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Revision as of 18:58, 16 August 2006

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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

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 Sensing

• Lactate lacI represses, IPTG induces ([http://partsregistry.org/Part:BBa_R0011 BBa_R0011] or [http://partsregistry.org/Part:BBa_R0010 BBa_R0010] )
• Tetracycline, TetR inhibitor, Tet inducer by inhibiting TetR (or aTc, it's analog) ([http://partsregistry.org/Part:BBa_R0040 BBa_R0040])
• combination thereof ([http://partsregistry.org/Part:BBa_I13614 BBa_I13614] / [http://partsregistry.org/Part:BBa_I13617 BBa_13617] / [http://partsregistry.org/Part:BBa_I13623 BBa_I13623] / [http://partsregistry.org/Part:BBa_I13624 BBa_I13624] / [http://partsregistry.org/Part:BBa_I13627 BBa_I13627] /

[http://partsregistry.org/Part:BBa_I13637 BBa_I13637] / [http://partsregistry.org/Part:BBa_I13653 BBa_I13653])

• simple sugar Arabinose ([http://partsregistry.org/Part:BBa_R0080 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.

PoPS --> 2x PoPS Converter

We will also need a device providing two times the same output signal, according to the input. This is needed to supply the AND and the XOR gate with the input signals, sensed by the system.

ToDo:

• Although the idea of this device is clear (I am going to put the idea here soon --Dimo 09:57, 16 August 2006 (EDT)), we have to ensure that the device is reusable, because we need two of it.
• Of course, this part should be tested in the lab.

Modelling

Selected XOR/AND Model Variants

• eth-parts-and-xor.pdf (∼0.5M) file versions
• eth-parts-and-xor.ppt (∼0.6M) file versions
• matlab_sim_and1.zip (∼0.6M) file versions
• matlab_sim_and2.zip (∼0.6M) file versions

Old

• eth-xor.pdf (483KB)
• eth-and.pdf (185KB)
• AND34.ppt

Parts

We have already reserved parts for the adder and the gates in the registry the description of which are still tentative:

• Half adder: [http://partsregistry.org/Part:BBa_J34000 BBa_J34000]
• AND gate: [http://partsregistry.org/Part:BBa_J34100 BBa_J34100]
• XOR gate: [http://partsregistry.org/Part:BBa_J34200 BBa_J34200]

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?