ETH 2006 Half adder
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Contents |
The Model
Overview
TO DO's
- Model the whole System with Sensing, Pop's duplexer and Half adder (Marco and Franz)
- Make a picture of the whole model with te different parts in it (Alexandra)
- Finish AND and XOR Gates DNA (Marko and Sven) to order it
- Read the literature on the XOR and AND Gates, check carefully for strains needed and compatibility of the parts
- Check wether the strains are available (Robert)
- Model the IPTG Sensing device (Robert)
- Ask for the Plasmid with the light sensing device (Olga)
- Model wether a different strength of input is necessary for the AND and XOR Gates (Who?)
- Finish modeling the second AND Gate and find a biological way to implement it and write the DNA and order it (Marco and Robert)
- Prepare a protocol for promoter testing (Olga and Alexandra)
- Promoter and degradation tagged reporter protein testing (Arthur, Olga and Alexandra)
Important: we should order the DNA as soon as possible then if we order it next week we would only have 1.5 weeks for testing our system
Idea: Pattern recognition
→ Illustration of the concepts:
- slides (pdf, 352KB)
- handout (pdf, 268KB)
- An implementation of a half-adder or full-adder: 1-bit adder with carry
→ half/full adder in wikipedia
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
From the ingenieur point of view
- Half Adder
- = opportunity to build an AND and an XOR Gate
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 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
Modeling
Modeling Overview
- Modeling Overview (pdf) (∼0.5M)
- Modeling Overview (ppt) (∼0.5M)
Matlab scripts for ODE simulation
unzip the file, each zip file contains 2 files: sim_xxx.m and ode_xxx.m.
-
ode_xxx.m: contains the differential equations, i.e. the model -
sim_xxx.m: sets the parameters, calls the simulator and plots the result (this is the one to run, but the other is also needed).
- matlab_sim_and1.zip (<0.1M) →simulation results → abandoned
- matlab_sim_and2.zip (<0.1M) →simulation results → the pursued version A
- matlab_sim_and3.zip (<0.1M) →simulation results → the pursued version B
- matlab_sim_and4.zip (<0.1M) →simulation results → abandoned
As a result of the meeting on August 17, we will from now on concentrate on the AND versions 2 and 3.
- matlab_sim_xor1.zip (<0.1M) →simulation results → the only pursued version
- matlab_sim_xor2.zip (<0.1M) →simulation results → abandoned
- matlab_sim_xor3.zip (<0.1M) →simulation results → abandoned
Parts
Reserved Parts in Registry
We have already reserved parts for the adder and the gates in the registry the description of which are still tentative:
- Half adder: BBa_J34000
- AND gate: BBa_J34100
- XOR gate: BBa_J34200
Chemical Sensing Device
Suggestions for Chemical Sensing Device:
- 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 / BBa_13617 / BBa_I13623 / BBa_I13624 / BBa_I13627 / BBa_I13637 / BBa_I13653)
- 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.
