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Natural Computing
Lecture 16

Michael Herrmann mherrman@inf.ed.ac.uk phone: 0131 6 517177 Informatics Forum 1.42

11/11/2011

Molecular Computing
11/11/2011 NAT16 J.M. Herrmann

Overview

Molecular computing Membrane computing

Video to last lecture: http://www.youtube.com/watch?v=4PKjF7OumYo

11/11/2011 NAT16 J.M. Herrmann

Current developments

Synthetic biology: Creating new biological functions and systems for computation and medical applications Self-assembly: On the molecular, supermolcular, as well as on the macroscopic scale.
Gross, R.; Dorigo, M.; , "Self-Assembly at the Macroscopic Scale," Proceedings of the IEEE , vol.96, no.9, pp.1490-1508, Sept. 2008

Molecular nanomachines: MAYA II plays TicTacToe
J. Macdonald et al.: Medium Scale Integration of Molecular Logic Gates in an Automaton. NANO LETTERS 2006 Vol. 6, No. 11 2598-2603

Autonomous molecular computers
Y. Benenson et al. An autonomous molecular computer. Nature 2004 Yurke, B.; Turbereld, A. J.; Mills, A. P., Jr; Simmel, F. C. & Neumann, J. L. (2000). "A DNA-fuelled molecular machine made of DNA". Nature 406 (6796): 605609.

How to design the DNA pieces needed in the machines?
T. B. Kurniawan et al. (2008) An Ant Colony System for DNA sequence design based on thermodynamics. Proc. 4th IASTED ACST '08, 144-149. 11/11/2011 NAT16 J.M. Herrmann

Genetic Algorithms in DNA Computing

Adleman's solution to the Hamiltonian path problem: checking all possible solutions (although brute force, it was nevertheless a breakthrough in natural computing) New algorithms for a DNA computer? Life hasn't tested all possible combinations of genes, neither do GAs Introduce and exploit structure of the search space



DNA genetic algorithm

Z Ezziane: DNA computing: applications and challenges. Nanotechnology 17 (2006) R27R39.

11/11/2011 NAT16 J.M. Herrmann

GA operators
100 dierent restriction enzymes are known, each of which cuts at its specic recognition...

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