# 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
• 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.

# Turing Machine Demonstration

Xturing machine (Java Applet Example)

# DNA Information

The above from John Kyrk's website that animates processes related to DNA. http://www.johnkyrk.com © 2007

# 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.

Any questions?