ele 523e computational nanoelectronics w6: molecular computing, 19/10/2015 fall 2015 mustafa altun...
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ELE 523E COMPUTATIONAL NANOELECTRONICS
W6: Molecular Computing, 19/10/2015FALL 2015
Mustafa AltunElectronics & Communication Engineering
Istanbul Technical University
Web: http://www.ecc.itu.edu.tr/
Outline
Molecular computing Working with individual molecules
Fundamentals Implementing arithmetic operations
DNA strand displacement DNA basics DNA strand displacement Implementing logic operations
Computing with Individual Molecules
9
6
7
cell/test tubetypes count
+
8
5
9
Discrete quantity of molecules
x
y
z
+x y 2z
Computing with Individual Molecules
9
6
7
types count
+
3
0
19
x
y
z
+x y 2z
What are the final quantities of molecules?
Write an equation with initial and final quantities.
Computing with Individual Molecules
+
+
+
slow
medium
fast
Reaction rates used for step-by-step procedure.
UNI or BI directional
Computing with Individual Molecules
+
+
+
slow
medium
fast
test tubeInitial condition
10 blue and 5 black
What will happen? Explain step-by-step.
Computing with Individual Molecules
+
+
+
slow
medium
fast
test tubeInitial condition
6 blue, 6 black, and 6 orange
What will happen? Explain step-by-step.
Addition
biochemical code
How to select reaction rates (slow or fast)?
Multiplication
pseudo-codebiochemical code
Exponentiation
biochemical code
pseudo-code
DNA Basics
Biological DNA stores hereditary information Width of the double helix: 2nm Distance between base pairs (bp): 0.34 nm Carsonella rudii (smallest non-viral genome): 160,000 bp Human genome: 3.2 Billion bp Lungfish (largest vertebrate genome): 130 Billion bp
DNA helix
DNA Basics: Nucleotides
DNA Basics: Strands
DNA Basics: Base Pairs
DNA Basics: Base Pairs
DNA Basics: Synthesis
DNA Basics: Complementary
DNA Basics: Binding
1) DNAs tend to have more binded (matched) parts!
Direction is important!
2) DNA binded strands tend to comprise minimum number of single strands!
DNA Basics: Binding
DNA Strand Displacement
Input and Gate
Input and Gate
Binding
ReplacingOutput and Gate
DNA Strand Displacement
x y
y
x
Outputs can be used as inputs. Inputs and outputs are single
strands Gates are double stranded Different types of strand
displacements with different reaction rates.
Waste molecules!
DNA Strand Displacement
What happens?
x y
y z
x
DNA Strand Displacement
x y z+
y z
x
Logic with DNA Strand Displacement
x z
y zx y z+
OR AND
Logic with DNA Strand Displacement
x z
y zOR
Logic with DNA Strand Displacement
x z
y zOR
Logic with DNA Strand Displacement
x z
y zOR
Logic with DNA Strand Displacement
x z
y zOR
DNA Strand Displacement Software
Suggested Readings
Soloveichik, D., Seelig, G., & Winfree, E. (2010). DNA as a universal substrate for chemical kinetics. Proceedings of the National Academy of Sciences, 107(12), 5393-5398.
http://www.technologyreview.com/featuredstory/400728/molecular-computing/
http://research.microsoft.com/en-us/projects/dna/