Physical Processes - Coastal Lagoons: Ecosystem Processes and Modeling for Sustainable Use and Development - page 73

form of roots. The organic matter associated with the roots will be mineralized by
bacteria and secondary producers, stimulating biological activity in sediment and
modifying the mechanical properties of sediment and, consequently, its erodability.
Plants also act on the bottom shear modifying the flow itself.
Filter feeders play two different roles. On one hand, they increase roughness of
the flow, increasing bottom shear stress and reducing conditions for gravitational
deposition of particulate matter. On the other hand, they extract particles from the
water column and build pseudo-faeces that are deposited on the bottom, increasing
the rate of accumulation of matter (including refractory organics) and also increasing
cohesiveness of bottom sediment.
Detailed information on biological boundary processes is given in Chapter 5.

3.5.2 S OLID B OUNDARY P ROCESSES

Lateral solid boundaries are usually artificial walls or created artificially in the model
due to the incapacity of the grid to continuously describe the bottom until it reaches
a negligible depth. Even if they are physical, there are no relevant biological pro-
cesses. Along these boundaries momentum can only be transferred through shear
diffusion. In a model these boundaries are represented imposing a null advective
flux and most often no diffusive flux.
In fact, the consideration of horizontal shear requires the use of a grid step smaller
than the boundary layer thickness; otherwise, the effect of the wall is propagated
artificially into the model domain. The case of a coarse grid lateral diffusion is
negligible when compared to the bottom shear diffusion due to the small value of the
lateral surface of boundary cells when compared with values of their bottom surface.
As a general rule, we can assume that horizontal diffusion in a model is relevant only
when the grid size is of the same order of magnitude as the depth near solid boundaries.

3.5.3 F REE S URFACE P ROCESSES

Through their free surfaces, aquatic systems can exchange mass, energy, and momen-
tum, according to atmospheric conditions. These fluxes control the biological activity
and the flow, except in tidal systems, where ocean-level oscillation can be the most
important mechanism forcing the flow.

3.5.3.1 Mass Exchange

Gases, vapors, and solid matter can be exchanged across the free surface. The
exchange of gases depends on relative partial pressures and can be in both senses.
It is mostly a result of biological activity, which in coastal lagoons is very much
related to land discharge of nutrients and organic matter. Globally, the aquatic system
tends to import CO 2 and export O 2 and N 2 . The rate of exchange depends on the
surface concentration on both sides of the surface layer and that depends on turbu-
lence intensities in the atmosphere and in the water column.
Mass can also be lost by the water in the form of vapor. This is mostly the case
with water, but it can be the case with floating liquids such as hydrocarbons. The rate