Biological Computing Intro
Walker Wheeler
What Is Biological Computing?
Biological Computing has 2 main sub categories:
- BioComputers - DNA based computing
- BioInformatics - Use of computers in biological research.
The Turing Machine
- Created by Alan Turing (1936)
- Composed of:
- Infinite Length of Tape
- Read/Write Head for Tape
- State Register
- State Transition Table
- Current State
- Current Tape Symbol
- Symbol to Write
- Tape Shift Direction
- New State
- Can be used to compute anything that has a computable algorithm.
DNA and Turing Machines
- Both systems process information stored in a string of symbols.
- Both operate by moving step by step along strings, modifying and adding symbols according to a given set of rules
These observed similarities encouraged investigation of DNA computation.
Adelman and the Traveling Salesman
Leonard Adelman was the first person to actually do BioComputing. While at the University of
Southern California, he used DNA to solve an instance of the Traveling Salesman problem.
He used DNA molecules to systematically encode connected cities and combined trillions of these
in a test tube. He then took advantage of the pairing affinities to achieve an answer within
a few minutes. The downside was that it took much longer at the time to retrieve the combinations
representing success.
A DNA based Turing Machine
This is an abstract model of how the DNA based Turing machine would work.
A DNA based Turing Machine (2)
The following image shows how the enzyme FokI will act as a turing machine
and how the various components map to the Turing Machine model in the previous slide.
A DNA based Turing Machine (3)
This image shows how a DNA computer would process it's input.
DNA Oragami
Although many seek to advantage of DNA's potential for computational power, some others have a more
entertaining use of it. Paul W. K. Rothemund has found yet another use of DNA. He has started to
build 2d images out of DNA that only take about 2 weeks from start to finish. Each of the images to
the right is only a few hundred nanometers across.