Downfront winds over buoyant coastal plumes

Author Posting. © American Meteorological Society, 2016. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 46 (2016): 3139-3154, doi:10.1175/JPO-D-16-0042.1.Downfront, or downwelling favorable, winds are commonly found over buoyant coastal plumes. It is known that these winds can result in mixing of the plume with the ambient water and that the winds influence the transport, spatial extent, and stability of the plumes. In the present study, the interaction of the Ekman velocity in the surface layer and baroclinic instability supported by the strong horizontal density gradient of the plume is explored with the objective of understanding the potential vorticity and buoyancy budgets. The approach makes use of an idealized numerical model and scaling theory. It is shown that when winds are present the weak stratification resulting from vertical mixing and the strong baroclinicity of the front results in near-zero average potential vorticity q. For weak to moderate winds, the reduction of q by diapycnal mixing is balanced by the generation of q through the geostrophic stress term in the regions of strong horizontal density gradients and stable stratification. However, for very strong winds the wind stress overwhelms the geostrophic stress and leads to a reduction in q, which is balanced by the vertical mixing term. In the absence of winds, the geostrophic stress dominates mixing and the flow rapidly restratifies. Nonlinearity, extremes of relative vorticity and vertical velocity, and mixing are all enhanced by the presence of a coast. Scaling estimates developed for the eddy buoyancy flux, the surface potential vorticity flux, and the diapycnal mixing rate compare well with results diagnosed from a series of numerical model calculations.This study was supported by NSF Grants OCE-1433170 (MAS) and OCE-1459677 (LNT).2017-04-0

Nonlinear stratified spindown over a slope

Author Posting. © Cambridge University Press, 2013. This article is posted here by permission of Cambridge University Press for personal use, not for redistribution. The definitive version was published in Journal of Fluid Mechanics 726 (2013): 371-403, doi:10.1017/jfm.2013.231.Nonlinear stratified spindown of an along-isobath current over an insulated slope is shown to develop asymmetries in the vertical circulation and vertical relative vorticity field. During spindown, cyclonic vorticity is weakened to a greater extent than anticyclonic vorticity near the boundary because of buoyancy advection. As a consequence, Ekman pumping is weakened over Ekman suction. Momentum advection can weaken Ekman pumping and strengthen Ekman suction. Time-dependent feedback between the geostrophic flow and the frictional secondary circulation induces asymmetry in cyclonic and anticyclonic vorticity away from the boundary. Buoyancy advection over a slope can modify the secondary circulation such that anticyclonic vorticity decays faster than cyclonic vorticity outside the boundary layer. In contrast, momentum advection can cause cyclonic vorticity to spin down faster than anticyclonic vorticity. A scaling and analytical solutions are derived for when buoyancy advection over a slope can have a more significant impact than momentum advection on these asymmetries. In order to test this scaling and analytical solutions, numerical experiments are run in which both buoyancy and momentum advection are active. These solutions are contrasted with homogeneous or stratified spindown over a flat bottom, in which momentum advection controls the asymmetries. These results are applied to ocean currents over continental shelves and slopes.2014-06-0

Asymmetries in vertical vorticity and vertical velocity arising during nonlinear homogeneous spindown

Author Posting. © The Author(s), 2012. This is the author's version of the work. It is posted here by permission of American Institute of Physics for personal use, not for redistribution. The definitive version was published in Physics of Fluids 24 (2012): 076601, doi:10.1063/1.4731280.During the spindown of a uni-directional, geostrophic current in a homogeneous fluid, asymmetry arises in the vertical velocity and vertical relative vorticity fields. A closed-form, time-dependent solution valid to order Rossby number is derived to explore these asymmetries. Momentum advection in the interior and the Ekman layer leads to competing tendencies in the vertical vorticity’s evolution. In the interior, momentum advection hastens spindown in cyclonic regions. In the Ekman layer, momentum advection weakens Ekman pumping over Ekman suction and thus tends to slow the spindown of cyclonic vorticity. It is shown that the former effect dominates, and hence cyclonic vorticity decays faster than anticyclonic vorticity

