Numerical Particle Tracking

well as near-surface temperature and salinity. To complement the PORTS, a new nowcast/forecast system (consistent with NOS procedures) has been constructed. This new nowcast/forecast system is based on the Finite Volume Coastal Ocean Model (FVCOM) using a computational domain, which extends from Rio Vista on the Sacramento River and Antioch on the San Joaquin River through Suisun and San Pablo Bays and Upper and Lower San Francisco Bay out onto the continental shelf. This paper presents the FVCOM setup, testing, and validation for tidal and hindcast scenarios. In addition, the San Francisco Bay Operational Forecast System (SFBOFS) setup within the NOS Coastal Ocean Model Framework (COMF) is discussed. The SFBOFS performance during a semi-operational nowcast/forecast test period is presented and the production webpage is also briefly introduced. FVCOM, the core of SFBOFS, has been found to run robustly during the test period. Amplitudes and epochs of the M2 S2, N2, K2, K1, O1, P1, an...

Thermaikos Gulf is an environmentally fragile coastal environment characterized by numerous anthropogenic and natural pressures. The environmentally protected areas along its western coasts and the large number of inhabitants that live over its northern and eastern coasts raise the need for systematic monitoring and prediction of the marine environment concerning the ocean circulation, weather conditions, sea level and wave characteristics, pollution events, coastal flooding, and freshwater input. Herein, we present recent advances of the Wave4Us operational platform that provides short-term forecasts of all the above conditions, freely accessed by local authorities, the research community, and the broader audience on a daily basis. Specified marine predictions (e.g., about pollution, flooding, and heatwaves) provide useful real-time information to first-level responders and managerial stakeholders during hazardous events that may threaten the quality of the coastal environment and the safety of the population residing on Thermaikos Gulf's littorals.

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.

A detailed physical model of Georges Bank, including M tidal recti"cation, realistic topography, Mellor-Yamada 2.5 mixed-layer dynamics, and time-varying wind forcing, was used to simulate plankton transport. Wind records from January 1 through March 4 of each year from 1968 through 1993 were selected to force the model. For each year, two model runs were made, one time-variant and the other using the mean wind stress for the entire period. Simulations using no wind and a 26-year climatological mean (1968}1998) also were conducted. Di!erences in net transport and 2-month mean currents between the vector-averaged and time-varying runs for a given year were slight. Plankton distribution in time-varying winds moved in response to transient wind events, but distributions at the end of the 60-day simulation period were remarkably similar to those from model runs using vector-averages of the same winds. Interannual di!erences were signi"cant; depending on the direction of the mean wind stress, tracers were transported to several di!erent regions on and o! the bank. The use of wind-stress averages over a 2-month period is supported for models addressing transport on that time scale. Interannual variability in winter wind stress may play a major role in determining transport and subsequent recruitment of plankton on the bank.

For the period 2005-2009, the abundance of resting cysts in bottom sediments from the preceding autumn was a first-order predictor of the overall severity of spring-summer blooms of Alexandrium fundyense in the western Gulf of Maine and southern New England. Cyst abundance off mid-coast Maine was significantly higher in autumn 2009 than it was preceding a major regional bloom in 2005. A seasonal ensemble forecast was computed using a range of forcing conditions for the period 2004-2009, suggesting that a large bloom was likely in the western Gulf of Maine in 2010. This did not materialize, perhaps because environmental conditions in springsummer 2010 were not favorable for growth of A. fundyense. Water mass anomalies indicate a regional-scale change in circulation with direct influence on A. fundyense's niche. Specifically, near-surface waters were warmer, fresher, more stratified, and had lower nutrients than during the period of observations used to construct the ensemble forecast. Moreover, a weaker-than-normal coastal current lessened A. fundyense transport into the western Gulf of Maine and Massachusetts Bay. Satellite ocean color observations indicate the 2010 spring phytoplankton bloom was more intense than usual. Early season nutrient depletion may have caused a temporal mismatch with A. fundyense's endogenous clock that regulates the timing of cyst germination. These findings highlight the difficulties of ecological forecasting in a changing oceanographic environment, and underscore the need for a sustained observational network to drive such forecasts.

