What is DNA Computing?

• For short, DNA Computing uses DNA molecules to solve the problems.
  One reason to use DNA molecules is that DNAs have massive parallelism. Since DNA computing is naturally parallel computing, we hope we can solve the hard problems -for example, NP-complete problems- using DNA computing methods.
  
  
• read these articles.
  • 한겨레 신문 interview (in Korean : 한계레 신문 [21C특별기획]인터뷰.뉴욕시립대 미치오 카쿠 교수 - 1998년 9월 3일자 신문)
  • 한겨레 신문 2000년 1월 14일자 국제면 기사
  • 한겨레21 2000.1.27 제293호 과학면 기사
  • 디지털 타임스 2001년 12월 7일자
  • The Technology Review May/Jun 2000
  • The Chronical of Higher Education, Nov. 28, 1997
• Discover Magazine published an article in comic strip format about Leonard Adleman's discovery of DNA computation.
  Not olny entertaing but also the most understandable explanation of molecualr computation.
• The article published in Scientific American, written by Adleman
• Introduction to DNA Computing (made by me)

• The most important paper in DNA Computing (the html version)
  L.M. Adleman, Molecular Computation of Solutions to Combinatorial Problems, Science, 266:1021-1024, 1994

• Tutorals and Introductive Papers
  • Genetic Programming 1998 Conference; Computing with DNA: An Introduction Tutorial, R. Deaton and S. A. Karl
  • Genetic and Evolutionary Conference 1999 Tutorial; Introduction to DNA Computing, 75-93, R. Deaton and S. A. Karl
  • Congress on Evolutionary Computation 1999 Tutorial
  • Genetic and Evoltuionary Conference 2000 Tutorial; Introduction to DNA Computing, 1-25, R. Deaton and J. Chen
  • C.C. Maley, DNA computation; Theory, Practice, and Prospects, Evolutionary Computation, 6(3):201-229, 1999.
  • M. Garzon and R. Deaton, Biomolecular Computing and Programming, IEEE Trans. on Evolutionary Computation, 3:3 (Sept. 1999), 236-250.

• DNA Computing Courses in the Universities
  • CS 881 : Dept. of Computer Science, Univ. of Western Ontario
    I think this course is the first DNA Computing Course in the University
    
  • Unconventional Compouting 1: DNA Computing, CS881b, Winter 2001 : Univ. of Western Ontario
    
  • MIS 214/CS 274 General Course Information (Spring '99)
  • Basic DNA Computing CICS 449/649, Fall 1999
  • Introduction to Computational Genomics Lecture 5 (Korea Univ. and KAIST in Korea)

• Ph. D Papers and other papers
  • The first Ph.D Thesis on DNA Computation by Martyn Amos in the University of Warwick (1997)
    
  • Erik Winfree's Ph.D thesis in the California Institute of Technology (1998)
  • If you want to find the more paper, I recomend this site
    A Bibliography of Molecular Computation and Splicing Sysmtes
  • also recomend this site The Collection of Computer Science Bibliographies (subject: DNA Computing etc.)
  • my papers on DNA computing is in the publications page

• Related Proceedings and Books
  • DIMACS Proceedins: DNA Based Computers I, II, III, IV (Special Issue of BIosystems), V, VI.
  • GP Proceedins: Genetic Programming 1 (1997), Genetic Programming 2 (1998), GECCO-99 (1999)
  • ICEC Proceedings: IEEE Internal Conference on Evolutionary Computation (1997), CEC99 (1999)

  • G. Paun (ed.), Computing with Biomolecules: Theory and Experiment, Springer-Verlag, Singapore, 1998
  • G. Paun et al. (eds.), DNA Computing: New Computing Paradigms, Springer-Verlag, Berlin, 1998
  • T. Gramss (ed.), Non-Standard Computation: Molecular Computation - Celluar Automata - Evolutionary Algorithms - Quantum Computers, 1998
  • C. S. Calude and G. Paun, Computing with Cells and Atoms: An intoruction to quantum, DNA and membrane computing, Taylor & Francis, 2001.
  • M. Amos, Theoretical and Experimental DNA Computation, Springer-Verlag, 2001.
  • Amazon.com search result (subject: Molecular computers)

• Related Conferences and Events
  • DNA Based Computers VII - This year
  • DIMACS Special Focus on DNA Computing 1997 - 1999
  • Erik's collection

• Related Organization or Research Groups
  • BioMip (in GMD)
  • The European Molecular Computing Consortium(EMCC)
  • Dreseden DNA Computation Group
  • Molecular Computer Project (Tokyo Univ.)
  • DNA Computing and Informatics at Surfaces (Univ. of Wisconsin)
  • Leiden Center for Natural Computing
  • Consortium for Biomolecular Computation
    • Status Reports for DNA computing
    • 1998 Report
    • 1997 Report
    • DARPA Web Report
    • DARPA Proposal
    • NSF Proposal

  • DNA Computing Researchers

• Erik's collections of informations about the field of DNA computing (such as some upcoming conferences, other events, and relevant journals) are here. This site is very useful! ^^

My major topic is DNA computing or molecular computation.

My works are

• developing NACST (Nucleic Acid Computing Simulation Toolbox)

  - Software tool for simulation and programming of DNA Computers
  

  I focus on bio-inspired intelligence technologies (bio-intelligence). I try to model the biological information processing at the molecular level and its application to construction of learning and adaptive systems for solving NP-complete problems. I and my professor developed the concept, Molecular Programming (MP), evolutionary algorithms designed for automatic programming of molecular (DNA) computers.
  

• DNA Computing for Network Optimization
  (You can see the abstract flows of network optimization using DNA computation method)
  

  Using the NACST system, I simulated Adleman's experiment (Hamiltonian Path Problem), Ouyang's experirment (Maximal Clique Problem), and I solved Travelling Salesman Problems.