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DNA as a solution of computational problems Radosław Łazarz

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. Why DNA?. ~750 mB

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DNA as a solution of computational problems Radosław Łazarz

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  1. DNA as a solution of computationalproblemsRadosław Łazarz An introductrion to DNA-basedcomputing Examples of succesfulimplementations: Hamiltonian path problem Turing-likefiniteautomaton Tic-Tac-Toe Predictionsaboutthefuture

  2. Why DNA? • ~750 mB • largenumber od parallelprocesses • extraordinary energy efficiency • survivedaround 3 billionyears of demandingtests as a data carrier • multiplesimilaritieswith Turing machine

  3. Hamiltonian Path Problem • Leonard M. Adelman (1994) • Tools: • Watson-Crickpairing • Polymerases • Ligases • Nucleases • Agarosegelelectrophoresis • DNA synthesis • Bruteforcealgorithm • 7 daysinlaboratory…

  4. Finiteautomaton • 2 states • 4 transitionrules • Fok I and ligase • no additional energy source • close to Turing completeness

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

  6. MolecularArray of YES and ANDANDNOT gates (MAYA) • allostericallyregulateddeoxyribozymes • input: oligonucleotides • output: fluorescencentmolecules • 15 minutes per move • MAYA II

  7. Whatnext? • Othersuccessfulapplications: • selfassembly of ‘Wang’ tiles • booleansatisfiability problem (SAT) • designing materials by specifying a series of DNA orders • Importantproblems: • designingenzymes • stochasticnature of biologicalprocesses • monitoring results • „But biology and computer science - life andcomputation - are related. I am confidentthat at their interface great discoveriesawait those who seek them.”

  8. Ifyou want to learnmore: • “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 DarkoStefanovic; Nature Bio­technology, September 2003 • “DNA Computers for Work and Play” - Joanne Macdonald, DarkoStefanovic and Milan N. Stojanovic; Scientific American, November 2008 • https://digamma.cs.unm.edu/wiki/bin/view/McogPublicWeb/MolecularAutomataMAYAII • “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 http://student.agh.edu.pl/~lazarz/MOwNiT

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