Information about seabed stability and sediment dynamics is part of the fundamental geoscience knowledge required for the extraction of tidal energy in the Bay of Fundy and for the integrated management of the Bay. Waves, tidal currents, and wind-driven and circulation currents were obtained from oceanographic models to assess the wave and current processes for the broader Bay of Fundy. The wave and current outputs were coupled with observed grain size in a sediment transport model to predict, for the first time, the seabed shear stresses, sediment mobility, and sediment transport patterns for the entire Bay. The root mean square tidal current, highest in the upper Bay (>1.4 m·s−1), is reduced to moderate in the central Bay (0.5–0.8 m·s−1) and decreases further in the outer Bay (0.2–0.5 m·s−1). The maximum tidal current occurs in the Minas Passage and is >5 m·s−1. The mean significant wave height, in contrast, is the greatest in the outer Bay (∼1.3 m) and gradually decreases t...

Vertical profiles of the adult epibenthic shrimp Neomysis americana and Crangon septemspinosus obtained during June 1985 were used to simulate possible rates of ascent from bottom (40 to 50 m) to near surface at night and return by day, and the consequence of these rates on their horizontal distribution. Numerical particles were released at the sampling site using archived model current fields with specified vertical rates (from no swim behavior to 20 mm s −1) and tracked for up to 30 d. The best match between observed and modeled vertical profiles was with a vertical swimming speed of 10 mm s −1 for N. americana and 2 mm s −1 for C. septemspinosus. Whereas N. americana rapidly swims towards the surface at dusk and descends to bottom by dawn, C. septemspinosus tends to only swim up to the middle of the water column at night. After 16 d, the simulation with 10 mm s −1 swim speed showed most particles were concentrated in an area centered around the 60 m isobath, where the tidal front was located. At 2 mm s −1 swim speed particles were concentrated more shoalward onto the western end of Georges Bank. N. americana are expected to be more closely associated with the tidal front, since they spend more time near the front surface convergence, but are more likely to be transported off the bank due to the southwestward-flowing surface tidal jet, whereas C. septemspinosus would be retained primarily on the bank, since they are found deeper in the water column during both day and night.

The circulation of the tidal front along the Southern Flank of the Georges Bank region during May 1999 is examined for the purpose of understanding the transport of larval fish for periods of days to a week. Assimilation of shipboard ADCP data from several Georges Bank cruises into 3-D models is used to produce the hindcast circulation. Adjustments to boundary nodal elevations are estimated to minimize the misfit between model and observations both in frequency and time domains as described in Lynch and Hannah (J. Atmos. Oceanic Technol 18 (2001) 962) and Lynch and Naimie (Cont. Shelf Res. 22 ). An intercomparison of different methods of applying the adjustments is completed using drifter records and dye patch trajectories to provide a measure of skill. The computed flow fields show a skill of 2:4 km day À1 when compared to (unassimilated) drifter trajectories. The tracking of a dye-patch recovers an observed near-bottom cross-bank flow component that is not present without assimilation. Using these flow fields we then investigate the importance of the front as a retention mechanism using passive particle simulations. Wind, heat flux, and tides control the circulation across and along the tidal mixing front. Three 3-day time periods, before, during and after a wind event during May 1999 were studied. Model simulations suggest a highly variable cell-like circulation in the frontal region (onshore near the bottom, upwelling shoalward of the front, offshore at mid-depth and downwelling seaward of the front) that controls the exchange and retention of particles. During the periods when the cell-like circulation is active the highest accumulation of particles occurs in the areas surrounding the front. r

