Theoretical and Experimental DNA Computation (Natural ...

56 3 Models of Molecular Computation
Bit
k
1 2 k
0 0 0
0 0 1
0 1 0
0 1 1
(a)
0 0
0 0
0 0
0 0
(b)
l
1 0 0
1 0 1
1 1 0
1 1 1
0 0
0 0
0 0
0 0
Fig. 3.2. (a) General memory strand scheme. (b) Complete (5,2) library
As in the models described previously, computations within the model consist
of sequences of operations taken from the available set. The final result is read
from the output tube by determining the contents of the memory strands it
contains; if the output tube is empty then this fact is reported.
The initial input to a computation consists of a library of memory strands.
A(k, l) library, where 1 ≤ l ≤ k, consists of memory strands with k substrands,
the first l of which may be on or off, and the last k − l of which are
off. Therefore, in an initial tube the first l substrands represent the input to
the computation, and the remaining k − l substrands are used for working
storage and representation of output. For example, a complete (5,2) library is
depicted in Fig. 3.2b.
1
4
(a)
2
3
5
5
3 4
2
1 5
1
3
C 1 C 2
4
3 4
C3 C4
Fig. 3.3. (a) Five possible objects. (b) Four different bags
(b)