Simulator Software for Autonomous DNA Nanomechanical Device
Capable of Universal Computation
and Universal Translational Motion
This software simulates the DNA ligation and restriction events
occuring in the autonomous DNA Universal Turing Machine. The output is
a graphical display of the reactions taking place with the Head
Molecules and the Symbol Molecules. The top array and bottom array
consists of Head Molecules and Symbol Molecules, respectively.
Screenshots of the Turing Machine
simulation for a binary counter of 2-digits.
The software package can be obtained by sending an email to sudheer@cs.duke.edu,
and it includes the following files:
1) Source code and executable for the the simulator.
2) Example Input files:
input.a.dir
The head of the Turing Machine
makes uni-directional motion and changes the color of the tape (the
Symbol Molecules).
input.bi.dir
The head of the Turing Machine
just moves
forward-backward without changing the color of the tape.
input.counter_base2.2
A 2-digit binary counter with 0
and 1 displayed in different colors.
input.counter_base3.2
A 2-digit base-3 counter with 0, 1 and 2 displayed in different colors.
input.univ
A 2-state and 5-symbol Universal Turing Machine. (Reference:
S. Wolfram, A new kind of science. Wolfram Media, Champaign, IL, 2002).
3) README
4) Perl script to construct the Rule Molecules of our
simulation from the specified transition rules for
the Turing Machine.
To run the code just type :
./a.out
input_file_name