Cyclic Mixture Mutagenesis \\ for DNA-Based Computing -- Large Tape Head Version<A NAME="2"> </A><A NAME="sec:fatTM"> </A>

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Large Tape Head Version

Next we have a system implementing a simple Turing machine using the method of having the encoding of the tape head symbol be a different size from the encoding of the tape symbols.

        :0      CATGCAGG
        :q0     CAGGCATGCAGG
        :1      ATCGCACA
 
        3'<- !0 !0 !q0 !0 !0 !0 !1 !0 ->5'
 
        5'- 0 0 q0 0 ->3'

This machine also uses the idea of flanking symbols. Below is a sample run of this machine at 60 C, skipping the alternate steps that involve exact replication. Also we ignore primers. Note that the machine moves both forwards and backwards, randomly.

----------------------------------------------------------------------
sim julia.olig -T 60 -n -t 600
Parameters: file = julia.olig, T = 333.15, c = 1e-07, t = 600,
            p = 0, s = 796559247
 
Command: ?
 
   [!0    ][!0    ][!q0       ][!0    ][!0    ][!0    ][!1    ][!0    ]
3'-GTACGTCCGTACGTCCGTCCGTACGTCCGTACGTCCGTACGTCCGTACGTCCTAGCGTGTGTACGTCC-5'
 
   ::::::::::::::::::::::::::::::::::::    DG0 = -27.4359
5'-CATGCAGGCATGCAGGCAGGCATGCAGGCATGCAGG-3' k = 1.02047e+18
   [0     ][0     ][q0        ][0     ]    p = 1.000000
 
           ::::::::::X:::X:::::::::::::::::::::    DG0 = -16.2482
        5'-CATGCAGGCATGCAGGCAGGCATGCAGGCATGCAGG-3' k = 4.62655e+10
           [0     ][0     ][q0        ][0     ]    p = 0.999784
 
Below .01 probability of binding:
 
                   ::X:::X:::X:::X:::::::::::::::::::::    DG0 = -5.06054
                5'-CATGCAGGCATGCAGGCAGGCATGCAGGCATGCAGG-3' k = 2097.56
                   [0     ][0     ][q0        ][0     ]    p = 0.000210
 
 
Command: 
 
Cycle = 1, time = 10:00, temp =  60.00.
[0     ][0     ][q0        ][0     ]                                
CATGCAGGCATGCAGGCAGGCATGCAGGCATGCAGG                                
::::::::::::::::::::::::::::::::::::                                
GTACGTCCGTACGTCCGTCCGTACGTCCGTACGTCCGTACGTCCGTACGTCCTAGCGTGTGTACGTCC
[!0    ][!0    ][!q0       ][!0    ][!0    ][!0    ][!1    ][!0    ]
 
Command: 
 
Cycle = 3, time = 10:00, temp =  60.00.
[0     ][0     ][q0        ][0     ]                                
CATGCAGGCATGCAGGCAGGCATGCAGGCATGCAGG                                
::::::::::::::::::::::::::::::::::::                                
GTACGTCCGTACGTCCGTCCGTACGTCCGTACGTCCGTACGTCCGTACGTCCTAGCGTGTGTACGTCC
[!0    ][!0    ][!q0       ][!0    ][!0    ][!0    ][!1    ][!0    ]
 
Command: 
 
Cycle = 5, time = 10:00, temp =  60.00.
        [0     ][0     ][q0        ][0     ]                        
        CATGCAGGCATGCAGGCAGGCATGCAGGCATGCAGG                        
        ::::::::::X:::X:::::::::::::::::::::                        
GTACGTCCGTACGTCCGTCCGTACGTCCGTACGTCCGTACGTCCGTACGTCCTAGCGTGTGTACGTCC
[!0    ][!0    ][!q0       ][!0    ][!0    ][!0    ][!1    ][!0    ]
 
Command: 
 
