3-SAT Problem
description
Transcript of 3-SAT Problem
![Page 1: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/1.jpg)
3-SAT Problem
• Sakamoto used hairpin formations in single stranded DNA (ssDNA) as a molecular computer.
• The formation of a hairpin shows that the problem was not satisfied.
![Page 2: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/2.jpg)
3-SAT Problem• 6 Inputs- A,B,C,D,E,F
• 10 Clauses- ex. (A or B or C), (C or D or -E)…– Expressed as (SA or SB or SC), (SC or SD or S-E)…In DNA sequence.
10 Clause 3-SAT Problem used by Sakamoto et al.
(a or c or d) (a or b or –c)
(a or –c or –d)(-a or –c or d)(a or –c or e)(a or d or –f)(-a or c or d)(a or c or –d)(-a or c or –d)
(-a or –c or –d)
![Page 3: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/3.jpg)
• A frameshift is a genetic mutation caused by the addition or deletion of nucleotides.
• Since codons are read in a series of three, the addition or deletion of nucleotides will disrupt the reading frame. This disruption will most likely cause the production of a nonfunctional protein.
![Page 4: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/4.jpg)
ATG CCC GAC g
The suppressor tRNA allows the 4 letter sequence to be read as a single codon, therefore, keeping the
protein on track.
A frameshift occurs and, if nothing is done, enzyme A will not be made,
meaning the clause will not be satisfied.
Start
![Page 5: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/5.jpg)
Supressor tRNA can Read Through a Frame Shift Keeping the Original
Protein Sequence
![Page 6: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/6.jpg)
Suppressor Suppressor Logic
• Based on Amber (UAG) and Opal (UGA) suppressor tRNAs
• PoPS inputs A or B control Amber or Opal suppressor production
• Repressors and/or activators control PoPS output
• Basic logic circuits produced
![Page 7: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/7.jpg)
OR Gate Using SSL
UAG
Activator
UGA
Activator
PoPS Input A PoPS Input B PoPS Output
0 0 0
1 0 1
0 1 1
1 1 1
Amber Suppressor tRNA
Opal Suppressor tRNA
PoPS Input A
PoPS Input B
PoPS OutputOFF to
ON
![Page 8: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/8.jpg)
NOR Gate Using SSL
PoPS Input A PoPS Input B PoPS Output
0 0 1
1 0 0
0 1 0
1 1 0
Amber Suppressor tRNA
Opal Suppressor tRNA
PoPS Input A
PoPS Input B
UAG
Repressor
UGA
Repressor
PoPS OutputON to
OFF
![Page 9: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/9.jpg)
AND Gate Using SSL
PoPS Input A PoPS Input B PoPS Output
0 0 0
1 0 0
0 1 0
1 1 1
Amber Suppressor tRNA
Opal Suppressor tRNA
PoPS Input A
PoPS Input B
UAG
Activator
UGA
PoPS OutputOFF to
ON
![Page 10: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/10.jpg)
NAND Gate Using SSL
PoPS Input A PoPS Input B PoPS Output
0 0 1
1 0 1
0 1 1
1 1 0
Amber Suppressor tRNA
Opal Suppressor tRNA
PoPS Input A
PoPS Input B
UAG
Repressor
UGA
PoPS OutputON to
OFF
![Page 11: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/11.jpg)
XOR Gate Using SSL
PoPS Input A PoPS Input B PoPS Output
0 0 0
1 0 1
0 1 1
1 1 0
Amber Suppressor tRNA
Opal Suppressor tRNA
PoPS Input A
PoPS Input B
UAG
Repressor
UGA
UAG
Activator
PoPS Output
UGA
ActivatorON to OFF
OFF to ON
![Page 12: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/12.jpg)
NXOR Gate Using SSL
PoPS Input A PoPS Input B PoPS Output
0 0 1
1 0 0
0 1 0
1 1 1
Amber Suppressor tRNA
Opal Suppressor tRNA
PoPS Input A
PoPS Input B
UAG
Repressor
UGA
UAG
Repressor
PoPS Output
UGA
Repressor
ON to OFF
ON to OFF
![Page 13: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/13.jpg)
Choosing Inputs
Sa Sg Sb Sh Sf Sl
The triangles are hix sites for hin recombination. If the first activator is the correct one then it will activate a repressor that shuts off the hin and, therefore, stops the recombination from happening. Then it will move on to the next activator.
Only forward activators are expressed.
![Page 14: 3-SAT Problem](https://reader035.fdocuments.us/reader035/viewer/2022062423/568145aa550346895db2a135/html5/thumbnails/14.jpg)
SSL and 3-SAT
This slide shows that if all ten logical clauses are satisfied green fluorescent protein (or any other protein you might want) is made