Rapid generation of upwelling at a shelf break caused by buoyancy shutdown

Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 294–312, doi:10.1175/JPO-D-14-0104.1.Model analyses of an alongshelf flow over a continental shelf and slope reveal upwelling near the shelf break. A stratified, initially uniform, alongshelf flow undergoes a rapid adjustment with notable differences onshore and offshore of the shelf break. Over the shelf, a bottom boundary layer and an offshore bottom Ekman transport develop within an inertial period. Over the slope, the bottom offshore transport is reduced from the shelf’s bottom transport by two processes. First, advection of buoyancy downslope induces vertical mixing, destratifying, and thickening the bottom boundary layer. The downward-tilting isopycnals reduce the geostrophic speed near the bottom. The reduced bottom stress weakens the offshore Ekman transport, a process known as buoyancy shutdown of the Ekman transport. Second, the thickening bottom boundary layer and weakening near-bottom speeds are balanced by an upslope ageostrophic transport. The convergence in the bottom transport induces adiabatic upwelling offshore of the shelf break. For a time period after the initial adjustment, scalings are identified for the upwelling speed and the length scale over which it occurs. Numerical experiments are used to test the scalings for a range of initial speeds and stratifications. Upwelling occurs within an inertial period, reaching values of up to 10 m day−1 within 2 to 7 km offshore of the shelf break. Upwelling drives an interior secondary circulation that accelerates the alongshelf flow over the slope, forming a shelfbreak jet. The model results are compared with upwelling estimates from other models and observations near the Middle Atlantic Bight shelf break.J. Benthuysen acknowledges support from the ARC Centre of Excellence for Climate System Science (CE110001028) and the MIT/WHOI Joint Program, where this work was initiated.2015-07-0

Moored observations of bottom-intensified motions in the deep Canada Basin, Arctic Ocean

Author Posting. © Sears Foundation for Marine Research, 2010. This article is posted here by permission of Sears Foundation for Marine Research for personal use, not for redistribution. The definitive version was published in Journal of Marine Research 68 (2010): 625-641, doi:10.1357/002224010794657137.In the deep Canada Basin, below the sill depth (about 2400 m) of the Alpha-Mendeleyev Ridge, potential temperature and salinity first increase with depth, then remain uniform from about 2600 m to the bottom (approximately 3500 m). Year-long moored measurements of temperature, salinity and pressure in these deep and homogeneous bottom waters reveal significant vertical excursions with periods of about 50 days. The observed isopycnal displacements have amplitudes up to 100 m at the top boundary of the bottom layer; moored profiler measurements in the intermediate water column indicate that the amplitudes of these vertical displacements decay toward the surface over a scale of about 1000 m. The subinertial excursions are consistent with a bottom-trapped topographic Rossby wave. Given the magnitude of the bottom slope in the vicinity of the mooring, the observed vertical velocities correspond to only weak (about 1 cm s−1) cross-slope horizontal velocities. The generation mechanism for the waves remains an open question.Funding was provided by the National Science Foundation Office of Polar Programs Arctic Sciences Section under awards ARC-0632201 and ARC-0806306

Wintertime observations of Subtropical Mode Water formation within the Gulf Stream

Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 36 (2009): L02607, doi:10.1029/2008GL035918.We study the structure of Subtropical Mode Water (STMW) within the eastward-flowing Gulf Stream as it forms during strong winter cooling. Shipboard observations using SeaSoar and ADCP reveal that while active mixing by gravitational instabilities is common, large vertical and lateral shears of the Gulf Stream play a central role in determination of the modes of active mixing. Evidence is presented that low static stability and large vertical shear can combine to cause slantwise convection/symmetric instabilities, while the large anticyclonic shears to the south of the Gulf Stream core can cause low absolute vorticity and precondition the Ertel potential vorticity to be small and more susceptible to instabilities. The area of active mixing driven by surface forcing in the presences of shear occupies a swath 50–90 km wide immediately south of the Gulf Stream core at the northern edge of the Sargasso Sea.Support came from the National Science Foundation grants OCE-0424865 (TJ and FB) and OCE-0549699 (LT)

CoaSim: A flexible environment for simulating genetic data under coalescent models

BACKGROUND: Coalescent simulations are playing a large role in interpreting large scale intra-specific sequence or polymorphism surveys and for planning and evaluating association studies. Coalescent simulations of data sets under different models can be compared to the actual data to test the importance of different evolutionary factors and thus get insight into these. RESULTS: We have created the CoaSim application as a flexible environment for Monte Carlo simulation of various types of genetic data under equilibrium and non-equilibrium coalescent processes for a variety of applications. Interaction with the tool is through the Guile version of the Scheme scripting language. Scheme scripts for many standard and advanced applications are provided and these can easily be modified by the user for a much wider range of applications. A graphical user interface with less functionality and flexibility is also included. It is primarily intended as an exploratory and educational tool CONCLUSION: CoaSim is a powerful tool because of its flexibility and ease of use. This is illustrated through very varied uses of the application, e.g. evaluation of association mapping methods, parametric bootstrapping, and design and choice of markers for specific question