Using observations of the densest waters found within the fjord during 1981 to 2002 ( Skogseth et al., 2005b) we vary the inflow salinity Apoptosis Compound Library cell assay S from 34.75 to 35.81. The flow rate Q is varied from 0.01 to 0.08 Sv, based on observations at the sill of a mean volume transport of 0.05 to 0.08 Sv ( Schauer and Fahrbach, 1999, Skogseth et al., 2005a and Geyer et al., 2009). In the present study we do not attempt to model the dense water formation process itself. The flow rate Q and the salinity S of the simulated overflow waters are intended to capture the parameters of the SFOW behind and at the sill. We employ the NEMO-SHELF model (O’Dea et al., 2012) at 1 km resolution

with a 109×109109×109 grid in the horizontal and 42 levels in the vertical. The baroclinic time step is 40s with time splitting for the barotropic component every 20 steps. O’Dea et al. (2012) describe in detail the modifications to NEMO (Madec, 2008) for use in shelf seas and regional studies. We include here only a brief summary of the differences as well as its configuration specific to this study and SCH772984 mouse our own modifications to the NEMO-SHELF code. A key departure of the NEMO shelf code from the open ocean is the use of a terrain-following s  -coordinate discretisation in the vertical instead of z  -coordinates.

The s  -coordinate system is well suited to the modelling of density currents (see e.g. Wobus et al., 2011), but the horizontal boundaries

between ambient layers ( Fig. 2(b)) would suffer numerical diffusion over areas of sloping topography where s  -levels intersect the isopycnals at an angle. We therefore modify the vertical coordinate system because neither the traditional s  -coordinate nor z  -coordinate systems suit our scenario where strong gradients are orientated vertically (in the ambient water) and also normal to the slope (at the upper plume boundary). The approach of blending s  - and z  -coordinates in this study can be traced back to Enriquez et al. (2005) who used a traditional s  -coordinate stretching function ( Song and Haidvogel, 1994) but achieved horizontal s  -levels over the interior of a basin by capping its bathymetry. Ivanov (2011) changed the traditional s  -coordinate formulation O-methylated flavonoid by introducing virtual seabeds at certain depth levels to maintain horizontal s  -levels closer to the slope. The levels designated as virtual seabeds (here called “shsh-levels”) follow the terrain only at shallower depths, while maintaining a prescribed depth over deep bathymetry. Our modified shsh-coordinate system1 refines the Ivanov (2011) approach by smoothing the transition between horizontal and terrain-following s-levels ( Fig. 3). The smoothing reduces errors in the calculation of the second derivative of the s-level slope. In this study we reserve 16 out of the 42 levels for a bottom layer of constant thickness (60 m).