الفهرس 
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Abstract
A major goal for nanoscince, nanotechnology and super molecular chemistry is to design synthetic molecular devices that are programmable and run autonomously. Programmable means that the behavior of the device can be modified without redesigning the whole structure. Autonomous means that it runs without externally mediated change to the work cycle.A finite-state machine (FSM) is an abstract mathematical model of computation used to design both computer programs and sequential logic circuits. DNA had been used to solve computational problems like FSA, the satisfiability problem for Boolean circuits. Furthermore, DNA computers can also solve optimization problems directly with solving several decision problems. Linking computer science with microbiology came out with a new science called computational biology. DNA computing is a branch of this novel science. However, DNA computing have many advantages over traditional computing techniques, like high speed, low energy consumption, and economical information storing.In this thesis, different implementations of DNA finite state machines are discussed, such as Restriction Enzymes FSM, FSM with DNA Polymers, and DNAzymes FSM. Moreover, a comparison was made to clarify the advantages and disadvantages of each kind of presented DNA finite state machines. A practical design of a DNA finite state machine, constructed in Duke University by John H. Reif and Sudheer Sahu [1], was presented. Such automata use massive parallel processing offered by molecular approach for computation and exhibits a number of advantages over traditional electronic implementations.A known finite state machine called Odd Parity Checker, was described. It is built on 10-23 DNAzymes [2] and give its procedure of both design and computation. The design of such a molecular parity checker incorporated ideas from the design of autonomous programmable DNAzyme nanorobotic devices; DNAzyme walker and VI DNAzyme FSM. The design procedure has two major phases. The first phase considers designing the language potential alphabet DNA strands. The second phase depends on the first to design the DNAzyme possible transitions.Due to fund, difficulties had been faced to implement the whole machine with all of its transitions in the wet lab. So, for simplicity, it was sufficient to demonstrate the feasibility of such a machine by one transition implementation. The primary result had been disappointing. So it had been decided to add 24 different constrains to the lab experiment, in order to choose the best result that proves what had been claimed in Reif and Sudheer’s theory. Again, the results were negative according to the theory claimed in [1]. Though their theory wasn’t fully proved in this thesis, there is a genuine spark to continue research on this area.Keywords: DNA computing, DNAzymes, Finite state automata, Self-Assembly, Restriction enzymes, Molecular devices, Miniaturization, Nanotechnology.