My model application

For my PhD project, I am doing 2 things:
1 - adding water quality state variable to SI3D. This will include nitrogen, phospohorus, algae, dissolved oxygen, and others. Here is a figure that shows all the state variables in my model. Each square is a state variable, and the lines that connect them represents an equation I need to solve. (NO3 is nitrate nitrogen, NH4 is ammonia, OrgN is Oragnic Nitrogen, DO is dissolved oxygen, SOD is sediment oxygen demand (the demand of oxygen from the bottom of the channel), BOD is biological oxygen demand (oxygen consumed by the death of biological material, usually originating from waste water treatment plants), A is algae, Z is zooplankton (little tiny swimming creatures, they eat algae), OrgP is Organic phosphorus and PO4 is orthophosphate.)


Each line also represents what can add to or subtract from each constituent. For example, NH4 can be broken down and become NO3, and during this process, oxygen is consumed. So, I have an equation that represents this.

2. I am applying my model to the Stockton Deep Water Ship Channel, part of the San Joaquin River and San Francisco Bay Estuary System. This stretch of river is of interest because it has low levels of dissolved oxygen. Low levels of dissolved oxygen put a stress on organisms. In particular, salmon have a hard time trying to pass through water that has less than 4 mg/L of dissolved oxygen. The salmon that pass through the Stockton Deep Water Ship Channel are endangered, so trying to improve their habitat and the likelihood that they can make it upstream to spawn is very important. One of the major factors causing a decrease in dissolved oxygen concentrations is an increase in algae growth. This is called eutrophication, and is a problem in many rivers, lakes and estuaries throughout the world, including the Gulf of Mexico and the Chesapeake Bay. Eutrophication is a process where excess nutrients are introduced into a system, which increases algae growth (algae need nitrogen and phosphorus to grow, so if more is introduced, more algae can grow) . This can be a natural process, but in more recent times, human interaction with nutrient cycles have sped it up. Agricultural fertilizers, fertilizers for golf courses, and waste water treatment plants are just a few of the processes that directly add nutrients (esp nitrogen and phosphorus) into water bodies. The San Joaquin River valley has thousands of acres of farmland, and some waste water treatment plants as well. The river carries all these nutrients into the Deep Water Ship Channel, which is deep. When the water gets to the ship channel, it slows down and the nutrients just sit. With the addition of the sun, algae can grow. But, at night, they all die and consume oxygen. The oxygen produced during the day (photosynthesis) is not enough to combat the death and decay during the night, so oxygen levels decrease. Bad for fish. Because of this, some government agencies, including the EPA, have introduced a TMDL (total maximum daily load - a hot topic in my field) mandating that dissolved oxygen concentrations in Stockton remain above 5 mg/L during most of the year, and above 6 mg/L in September - October when fish migrate through the system. A TMDL is supposed to impose fines to people in the basin if the TMDL is not met, but figuring out who is to blame is the hard part. The goal of my model is to figure out the causes, and I think most importantly, use it to try and figure out solutions.