Professor Laura Landweber
A changing view of biology has given rise to the new field of "DNA computers". This field seeks to use biological molecules such as DNA and RNA to solve basic mathematical problems. Fundamentally, many of these experiments recapitulate natural evolutionary processes that take place in biology, especially during the early evolution of life and the creation of genes. This seminar will explore both new uses of nucleic acids as the building blocks of life but also complex architectural structures and even biomolecular-computing "hardware". We will also examine the information processing in cells that have had billions of years to evolve and to perfect a "molecular computer". This seminar concludes by examining the "biological software" invented by nature. We ask whether we can tap into these processes and harness the parallel processing ability of DNA to tackle really hard problems? The ultimate challenge is to find the right questions and to identify the type of problem that molecules can solve in a tiny drop of solution.
WeekClick on links to obtain selected readings for that week.
2/4 DNA ArchitectureFrom Microsoft to "Bio-soft"
Principles of molecular biology
2/11 Fundamentals of ComputingHistory of Computing
Turing Machines, NP-Completeness, Universal Computers
read: Garey and Johnson chapters 1 and 2
2/18The Traveling Salesman: A DNA Computer
3/4Evolution in a Test Tube I: The RNA World
3/11DNA as Lego: Universal Computation by Self-Assembly of DNA
3/25 Evolution in a Test Tube II: Solvinghard problems
4/1 More Molecular TinkertoysNanostructures and Semiconductors
4/8 BuildingGenetic Codes
4/15 Development and EvolutionThe Burgess Shale and the Cambrian Explosion
4/22 RNA Editing and Gene ScramblingCellular Computation
Molecular Evolution and
4/29 Genetic regulation and amorphous computing
Towards in vivo digital circuits