Two approaches to the quantitative characterization of Lagrangian circulation in three-dimensional (3D) timeperiodic current fields are used to describe major features of a model-derived flow field for barotropic tidal rectification on Georges Bank. The first approach is an extension of the 2D ''saddlepoint'' method used by Ridderinkhof and Loder to describe the vertically averaged Lagrangian circulation associated with various forcings over outer Gulf of Maine banks. Application of the method to representative sigma (terrain-following) surfaces and comparison with particle trajectories in the 3D current field indicate that the circulation saddlepoints and associated separation lines (between recirculation and throughflow regions) in the vertically averaged flow over Georges Bank are qualitatively representative of the entire water column, but that there is significant vertical structure in the Lagrangian circulation. In particular, the horizontal extent of the tidally rectified clockwise gyre on Georges Bank is greater in the lower water column, due to an on bank component of near-bottom Lagrangian flow. The second approach-evaluation of the 3D Lagrangian residual displacement field from particle tracking in the 3D current field-confirms the presence of a significant Stokes velocity associated with tidal rectification on Georges Bank. The around-bank component of the Stokes velocity is counterclockwise with magnitude approximately one-third that of the mean Eulerian velocity arising from tidal rectification, thereby partially offsetting the mean Eulerian velocity. The cross-bank component of the Stokes velocity also generally opposes the mean Eulerian flow and has a comparable magnitude. It accounts for the onbank near-bottom Lagrangian flow on the southern flank and northern edge of the bank (and hence the expanded gyre in the near-bottom region), and illustrates the importance of including the tidal velocity in model studies of Lagrangian circulation in tidally energetic regions.

Results of a modeling study designed to explore the influences of physical advection and certain biological mechanisms on the distribution of cod (Gadus morhua) and haddock (Melanogrammus aegkfinus) early life stages on Georges Bank are described. Using a latewintedearly-spring 3-D circulation field driven by the Mz tidal current, mean wind stress and Scotian Shelf inflow, we examine the distribution of cod and haddock larvae spawned on the Northeast Peak of the Bank. The sensitivity to a March-April baroclinic field is also explored. Results indicate that larvae remaining in the surface Ekman layer are generally advected off-bank. However, downwelling associated with Ekman layer convergence near the shelf break provides a mechanism for larvae to exit from the off-bank surface drift. Larvae below the surface layer are transported south-westward along the southern flank of Georges Bank and are retained on the Bank if their position immediately upstream of the Great South Channel is shoalward of (roughly) the 70 m isobath. Within the Great South Channel region and between the 50 and 70 m isobaths, retention can depend on the phase of the tide. Spawning shoalward of the 50 m isobath on the Northeast Peak greatly increases the chances of retention. These results apply to passive larvae and to those with specified vertical distributions and migration based on observations. Directional on-bank swimming at rates of 0.5 to 1 body length per second would substantially enhance shoalward displacement, resulting in larval distributions during the first 2 months that are consistent with field observations.

The seasonal and geographical patterns of spawning for Georges Bank cod (Gadus morhua) and haddock (Melanogrammus aegle®nus) are estimated using composite distributions of stage I eggs derived from the Marine Resources Monitoring, Assessment and Prediction (MARMAP) data set (1977±1987). The inferred mean spawning locations are compared with patterns in particle residence times derived from a three-dimensional prognostic circulation model that estimates the tidal and seasonal mean circulation. The comparisons indicate that cod and haddock spawning occurs at times and locations characterized by model residence times in excess of 35 d. The results are discussed in the context of ®sh population regulation theory, particularly the member/vagrant hypothesis and the concept of abundance-dependent vagrancy.

The previous larval-trajectory modeling studies on Georges Bank were assessed through process-oriented Lagrangian-tracking comparison experiments using the high-resolution Gulf of Maine ⁄ Georges Bank Finite-Volume Coastal Ocean Model (GOM-FVCOM). The results indicate that in a strong nonlinear system such as Georges Bank, the passive tracer movement is driven by a fully three-dimensional Lagrangian flow field that varies in space and time due to large tidal excursion and steep bottom topography. The particle-tracking methods developed based on the assumption of weak nonlinearity of the flow field are not applicable to Georges Bank. The results of previous larval transport studies driven by circulation fields constructed under the weak-nonlinearity assumption need to be interpreted with caution. In the present work, the influence of model physical setups on sea scallop larval dispersal and settlement on Georges Bank and adjacent shelf regions is examined. Distinct differences in the spatial distribution of the passive larvae predicted by the model under various physical conditions suggest that a fully nonlinear model driven by realistic spatially and temporally varying forcing should be employed for Lagrangian-based studies of fishery population dynamics on Georges Bank.

