From a biochemical point of view, the DNA computer works by sequentially cutting and joining DNA molecules with the RE FokI and DNA ligase.
#FINITE AUTOMATON SOFTWARE#
These first constructions of DNA computers used one restriction enzyme (RE) as the hardware and DNA fragments as the software and input/output signals.
Although some of this research provided only theoretical solutions without practical laboratory implementation, e.g., biomolecular representations of the Turing machine (Rothemund, 1995) or the pushdown automaton (Cavaliere et al., 2005 Krasinski et al., 2012), there have been prominent excep- tions, including a stochastic automaton ) and a finite automaton (Benenson et al., 2001(Benenson et al.,, 2003. An inter- esting trend in DNA computing has been the development of biomolecular solutions for well-known models in theo- retical computer science, such as finite automata, pushdown automata or Turing machines. Other areas of research have attempted to apply DNA computing in medi- cine, e.g., for cancer therapy ) or 'miRNA' level diagnostics (Seelig et al., 2006). Some studies have focused on se- lected, well-known problems in mathematics and computer science, e.g., the tic-tac-toe algorithm (Stojanovic and Stefanovic, 2003), the Knight problem (Faulhammer et al., 1999) or the SAT problem (Lipton, 1995). Over the next two decades, numerous reports on DNA computing appeared. The first attempt to develop a DNA computer was by Adleman (1994), who solved some computational problems in a laboratory test- tube. computers are the answer to problems associated with the development of traditional, silicon- based computers, particularly their miniaturization, as im- plied by the Heisenberg uncertainty principle, and to limita- tions in data transfer to and from the main memory by the central processing unit (Amos, 2005). Based on this experiment, we conclude that it is possible to construct more complex finite automata using several re- striction. The positive re- sult of our experiment (Figure 10) proved that a multistate biomolecular automaton may act with four endonucleases. Detection of the 614 bp fragment in gel electrophoresis indicated the accep- DNA computer tance of the input word by the automaton. Since the detection molecule had no restriction sequence charac- teristic for any of the REs, DNA molecules 614 bp long were obtained (the previous steps produced much shorter fragments, as seen in Figures 9 and 10). If a sticky end CGTT is obtained in terminator t of the input word then the detection molecule will ligate to the input molecule. These experi- ments focused on the key automaton element that is essen- tial to the action of automata, namely, the autonomous and alternating action of four REs (Figure 9). tested the action of automaton M 1 in Figure 5B by running it on the accepted input word abba. The transition function returns a state which can be called as the next state. The two parameters mentioned below are the passes to this transition function. The transition table is as follows − State/input symbol
Column corresponds to the input symbol.Īn example of transition table is as follows −.In transition table, the following factors are considered − It is basically a tabular representation of the transition function that takes two arguments (a state & a symbol) and returns a value (the ‘next state’). It is a directed graph associated with the vertices of the graph corresponding to the state of finite automata.Īn example of transition diagram is given below − δ: Q × Σ → Q is the transition function.įinite Automata can be represented as follows −.The finite automata can be represented in three ways, as given below − It is a mathematical model of a system with discrete inputs, outputs, states and a set of transitions from state to state that occurs on input symbols from the alphabet Σ. Finite automata is an abstract computing device.
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