| This thesis is a compilation of published manuscripts and unpublished results detailing the conceptual design, optimization and development of biomolecular logic systems. The majority of results presented herein demonstrate the usage of a biomolecule as an input introduced into a system which induces a chemical change detected as an output. This distinction is significant, as it diverges from earlier demonstrations which utilize chemicals as input signals.;Initially, biochemical systems demonstrating Boolean logic operations, AND, OR, XOR and InhibA, were developed using soluble compounds representing the chemical "devices" and enzymes operating as the input signals that activate the logic gates. Next, a biochemical system using immune-specific and biocatalytic reactions was designed, and the generated output signals were analyzed by AFM and optical means. Logic gate optimization was demonstrated both experimentally and theoretically; the analog noise generation by a single enzymatic AND gate can be dramatically reduced to yield gate operation with virtually no input noise amplification.;Following the initial demonstration and optimization of biomolecular logic systems, the construction of a "toolbox" including examples of biochemical information processing with specific functionalities is presented. The first example is a novel approach toward the assembly of a biomolecular keypad lock using a biocatalytic cascade triggered by the chronological introduction of three immobilized biocatalysts. Next, an enzyme-based set-reset flip-flop memory system was designed with the core part composed of horseradish peroxidase and diaphorase biocatalyzing oxidation and reduction of redox species. One of the unique "tools" in the "toolbox" is the chemically induced actuation of a polypyrrole (Ppy) artificial muscle controlled by biocatalytic reactions resulting in the changes of the redox state of the polymer film mediated by soluble redox species. The biocatalytic reactions governing the chemical actuator can be extended to multi-step cascades processing various patterns of biochemical signals mimicking logic networks.;Lastly, a stable bioelectronic interface allowed for a programmable response in amperometric output signal caused by controllable changes in the input feed. The methodology facilitates the practical demonstration of a directly-readable barcode generated from the electrocatalytic response of a biocatalyst. |
