DNA Chemical Reaction Network Design Synthesis and Compilation
The advantages of biomolecular computing include 1) the ability to interface with, monitor, and intelligently protect and maintain the functionality of living systems, 2) the ability to create computational devices with minimal energy needs and hazardous waste production during manufacture and lifecycle, 3) the ability to store large amounts of information for extremely long time periods, and 4) the ability to create computation analogous to human brain function. To realize these advantages over electronics, biomolecular computing is at a watershed moment in its evolution. Computing with entire molecules presents different challenges and requirements than computing just with electric charge. These challenges have led to ad-hoc design and programming methods with high development costs and limited device performance. At the present time, device building entails complete low-level detail immersion. We address these shortcomings by creation of a systems engineering process for building and programming DNA-based computing devices. Contributions of this thesis include numeric abstractions for nucleic acid sequence and secondary structure, and a set of algorithms which employ these abstractions. The abstractions and algorithms have been implemented into three artifacts: DNADL, a design description language; Pyxis, a molecular compiler and design toolset; and KCA, a simulation of DNA kinetics using a cellular automaton discretization. Our methods are applicable to other DNA nanotechnology constructions and may serve in the development of a full DNA computing model.
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