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Contents 1 Half-adder or Full-adder 1.1 Idea: Pattern recognition 1.1.1 Main Goal: 1.1.2 Implementation from the ingenieur point of view 1.1.3 Implementation from the biologist point of view 1.1.4 Chemical 1.1.5 Parts 1.1.5.1 Overview, Light Sensing, XOR Variants 1.1.5.2 AND Variants 1.1.6 Pro's & Con's

Half-adder or Full-adder

An implementation of a half-adder or full-adder: 1-bit adder with carry

• [http://en.wikipedia.org/wiki/Full_adder half/full adder in wikipedia]

Idea: Pattern recognition

→ Illustration of the concepts:

• slides (pdf, 352KB)
• handout (pdf, 268KB)

Main Goal:

• Write something with a chemical on a petri plate (like ETH for example)
• Let Bacteria grow uniformly on the plate
• Expose the plate to a picture (black and white) of the same pattern
• Result:
  • Bacteria gets green when pattern on the plate and picture match (light and chemical)
  • Bacteria does not express fluorescent protein when pattern on the plate and picture match (no light and no chemical)
  • Bacteria gets red when pattern on the plate and picture do not match

Implementation from the ingenieur point of view

• Half Adder
• = opportunity to build an AND and an XOR Gate

Implementation from the biologist point of view

• AND Gate: presence of chemical induces the production of an inactive protein, which is activated by a second protein (produced when light is present): the first protein is then activating GFP production
• XOR Gate: I think Marko had a good idea about that (I didn't really got it)
• a light sensible promoter (there are some, see [http://partsregistry.org/Featured_Parts:Light_Sensor here])
• a chemical sensible promoter (chemical to be defined)
• we would need to give a kind of first signal to the system (to don't have light reactions before a certain moment, otherwise we have to work in a dark room...), an activation signal after the bacterias have grown on the plate

Chemical

• Lactate lacI represses, IPTG induces (BBa_R0011 or BBa_R0010 )
• Tetracycline, TetR inhibitor, Tet inducer by inhibiting TetR (or aTc, it's analog) (BBa_R0040)
• combination thereof BBa_I13614 / 17 / 23 / 24 / 27 / 37 / 53)
• simple sugar Arabinose (BBa_R0080)
• I see the main difficulty in the spatial separation as the cells are growing in the petri dishes. since the inducers are water-soluble we would have to fix the chemicals onto the petro dish.

Parts

Overview, Light Sensing, XOR Variants

• eth-xor.pdf (483KB)

AND Variants

• eth-and.pdf (185KB)

Pro's & Con's

Pro's:

• meaningful from engineering point
• valuable parts for synthetic biology
• stepwise proceeding applicable (→ intermediate and partial results!)
• experiments visually attractive
• probably simple enough

Con's:

• cheap copy of “bio-film” project ([http://partsregistry.org/cgi/htdocs/SBC04/index.cgi iGEM 2004])
• sensational experiments, have little in common with half adder
• maybe that a big vision is lacking
• general/practical benefit? (counter-argument: is this required?)
• too simple?