1] 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.

1] 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.

The photogrammetric determination of three-dimensional particle coordinates from a 3-camera system is described in Part I. In Part II we describe a fully automated tracking scheme for the determination of a sequence of velocity vectors within a three-dimensional observation volume of a fluid flow. From this sequence long-time particle trajectories are reconstructed. The tracking scheme is tested on trajectories obtained using the Kinematic Simulation Inertial Model (KSIM). Estimates of the yield of links between adjacent data sets of particle positions and of the yield of long-time particle trajectories are obtained. The limits of efficient tracking as a function of the spacing-displacement ratio p= Ao/u'A~ are also obtained. The effect of noise, in the form of the apparent appearance and disappearance of particles between one image and the next, and of jitter, which is the error in the determination of particle coordinates, is examined. It is shown that noise reduces the number of links per frame, but does not increase the number of erroneous links which is always small. However, the yield of long trajectories drops sharply with increasing noise. A small level of jitter, on the other hand, does not significantly influence any of the results. The tracking scheme is used on two sets of particle coordinate data obtained from real flows: a non-turbulent flow in a small water tank and a turbulent open channel flow.

Particle Tracking Velocimetry (PTV) is one of the evolving techniques which can cover the increasing need for measurements in a Lagrangian frame. Here some recent developments and the validation of the tracking scheme on the Kinematic Simulation Inertial Model (KSIM) test flow field is presented.

Acoustic backscatter from an active sonar system over a range of six frequencies between 265 kHz and 3 MHz in the tidally dominated Damariscotta River estuary, Maine, United States, revealed that the major emergence event of the night commenced on the first tidal deceleration after dark (3.5-4 h after local slack), irrespective of flow direction. Emergence traps identified the mysid shrimp, Neomysis americana, as the dominant migrator. Water-column-integrated, acoustically estimated biovolume at our 10-m deep study location increased by a factor of about 6 during these large events, entirely dominating the holoplanktonic contribution and likely being a major component in benthic-pelagic coupling. Application of the same algorithm used to locate this nighttime emergence revealed a parallel but considerably smaller daytime emergence event near the same phase of the tide. Daytime trap samples failed to recover the organisms responsible, but transmissometry rejected the alternative hypothesis that we observed resuspension events. We suspect, but have yet only weak evidence, that animals emerging in daylight are copepods rather than mysids.

Results of a modeling study designed to explore the influences of physical advection and certain biological mechanisms on the distribution of cod (Gadus morhua) and haddock (Melanogrammus aegkfinus) early life stages on Georges Bank are described. Using a latewintedearly-spring 3-D circulation field driven by the Mz tidal current, mean wind stress and Scotian Shelf inflow, we examine the distribution of cod and haddock larvae spawned on the Northeast Peak of the Bank. The sensitivity to a March-April baroclinic field is also explored. Results indicate that larvae remaining in the surface Ekman layer are generally advected off-bank. However, downwelling associated with Ekman layer convergence near the shelf break provides a mechanism for larvae to exit from the off-bank surface drift. Larvae below the surface layer are transported south-westward along the southern flank of Georges Bank and are retained on the Bank if their position immediately upstream of the Great South Channel is shoalward of (roughly) the 70 m isobath. Within the Great South Channel region and between the 50 and 70 m isobaths, retention can depend on the phase of the tide. Spawning shoalward of the 50 m isobath on the Northeast Peak greatly increases the chances of retention. These results apply to passive larvae and to those with specified vertical distributions and migration based on observations. Directional on-bank swimming at rates of 0.5 to 1 body length per second would substantially enhance shoalward displacement, resulting in larval distributions during the first 2 months that are consistent with field observations.

