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How many computers can fit into a drop of water?
Udi Shapiro
Ehud Shapiro
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Medicine in 2050: “Doctor in a Cell”
Programmable Computer
Molecular Input
Molecular Output
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micronmicronin Pentium IIin Pentium II
Scaling electro and bio devices
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E. ColiE. Coli
1 micron1 micron
micronmicronin Pentium IIin Pentium II
Scaling electro and bio devices
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E. Coli
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E. Coli internals
(1Mbyte)
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Ribosomes in operation
Ribosomes translate RNA to Proteins
RNA Polymerase transcribes DNA to RNA
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A mechanical computer
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1122
33
4455
AA
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BB
FrontFront BackBack
1a1a
1b1b
2a2a
2b2b3a3a
3b3b
4a4a
4b4b
5a5a
5b5b
5a5a
5b5b
4a4a4b4b
3a3a
3b3b
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Medicine in 2050: “Doctor in a Cell”
Programmable ComputerProgrammable Computer
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S0 S1
a a
b
b
A1: even number of b’s
Automaton A1 accepting inputs with an even number of b ’s
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0 1 0 0 1 1 0 0 1 0 0 1 1 0 ............
S0,0 S0
S1,0 S1
S0,1 S1
S1,1 S0
State transition rules
Turing Machine and Finite AutomatonTuring Machine and Finite Automaton
S0 S1
1
1
00
State transition diagram
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Example ComputationExample Computation
S0,0 S0
S1,0 S1
S0,1 S1
S1,1 S0
State transition rules
0 1 0 0 1 0 0
S0
initial state: S0
<S0, 0100100>
S1
0 1 0 0 1 0 0 <S1, 00100>
S0,1 S1
S1
0 1 0 0 1 0 0 <S1, 0100>
S1,0 S1
S1
0 1 0 0 1 0 0 <S1, 100>
S1,0 S1
0 1 0 0 1 0 0
S0
<S0, 00>
S1,1 S0
0 1 0 0 1 0 0
S0
final state: S0 <S0, 0>
S0,0 S0
0 1 0 0 1 0 0
S0
<S0, 100100>
S0,0 S0
S0 S1
1
1
00
State transition diagram
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S0-abaaba (S0 S0)
S0-baaba (S0 S1)
S1-aaba (S1 S1)
S1-aba (S1 S1)
S1-ba (S1 S0)
S0-a (S0 S0)
S0 (final state)
The input is accepted
⏐ →⏐ a
⏐ →⏐ a
⏐ →⏐ a
⏐ →⏐ a
⏐ →⏐ b
⏐ →⏐ b
An example computation over abaaba
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T1: S0 S0
T2: S0 S1
T3: S0 S0
T4: S0 S1
T5: S1 S0
T6: S1 S1
T7: S1 S0
T8: S1 S1
⏐ →⏐ a
⏐ →⏐ a
⏐ →⏐ a
⏐ →⏐ a
⏐ →⏐ b
⏐ →⏐ b
⏐ →⏐ b
⏐ →⏐ b
A list of all 8 possible transition rules
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S0 S1
a a
b
A2: at most one b
b
A6: no a after b
S0 S1
a b
S0 S1
a
b
a
A4: no two consecutive b’s
S0
a
A5: only a’s
S0 S1
a a
b b
A3: at least one b
S0 S1
b a
a b
A7: starts with a and ends with b
Automata programs used to test the molecular implementation
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Molecular realization of Finite Automata
•Input: DNAS, a rest a’
•Software: DNA
S, aFokI
•Hardware: Class-II restriction enzyme FokI, DNA Ligase, ATP as fuel
Fok I Ligase