426 B DNA

By srinivasan krishnamurthy
Introduction:
What is DNA computing ? Around 1950 first idea (precursor Feynman) First important experiment 1994: Leonard Adleman Molecular level (just greater than Massive parallelism. In a liter of water, with only 5 grams of DNA we get around 1021 bases ! Each DNA strand represents a processor !
10-9 meter)
Introduction to DNA:
A bit of biology
The DNA is a double stranded molecule. Each strand is based on 4 bases: Adenine (A) Thymine (T) Cytosine (C) Guanine (G) Those bases are linked through a sugar (desoxyribose)
IMPORTANT: The linkage between bases has a direction. There are complementarities between bases (Watson-Crick). (A) (T) (C)(G)
DNA manipulations
So instead of using physical processes, we would have to use natural ones, more effective: for lengthening: polymerases for cutting: nucleases (exo/endonucleases) for linking: ligases
If we want to use DNA as an information bulk, we must be able to manipulate it .
However we are talking of handling molecules
Serialization: 1985: Kary Mullis PCR(polymerase chain reaction)
ENZYMES = Natural CATALYSERS.
Thank this reaction we get millions of identical strands, and we are allowed to think of massive parallel computing.
And what now ?

Molecular level.
Situation:
Lots of agents. (strands) Tools provided by nature. (enzymes)
How can we use all this? If there is a utility
Coding the information:

Given a directed graph can we find an hamiltonian path (more complex than the TSP).
1994: THE Adlemans experiment.
In this experiment there are 2 keywords: massive parallelism (all possibilities are generated) complementarity (to encode the information)
This experiment proved that DNA computing wasnt just a theoretical study but could be applied to real problems like cryptanalysis (breaking DES )
Adleman experiment:
Each node is coded randomly with 20 bases.
Each Si is decomposed into 2 sub strands of length 10_9 Si = Si Si
Let Si be a code, h be the complementarity mapping. h(ATCG) = TAGC.
Edge(i,j) will be encode as h(SiSj)( preserve edge orientation).
Code: Input(N) //All vertices and edges are mixed, Nature is working NB(N,S0) //S0 was chosen as input vertice. NE(N,S4) //S4 was chosen as output vertice. NE(N,<=140) // due to the size of the coding. For i=1 to 5 do N+N(N, Si) //Testing if hamiltonian path Detect(N) //conclusion
New generation of computers?

In the second part of [1], it is proven through language theory that DNA computing guarantees universal computations.
Many architectures have been invented for DNA computations.
The Adleman experiment is not the single application case of DNA computing
Mother Board
DNA molecule Arrangement in Chip
Stickers model:
Memory complex = Strand of DNA (single or semidouble).
Stickers are segments of DNA, that are composed of a certain number of DNA bases.
To use correctly the stickers model, each sticker must be able to anneal only at a specific place in the memory complex.
About a stickers machine?
However for a mere computation (DES):
Great number of tubes is needed (1000). Huge amount of DNA needed as well.
Tubes are considered (cylinders with two entries) Simple operations: merge, select, detect, clean.
Why dont we see DNA computers everywhere?
DNA computing has wonderful possibilitie s: Reducing the time of computat ions* (parallelis m) Dynamic program ming !
However one importan t issue is to find the killer applicati on.
Great hurdles to overcome
Some hurdles:
Operations done manually in the lab.
Natural tools are what they are
Formation of a library (statistic way)
Operations problems
Features of DNA computer:

Storage capacity: The information density could go up to 1 bit
Speed: Although the elementary operations (electrophoresis separation, legation, and PCR-amplifications) would be slow compared to electronic computers, their parallelism would strongly prevail, so that in certain models the number of operations per second could be in an order
High parallelism: every molecule could act as a small processor on nanoscale and the number of such processors per volume would be potentially enormous. In an in vitro assay we could handle easily with about 1018 processors working in parallel.
Conclusion:
The paradiagram of DNA computing has lead to a very important theoretical research.
NO ! Wet computi ngstill alive to impleme nt
However DNA computers wont flourish soon in our daily environment due to the technologic issues.
Is all this work lost ?
Adleman renouncemen t toward electronic computing.
THANK YOU

426 B DNA

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426 B DNA

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By srinivasan krishnamurthy

If we want to use DNA as an information bulk, we must be able to manipulate it .

However we are talking of handling molecules

Serialization: 1985: Kary Mullis PCR(polymerase chain reaction)

ENZYMES = Natural CATALYSERS.

And what now ?

Lots of agents. (strands) Tools provided by nature. (enzymes)

How can we use all this? If there is a utility

Coding the information:

1994: THE Adlemans experiment.

Let Si be a code, h be the complementarity mapping. h(ATCG) = TAGC.

Edge(i,j) will be encode as h(SiSj)( preserve edge orientation).

New generation of computers?

Many architectures have been invented for DNA computations.

DNA molecule Arrangement in Chip

Memory complex = Strand of DNA (single or semidouble).

About a stickers machine?

However for a mere computation (DES):

Why dont we see DNA computers everywhere?

However one importan t issue is to find the killer applicati on.

Great hurdles to overcome

Operations done manually in the lab.

Natural tools are what they are

Formation of a library (statistic way)

Features of DNA computer:

NO ! Wet computi ngstill alive to impleme nt

Is all this work lost ?

Adleman renouncemen t toward electronic computing.

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