1. DNA as a solution of computational problems Radosław Łazarz
An introductrion to DNA-based computing
Examples of succesful implementations:
Hamiltonian path problem
Turing-like finite automaton
Tic-Tac-Toe
Predictions about the future

2. Why DNA? ~750 mB large number od parallel processes
extraordinary energy efficiency
survived around 3 billion years of demanding tests as a data carrier
multiple similarities with Turing machine

3. Hamiltonian Path Problem
Leonard M. Adelman (1994)
Tools:
Watson-Crick pairing
Polymerases
Ligases
Nucleases
Agarose gel electrophoresis
DNA synthesis
Bruteforce algorithm
7 days in laboratory…

4. Finite automaton 2 states 4 transition rules Fok I and ligase
no additional energy source
close to Turing completeness

5. DNA Doctor? in vitro vs. in vivo input: mRNA as disease indicators
output: antisense DNA molecule

6. Molecular Array of YES and ANDANDNOT gates (MAYA)
allosterically regulated deoxyribozymes
input: oligonucleotides
output: fluorescencent molecules
15 minutes per move
MAYA II

7. What next? Other successful applications: Important problems:
self assembly of ‘Wang’ tiles
boolean satisfiability problem (SAT)
designing materials by specifying a series of DNA orders
Important problems:
designing enzymes
stochastic nature of biological processes
monitoring results
„But biology and computer science - life and computation - are related. I am confident that at their interface great discoveries await those who seek them.”

8. If you want to learn more:
“Computing with DNA” - Leonard M. Adleman; Scientific American, August 1998
“Molecular Computation of Solutions to Combinatorial Problems.” - Leonard M. Adleman; Science, November 1994.
“DNA Solution of Hard Computational Problems.” - Richard J.Lipton; Science, April 1995.
“Bringing DNA Computers to Life.” - Ehud Shapiro, Yaakov Benenson; Scientific American, May 2006
“A Deoxyribozyme-Based Molecu­lar Automaton.” - Milan N. Stojanovic and Darko Stefanovic; Nature Bio­technology, September 2003
“DNA Computers for Work and Play” - Joanne Macdonald, Darko Stefanovic and Milan N. Stojanovic; Scientific American, November 2008
“Logical Computation Using Algorithmic Self-Assembly of DNA Triple Crossover Molecules.” - Chengde Mao, Thomas H. LaBean, John H. Reif, Nadrian C. Seeman; Nature, September 2000
“Nanotechnology and the Double Helix” - Nadrian C. Seeman; Scientific American, June 2004