20.20(S10):Notebook/BEI/2010/03/17

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System-Level Design
2020(S10)_Lecture:week_7#Week_7_Studio Breaking down a complicated problem into simpler parts: System > Device > Part > DNA


 * Nutrient recycling
 * Main nutrients: P, N, K, Ca, Mg, S
 * Focus on metabolic engineering for just two


 * Codependence
 * Should not be too difficult, known art. endocrine signals.
 * Biomolecules as signals which diffuse, NOT proteins (which only work if cells right next to each other) b/c bacteria and algae are fairly far apart in tank
 * Term is (not sure) commensalism?


 * Decontamination
 * Against mold, insects, etc.
 * Goals: inexpensive, not environmentally harmful, not easy to evolve resistance to
 * Engineer bac and alg to tolerate cold? But probably decreased efficiency
 * Look at extremophiles


 * Worries
 * Algae output locked up in algae?
 * Bacteria growing out of control and crashing?


 * System Diagram image:


 * Components that need biological engineering:
 * Oil secretion
 * Nutrient recycling
 * Steady state (constitutively attempt recycle nutrients) or what?
 * If constitutively, will always have enough nutrients, but energy costs and possibly bacteria population crash
 * Worry about start state
 * Especially if know that going to be rebooting frequently, start state becomes important


 * Notes
 * Investigate prior arr: Commensalism, there's previous research. Yeast and tryptophan, also something about mammalian cells
 * Growth temperature syncing
 * Worry about Mutations in our algae / bacteria
 * Biology: not absolute, probabilities
 * Perhaps have an expected "shelf life"
 * Have the bacteria produce antibodies, and only system reboot when superbug comes along

General Factory Design Parameters
From a mechanical perspective, we expect our systems to require nothing more than an initial investment of resources and continued water input. To this end, we would have to safeguard against such issues as cold weather or rain. A simple safeguard would be a small rollover shutter that could be used to cover the normally open ponds. Furthermore, we have envisioned two tanks, with the bacterial tank being lower than the algal tank and connected via a water bridge.

General Management Concerns
The construction of our reactor is straightforward. Begin with two long raceway ponds connected by a slanting water bridge. One should be elevated above the other. Add transgenic algae, signal compounds, the required nutrient fertilizer, and a proper saltwater solution. (Note that the use of saltwater allows for extension of our system to coastal locations rather than crop-producing areas, and has no impact on water use pressures.) After one algal life cycle- for our strain, roughly seven-ten days- add the bacterial cultures to the lower raceway pond. From here on out, the bacteria will feed on sedimenting dead algae, produce our customized antibiotic, and recycle system nutrients to the algae tank. No inputs other than occasional saltwater will be necessary. Assuming sufficiently warm weather, heating will be unnecessary. The algae will produce hydrocarbons that will rise to the top of the first raceway pond and may be siphoned off via vertical descent into a reservoir. Similarly, the bacteria will produce ethanol through the use of the dead algae, which will bubble upward and be restricted to yet another reservoir. Potential fermentation may also allow for methane and CO2 production; the former would be isolated while the latter would be released back to the growing algae.

Issues with antibiotic-resistant bacteria, while exceedingly unlikely given a concentrated saltwater medium combined with high antibiotic concentrations, are possible. In this case, we recommend complete purification and rebooting of the system via (environmentally sound) dumping and ethanol cleaning. For the purpose of rebooting, we propose to store at low Celsius temperatures no less than 10 identical strains of our algal and bacterial cultures. Although the transient state preceding steady energy production is presently assumed to last no more than two weeks, it is crucial to ensure the integrity of the system during these early days. As such, we recommend system isolation and low-scale energy siphoning- if any energy is, in fact, produced. Once the system is stable, as noted above, we anticipate no requirement for tank cleaning or costly/labor intensive oil/gas reclamation. That being said, the initial investment for our system is likely to be on the higher side of a simple two-pond system; we are at present unsure how many years of steady production would be necessary to recoup these losses.

(Note: This assumes implementation of all element pathways. It may be the case that fertilizer costs are merely reduced by 90-95% rather than completely eradicated, but this could theoretically be improved to 100% with further modification.)

Literature to be Considered

 * 1) Commensalism Papers: Yeast (Tryptophan) Mammalian/Bacteria
 * 2) Present Day Algae Fuel Factory Requirements
 * 3) Present Day Efforts with Multi-Organism Factories (Microbial Fuel Cells and Beyond)
 * 4) Examination of Ideal Algae, Nutrient Recycling Bacteria, and Fermentation Bacteria
 * 5) Examination of Suitable Antibiotics
 * 6) Examination of Useful Small Molecule Regulators
 * 7) Possible Applications to Wastewater, Brackish Water, and Generally Nonsaline Media

Algae Growth Requirements

 * 1) Water (Hydrogen & Oxygen)
 * 2) Carbon Dioxide (Carbon)
 * 3) Sunlight (Energy)
 * 4) Nitrogen Cycling
 * 5) Phosphorus Cycling
 * 6) Potassium Cycling
 * 7) Sulfur Cycling
 * 8) Calcium Cycling
 * 9) Magnesium Cycling
 * 10) Boron Cycling
 * 11) Cobalt Cycling
 * 12) Copper Cycling
 * 13) Iron Cycling
 * 14) Manganese Cycling
 * 15) Molybdenum Cycling
 * 16) Zinc Cycling

Nutrient Cycling Ideas
First, decompose dead algae to subproducts. Then process subproducts using bacteria into nutrients the live algae need.


 * 1) (Dead Algae) --> [Decomposer] --> (Algae Subproduct Ao, A1, A2, A3, A4, etc.)
 * 2) (Ao) --> [Nitrogen Recycling System: -step1- --> -step2- --> -step3-] --> NH4+ (Example)


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