The seasonal and geographical patterns of spawning for Georges Bank cod (Gadus morhua) and haddock (Melanogrammus aegle®nus) are estimated using composite distributions of stage I eggs derived from the Marine Resources Monitoring, Assessment and Prediction (MARMAP) data set (1977±1987). The inferred mean spawning locations are compared with patterns in particle residence times derived from a three-dimensional prognostic circulation model that estimates the tidal and seasonal mean circulation. The comparisons indicate that cod and haddock spawning occurs at times and locations characterized by model residence times in excess of 35 d. The results are discussed in the context of ®sh population regulation theory, particularly the member/vagrant hypothesis and the concept of abundance-dependent vagrancy.

The circulation of the tidal front along the Southern Flank of the Georges Bank region during May 1999 is examined for the purpose of understanding the transport of larval fish for periods of days to a week. Assimilation of shipboard ADCP data from several Georges Bank cruises into 3-D models is used to produce the hindcast circulation. Adjustments to boundary nodal elevations are estimated to minimize the misfit between model and observations both in frequency and time domains as described in Lynch and Hannah (J. Atmos. Oceanic Technol 18 (2001) 962) and Lynch and Naimie (Cont. Shelf Res. 22 (2002) 2191). An intercomparison of different methods of applying the adjustments is completed using drifter records and dye patch trajectories to provide a measure of skill. The computed flow fields show a skill of when compared to (unassimilated) drifter trajectories. The tracking of a dye-patch recovers an observed near-bottom cross-bank flow component that is not present without assimilatio...

From a grid of stations across the southern #ank of Georges Bank in May 1997, larval haddock and cod were observed to be concentrated across the tidal front in a band 10}20 km wide. Several cross-bank CTD and acoustic Doppler current pro"ler (ADCP) sections indicated a narrow ((10 km) but signi"cant tidal-front jet with residual currents moving southwest along the 60-m isobath at 10}20 cm/s in the upper water column ((35 m), consistent with a satellite-tracked drifter that logged a mean residual velocity of 13 cm/s for over a week. The tidal-front jet moved laterally with the strong M2 tide, but generally occurred in the region of maximum cross-bank density gradient. Evidence is provided for a two-cell secondary circulation pattern, with upwelling #ow on the mixed side of the front and a surface convergence and downwelling on the strati"ed side. A surface convergence zone was observed with drifters and also predicted from a modeled #ow "eld within 10 km of the jet on the strati"ed side, which generally coincided with the highest concentration of larvae. Model simulations, initialized with observed density structure from a CTD survey, suggest that larvae located in the convergence zone could be advected onto the shoals, under the jet in the near-bottom ('35 m), cross-isobath residual #ow (0.6}1.2 cm/s).

1] 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.

Results of a modeling study designed to explore the influences of physical advection and certain biological mechanisms on the distribution of cod (Gadus morhua) and haddock (Melanogrammus aegkfinus) early life stages on Georges Bank are described. Using a latewintedearly-spring 3-D circulation field driven by the Mz tidal current, mean wind stress and Scotian Shelf inflow, we examine the distribution of cod and haddock larvae spawned on the Northeast Peak of the Bank. The sensitivity to a March-April baroclinic field is also explored. Results indicate that larvae remaining in the surface Ekman layer are generally advected off-bank. However, downwelling associated with Ekman layer convergence near the shelf break provides a mechanism for larvae to exit from the off-bank surface drift. Larvae below the surface layer are transported south-westward along the southern flank of Georges Bank and are retained on the Bank if their position immediately upstream of the Great South Channel is shoalward of (roughly) the 70 m isobath. Within the Great South Channel region and between the 50 and 70 m isobaths, retention can depend on the phase of the tide. Spawning shoalward of the 50 m isobath on the Northeast Peak greatly increases the chances of retention. These results apply to passive larvae and to those with specified vertical distributions and migration based on observations. Directional on-bank swimming at rates of 0.5 to 1 body length per second would substantially enhance shoalward displacement, resulting in larval distributions during the first 2 months that are consistent with field observations.

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 crossfrontal bias.

