UNCONVENTIONAL COMPUTING I: DNA COMPUTING, CS 881b, Winter 2000

Announcements

• Deadline for submissions of the research paper: Monday, April 17, midnight (file, paper copy, transparencies). Details of submission.
• Class schedule: Wednesdays, 1:00-3:00pm, MC 320
• How to print a .ps file

Course outline

Office hours

• Friday, 11:10am - 1:10 pm, MC 361, Lila Kari.

Invited speakers

• Greg Gloor , Dept. of Biochemistry, UWO
• Lars Konermann , Dept. of Chemistry, UWO
• Jim Crutchfield , Santa Fe Institute
• Mark Daley , Computer Science Dept, UWO.
• Rob Kitto, Computer Science Dept, UWO

Schedule

• Wed., January 12, Introduction. Lila Kari.
• Wed., January 19, Adleman's first experiment in DNA computing. Lila Kari. Suggested readings:
  • DNA computing: arrival of biological mathematics (first two sections)
    Fig.1 , Fig.2 , Fig.3 , Fig.4 , Fig.5 , Fig.6 , Fig.7
• Wed., January 26, Basic concepts used in DNA computing (nucleotides, DNA, proteins, amino-acids). Greg Gloor. Suggested readings:
  • Chapter 1 from "DNA Computing: new computing paradigms." G.Paun, G.Rozenberg, A.Salomaa, Springer Verlag 1998. CS I/O counter.
  • Copies of the slides. CS I/O counter.
  • Nucleic acid structure and function
  • A computer scientist's guide to molecular biology
• Wed., February 2, Potential bio-operations; molecular procedures (PCR, biotin-avidin purification, hybridization, etc.). Greg Gloor. Suggested readings:
  • From Readings Jan.19: first two sections, and last 2 sections on implementation techniques and meta-thoughts.
  • Copies of the slides at the CS I/O counter.
  • Program (cgi)to predict the metling temperature of an oligonucleotide (updated).
• Wed., February 9, Implementing logic with proteins and DNA. Lars Konermann, Lila Kari. Readings:
  • Solving the Satisfiability Problem with DNA
• Wed., February 16, Cells do computations. . Lila Kari. Suggested readings:
  • Computational power of gene rearrangement (@AMS Press) .
  • Reversible molecular computation in ciliates (@Springer Verlag) .
• Wed., February 23- Conference week.
• Wed., March 1, Molecular expert systems , Rob Kitto. Circular insertions and deletions , Mark Daley. Suggested readings:
  • Circular insertions/deletions with applications to biomolecular computation (@IEEE CS Press)
  • Molecular expert systems
• Wed., March 8
  • Jiang Jiang Wang, "Evaluating Boolean formulas with DNA".
  • Xiaomei Liu, "DNA encoding and error resistance".
  • Zhiduo Lotus Zhao, "DNA sequencing methods".
  • Maia Hoeberechts, "Autonomous DNA computers".
• Wed., March 15. This class will be replaced by the talk When Evolution is Revolution March 24 , 3pm-4pm, MC 320, by James Crutchfield followed by the presentation by Xixiao Guo, "Time Complexity in DNA computation", 4pm-5pm.