CMPS 290A, Winter 2000

Moleculal Computation


Lecture times
Tu, Th, 2-3:45pm, Applied Sciences 165
Room permanently switched from 169 to 165 !!!

Instructor
Prof. Manfred Warmuth (manfred@cse.ucsc.edu)
Phone: (831) 459-4950
Office: 331 Applied Sciences
Office Hours: We 1-2, F 11-12

Course Decsription
Lecture 1: Tu, 1-4-00, Manfred Warmuth
Outline, main questions, simple in-vitro selection algs, Aldleman's Hamiltonian path implementation, size limits, electronic versus molecular computation, overview of class

Adleman's original paper

Maley's survey article on DNA computation

Bibliography of molecular computation and splicing systems
For an excellent overview check out Erik Winfree's DNA computation page
In particular look at the link "Some people and their papers"
Lecture 2: Th 1-6-00, Manfred Warmuth
Can a universal computer be built based on DNA
Lecture 3: Tu 1-11-00, Andrew Wedel
An intro to vitro selection
Lecture 4: Th 1-13-00, Andrew Wedel
More advanced methods for in vitro selection
How is crossover used to get rid of bad genes
Lecture 5: Th 1-18-00, Manfred Warmuth
We covered an elegant paper on a sticker-based model of DNA computation
Lecture 6: Th 1-20-00, Manfred Warmuth
The connection between multiplicative updates of on-line learning algorithm and amplification via PCR
Can we select for groups of molecules to solve a tasks cooperatively
Homework 1
Lecture 7: Th 1-25-00, Dave Deamer
Origins of life
Artificial life in lipid vessicles
Lecture 8: Th 1-27-00, Manfred Warmuth
DNA computation on surfaces
Building a large associative memory using DNA
More on selection for groups of molecules
Lecture 9: Th 2-1-00, Ali Shakouri
Why is electronics so successful:
large variability of properties
Doping, lithography, edging, plasma deposition, molecular beam epidaxy
Fiber optics, micro electric systems, scanning microscop, mass fabrication
Lecture 10: Th 2-4-00, Manfred Warmuth
Solution of the homework
Overview of enzymes
Insertion and deletion systems -
simple rewriting systems that are as powerful as Turing machines
Lecture 11: Tu 2-8-00, Manfred Warmuth
Using annealing to compute
and build DNA nano-structures
Winfree's articles on self-assembly
Seeman's survey on DNA nanotechnology
Lecture 12: Tu 2-10-00, cancelled due to sickness

Lecture 13: Tu 2-15-00, Charles Apel
Delineating space filling systems
Computing the number of possible color coding schemes of simple polyhedra
Chirality and modeling of a solution to the protein folding problem

Lecture 14: Th 2-17-00, Lilly Spirkovska
Intro to genetic algs. and genetic progr.

Lecture 15: Tu 2-22-00, Manfred Warmuth
Discussion of genetic algs. and genetic progr. versus biological evolution
How do the concentrations of different strands evolve during PCR

Lecture 16: Tu 2-29-00
Part one:
John Vieceli: Electronically configurable molecular-based logic gates ( paper)
Part two:
Manfred Warmuth: RNA solutions to chess problems ( paper)

Lecture 17: Th 3-1-00
Part one:
Rebecca Braslau: Living free radical polymerization
Part two:
Manfred Warmuth: Minimum genome - Quantitative PCR

Lecture 18: Th 3-7-00
Part one:
Eric Thorne: Quantom Mirages - AFM and STM microscopes
Part two:
Manfred Warmuth: Cellular automata - Game of Life and its universality

Lecture 19: Th 3-9-00
Part two:
Allessandra Cassar: Simulating interactive evolutionary games with SWARM
Part two:
Manfred Warmuth: Nano tweezers, how to grow and manufacture nanotubes

Lecture 20: Th 3-14-00
Eric Thorne: Presentation on Nanotube Tips for AFMs
Eric's final paper on Quantum Corrals and Nanotube Tips

Lilly Spirkovska: Genetic Alg. Design of Two-Way Crossover Circuits.
presentation (Figures) and final paper

Mike Mathieson and Jonathon Panttaja:
Simulating the Evolution of Phenotype and Genotype
Presentation and final paper (part one, part two )

Eric Rice: Presentation on the DNA mirco array technology

Overview of class by Manfred

Questions regarding about page content should be directed to
manfred@cse.ucsc.edu
 Last modified Thursday, 30-Mar-2000 17:43:54 PST.

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