Results of a modeling study designed to explore the influences of physical advection and certain biological mechanisms on the distribution of cod (Gadus morhua) and haddock (Melanogrammus aegkfinus) early life stages on Georges Bank are described. Using a latewintedearly-spring 3-D circulation field driven by the Mz tidal current, mean wind stress and Scotian Shelf inflow, we examine the distribution of cod and haddock larvae spawned on the Northeast Peak of the Bank. The sensitivity to a March-April baroclinic field is also explored. Results indicate that larvae remaining in the surface Ekman layer are generally advected off-bank. However, downwelling associated with Ekman layer convergence near the shelf break provides a mechanism for larvae to exit from the off-bank surface drift. Larvae below the surface layer are transported south-westward along the southern flank of Georges Bank and are retained on the Bank if their position immediately upstream of the Great South Channel is shoalward of (roughly) the 70 m isobath. Within the Great South Channel region and between the 50 and 70 m isobaths, retention can depend on the phase of the tide. Spawning shoalward of the 50 m isobath on the Northeast Peak greatly increases the chances of retention. These results apply to passive larvae and to those with specified vertical distributions and migration based on observations. Directional on-bank swimming at rates of 0.5 to 1 body length per second would substantially enhance shoalward displacement, resulting in larval distributions during the first 2 months that are consistent with field observations.

Vertical profiles of the adult epibenthic shrimp Neomysis americana and Crangon septemspinosus obtained during June 1985 were used to simulate possible rates of ascent from bottom (40 to 50 m) to near surface at night and return by day, and the consequence of these rates on their horizontal distribution. Numerical particles were released at the sampling site using archived model current fields with specified vertical rates (from no swim behavior to 20 mm s−1) and tracked for up to 30 d. The best match between observed and modeled vertical profiles was with a vertical swimming speed of 10 mm s−1 for N. americana and 2 mm s−1 for C. septemspinosus. Whereas N. americana rapidly swims towards the surface at dusk and descends to bottom by dawn, C. septemspinosus tends to only swim up to the middle of the water column at night. After 16 d, the simulation with 10 mm s−1 swim speed showed most particles were concentrated in an area centered around the 60 m isobath, where the tidal front was located. At 2 mm s−1 swim speed particles were concentrated more shoalward onto the western end of Georges Bank. N. americana are expected to be more closely associated with the tidal front, since they spend more time near the front surface convergence, but are more likely to be transported off the bank due to the south- westward-flowing surface tidal jet, whereas C. septemspinosus would be retained primarily on the bank, since they are found deeper in the water column during both day and night.

The life cycle of Alexandrium fundyense in the Gulf of Maine includes a dormant cyst stage that spends the winter predominantly in the bottom sediment. Wave-current bottom stress caused by storms and tides induces resuspension of cyst-containing sediment during winter and spring. Resuspended sediment could be transported by water flow to different locations in the Gulf and the redistribution of sediment containing A. fundyense cysts could alter the spatial and temporal manifestation of its spring bloom. The present study evaluates model near-bottom flow during storms, when sediment resuspension and redistribution are most likely to occur, between October and May when A. fundyense cells are predominantly in cyst form. Simulated water column sediment (mud) concentrations from representative locations of the Gulf are used to initialize particle tracking simulations for the period October 2010–May 2011. Particles are tracked in full three-dimensional model solutions including a sinking velocity characteristic of cyst and aggregated mud settling (0.1 mm s−1). Although most of the material was redeposited near the source areas, small percentages of total resuspended sediment from some locations in the western (~4%) and eastern (2%) Maine shelf and the Bay of Fundy (1%) traveled distances longer than 100 km before resettling. The redistribution changed seasonally and was sensitive to the prescribed sinking rate. Estimates of the amount of cysts redistributed with the sediment were small compared to the inventory of cysts in the upper few centimeters of sediment but could potentially have more relevance immediately after deposition.

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 thedeep basin in the central Bay of Fundy and strong tidal mixing on the shallow flanksaround Grand Manan Island and western Nova Scotia. Spring river discharge has animportant 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 theresidual 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.

Particle Tracking Velocimetry (PTV) is one of the evolving techniques which can cover the increasing need for measurements in a Lagrangian frame. Here some recent developments and the validation of the tracking scheme on the Kinematic Simulation Inertial Model (KSIM) test flow field is presented.