a physical–biological model

2005-04-27 , McGillicuddy, Dennis J. , Anderson, Donald M. , Lynch, Daniel R. , Townsend, David W.

Observations of Alexandrium fundyense in the Gulf of Maine indicate several salient characteristics of the vegetative cell distributions: patterns of abundance are gulf-wide in geographic scope; their main features occur in association with the Maine Coastal Current; and the center of mass of the distribution shifts upstream from west to east during the growing season from April to August. The mechanisms underlying these aspects are investigated using coupled physical-biological simulations that represent the population dynamics of A. fundyense within the seasonal mean flow. A model that includes germination, growth, mortality, and nutrient limitation is qualitatively consistent with the observations. Germination from resting cysts appears to be a key aspect of the population dynamics that confines the cell distribution near the coastal margin, as simulations based on a uniform initial inoculum of vegetative cells across the Gulf of Maine produces blooms that are broader in geographic extent than is observed. In general, cells germinated from the major cyst beds (in the Bay of Fundy and near Penobscot and Casco Bays) are advected in the alongshore direction from east to west in the coastal current. Growth of the vegetative cells is limited primarily by temperature from April through June throughout the gulf, whereas nutrient limitation occurs in July and August in the western gulf. Thus the seasonal shift in the center of mass of cells from west to east can be explained by changing growth conditions: growth is more rapid in the western gulf early in the season due to warmer temperatures, whereas growth is more rapid in the eastern gulf later in the season due to severe nutrient limitation in the western gulf during that time period. A simple model of encystment based on nutrient limitation predicts deposition of new cysts in the vicinity of the observed cyst bed offshore of Casco and Penobscot Bays, suggesting a pathway of re-seeding the bed from cells advected downstream in the coastal current. A retentive gyre at the mouth of the Bay of Fundy tends to favor re-seeding that cyst bed from local populations.

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Article

Data assimilative hindcast of the Gulf of Maine coastal circulation

2005-10-12 , He, Ruoying , McGillicuddy, Dennis J. , Lynch, Daniel R. , Smith, Keston W. , Stock, Charles A. , Manning, James P.

A data assimilative model hindcast of the Gulf of Maine (GOM) coastal circulation during an 11 day field survey in early summer 2003 is presented. In situ observations include surface winds, coastal sea levels, and shelf hydrography as well as moored and shipboard acoustic Doppler D current profiler (ADCP) currents. The hindcast system consists of both forward and inverse models. The forward model is a three-dimensional, nonlinear finite element ocean circulation model, and the inverse models are its linearized frequency domain and time domain counterparts. The model hindcast assimilates both coastal sea levels and ADCP current measurements via the inversion for the unknown sea level open boundary conditions. Model skill is evaluated by the divergence of the observed and modeled drifter trajectories. A mean drifter divergence rate (1.78 km d−1) is found, demonstrating the utility of the inverse data assimilation modeling system in the coastal ocean setting. Model hindcast also reveals complicated hydrodynamic structures and synoptic variability in the GOM coastal circulation and their influences on coastal water material property transport. The complex bottom bathymetric setting offshore of Penobscot and Casco bays is shown to be able to generate local upwelling and downwelling that may be important in local plankton dynamics.

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Technical Report

Kings Bay, Cumberland Sound, Georgia part II : numerical modeling

1987-03 , Aubrey, David G. , Fry, Virginia A. , Lynch, Daniel R.

As a complement to field measurements of waves, surface tides, currents, and sediment transport, numerical modeling of King's Bay/ Cumberland Sound was initiated. Diagnostic numerical models 1 (both 1- and 2-dimensional) were applied to determine their applicability to estuaries of the same scale as King's Bay. One-dimensional models showed the estuarine system to be ebb-dominant, in accord with observations. This model did not reveal any extreme system sensitivity to changes in channel geometry on the scale expected from maintenance dredging. The two-dimensional model (a finite element model having a moving boundary formulation) was run to examine its applicability for diagnostic modeling of these systems. Preliminary results indicate the method is promising, but some model developments are indicated. Suggested model developments include: semi-implicit algorithm to reduce run-time: mass-conserving boundary conditions at tidal boundaries: implementation of a two-level momentum equation: algorithm development to extend the deforming element concept for smaller estuarine space scales: and formulation of a comprehensive interactive graphical package to facilitate model formulation, boundary and domain gridding, and presentation of results. This latter graphical task is essential for successful application of these numerical models. Results from these studies suggest that diagnostic models of shallow estuaries will be a valuable tool to be used in conjunction with more expensive "predictive" models, to understand circulation and transport processes under natural and impacted conditions.