Math 297/Biol 497
Biomolecular Computing in
Nature
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January 23, 2008
- General remarks about the course
January 25, 2008
- DNA and RNA structure
- Unit of measurement: base pairs, bp
- DNA-to-RNA-to-protein
January 28, 2008
- Transcription, splicing, ligation.
- A functional difference between macronuclei and micronuclei
January 30, 2008
- Replication, nuclease-activity, methylation.
- Difference in DNA organization between macronuclei and micronuclei
- MDSs
- Collected Assignment 1
February 1, 2008
- Returned Assignment 1.
- The conjugation pathway
- MDS, IES
- Collected Assignment 2
February 4, 2008
- Steps of micronuclear decryption: Chromosome polytenization.
- DNA Excision: Scrambled micronuclear versions of genes
- MDSs, IESs and pointers
February 6, 2008
- Steps of micronuclear decryption: Chromosome fragmentation.
- Telomere addition.
- CFSs, CBSs and BESs.
- Returned Assignment 2.
- Collected Assignment 3.
February 8, 2008
- Discuss ActinI in Oxytricha Trifallax
- Returned Assignment 3.
- Collected Assignment 4.
February 11, 2008
- Discuss ActinI in several species
- Download Dr. Hampikian's presentation materials
February 13, 2008
- The DNA Template model for IES excision
February 15, 2008
- An ad-hoc application of the DNA Template model for IES excision
February 20, 2008
- Alteration of the DNA Template model for IES excision
February 22, 2008
- Defining molecular operations dlad, ld and hi, mediated by templates in the altered template model.
February 25, 2008
- Using molecular operations dlad, ld and hi, mediated by templates to descramble Actin I in Sterkiella Histriomuscorum.
February 27, 2008
- Guest lecture by Professor Hampikian.
February 29, 2008
- Using molecular operations dlad, ld and hi, mediated by templates to descramble a hypothetical gene.
March 3, 2008
March 5, 2008
- Molecular implementation of two-state, two-symbol alphabet finite automata
March 7, 2008
- Molecular implementation of two-state, two-symbol alphabet finite automata (II)
- Remarks about molecular operations
March 10, 2008
- Concatenation of two automata
- Adleman's Experiment.
March 17, 2008
- Guest lecture by Dr. Jorczyk.
March 19, 2008
- The satisfiability problem in propositional logic.
- Lipton's DNA algorithm for the satisfiability problem.
March 21, 2008
- Remarks about Turing machines.
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April 4, 2008
- Discussion of 8-puzzle and dlad enzyme.
- Remarks about Turing machines.
April 7, 2008
- Small universal Turing machines.
April 9, 2008
April 11, 2008
April 14, 2008
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Continutation of guided recombination model: splicing schemas and the operations SD and SR.
April 16, 2008
April 18, 2008
- Guided recombination model: circular words/plasmids.
April 21, 2008
- Guided recombination model: Multisets.
April 23, 2008
- Guided recombination model: Derivations of multisets, language accepted by....
April 25, 2008
- Turing machines abridged for the guided recombination model.
April 28, 2008
- Fundamental Theorem of Guided Recombination Systems: Simulating Turing machines.
April 30, 2008
- Fundamental Theorem of Guided Recombination Systems: The splicing schema.
May 2, 2008
- Fundamental Theorem of Guided Recombination Systems: Outline of an inductive proof.
- Returned graded assignments.
- No further homeworks will be assigned or accepted.
May 5, 2008
- Project Presentation: Carpenetti
May 5, 2008
- Project Presentation: Farrar
- Project Presentation: Graff
- Final examination posted: Hardcopy due 11:00 am on May 15