Cycle = 7, time = 10:00, temp =  60.00.
        [0     ][0     ][q0        ][0     ]                        
        CATGCAGGCATGCAGGCAGGCATGCAGGCATGCAGG                        
        ::::::::::::::::::::::::::::::::::::                        
GTACGTCCGTACGTCCGTACGTCCGTCCGTACGTCCGTACGTCCGTACGTCCTAGCGTGTGTACGTCC
[!0    ][!0    ][!0    ][!q0       ][!0    ][!0    ][!1    ][!0    ]
 
Command: 
 
Cycle = 9, time = 10:00, temp =  60.00.
                [0     ][0     ][q0        ][0     ]                
                CATGCAGGCATGCAGGCAGGCATGCAGGCATGCAGG                
                ::::::::::X:::X:::::::::::::::::::::                
GTACGTCCGTACGTCCGTACGTCCGTCCGTACGTCCGTACGTCCGTACGTCCTAGCGTGTGTACGTCC
[!0    ][!0    ][!0    ][!q0       ][!0    ][!0    ][!1    ][!0    ]
 
Command: 
 
Cycle = 11, time = 10:00, temp =  60.00.
                [0     ][0     ][q0        ][0     ]                
                CATGCAGGCATGCAGGCAGGCATGCAGGCATGCAGG                
                ::::::::::::::::::::::::::::::::::::                
GTACGTCCGTACGTCCGTACGTCCGTACGTCCGTCCGTACGTCCGTACGTCCTAGCGTGTGTACGTCC
[!0    ][!0    ][!0    ][!0    ][!q0       ][!0    ][!1    ][!0    ]
 
Command: 
 
Cycle = 13, time = 10:00, temp =  60.00.
        [0     ][0     ][q0        ][0     ]                        
        CATGCAGGCATGCAGGCAGGCATGCAGGCATGCAGG                        
        ::::::::::::::::::X:::X:::::::::::::                        
GTACGTCCGTACGTCCGTACGTCCGTACGTCCGTCCGTACGTCCGTACGTCCTAGCGTGTGTACGTCC
[!0    ][!0    ][!0    ][!0    ][!q0       ][!0    ][!1    ][!0    ]
 
Command: 
 
Cycle = 15, time = 10:00, temp =  60.00.
        [0     ][0     ][q0        ][0     ]                        
        CATGCAGGCATGCAGGCAGGCATGCAGGCATGCAGG                        
        ::::::::::::::::::::::::::::::::::::                        
GTACGTCCGTACGTCCGTACGTCCGTCCGTACGTCCGTACGTCCGTACGTCCTAGCGTGTGTACGTCC
[!0    ][!0    ][!0    ][!q0       ][!0    ][!0    ][!1    ][!0    ]
 
Command: 
 
Cycle = 17, time = 10:00, temp =  60.00.
[0     ][0     ][q0        ][0     ]                                
CATGCAGGCATGCAGGCAGGCATGCAGGCATGCAGG                                
::::::::::::::::::X:::X:::::::::::::                                
GTACGTCCGTACGTCCGTACGTCCGTCCGTACGTCCGTACGTCCGTACGTCCTAGCGTGTGTACGTCC
[!0    ][!0    ][!0    ][!q0       ][!0    ][!0    ][!1    ][!0    ]
 
Command: 
 
Cycle = 19, time = 10:00, temp =  60.00.
        [0     ][0     ][q0        ][0     ]                        
        CATGCAGGCATGCAGGCAGGCATGCAGGCATGCAGG                        
        ::::::::::X:::X:::::::::::::::::::::                        
GTACGTCCGTACGTCCGTCCGTACGTCCGTACGTCCGTACGTCCGTACGTCCTAGCGTGTGTACGTCC
[!0    ][!0    ][!q0       ][!0    ][!0    ][!0    ][!1    ][!0    ]
 
----------------------------------------------------------------------

- Michael P. Frank, September 12, 1995. Formatted using HyperLaTeX-1.3.