This thesis focuses on decentralized deadbeat output regulation of discrete-time nonlinear plants that are composed of multiple agents. These agents interact, via scalar-valued signals, in a known structured way represented with a graph. This work is motivated by applications where it is infeasible and/or undesirable to introduce control action within each plant agent; instead, control agents are introduced to interact with certain plant agents, where each control agent focuses on regulating a specific plant agent, called its target. Then, two analyses are carried out to determine if regulation is achieved: targeting analysis is used to determine if control laws can be found to regulate all target agents, then growing analysis is used to determine the effect of those control laws on non-target plant agents. The strength of this novel approach is the intuitively-appealing notion of each control agent focusing on the regulation of just one plant agent. This work goes beyond previous research by generalizing the class of allowable plant dynamics, considering not only arbitrary propagation times through plant agents, but also allowing for non-symmetrical influence between the agents. Moreover, new necessary and sufficient algebraic conditions are derived to determine when targeting succeeds. The main contribution of this work, however, is the development of new easily-verifiable conditions necessary for targeting and/or growing to succeed. These new conditions are valuable due to their simplicity and scalability to large systems. They concern the positioning of control agents and targets as well as the propagation time of signals through the plant, and they help significantly with design decisions. Various graph structures (such as queues, grids, spiders, rings, etc.) are considered and for each, these conditions are used to develop a control scheme with the minimum number of control agents needed.

This thesis focuses on decentralized deadbeat output regulation of discrete-time nonlinear plants that are composed of multiple agents. These agents interact, via scalar-valued signals, in a known structured way represented with a graph. This work is motivated by applications where it is infeasible and/or undesirable to introduce control action within each plant agent; instead, control agents are introduced to interact with certain plant agents, where each control agent focuses on regulating a specific plant agent, called its target. Then, two analyses are carried out to determine if regulation is achieved: targeting analysis is used to determine if control laws can be found to regulate all target agents, then growing analysis is used to determine the effect of those control laws on non-target plant agents. The strength of this novel approach is the intuitively-appealing notion of each control agent focusing on the regulation of just one plant agent. This work goes beyond previous research by generalizing the class of allowable plant dynamics, considering not only arbitrary propagation times through plant agents, but also allowing for non-symmetrical influence between the agents. Moreover, new necessary and sufficient algebraic conditions are derived to determine when targeting succeeds. The main contribution of this work, however, is the development of new easily-verifiable conditions necessary for targeting and/or growing to succeed. These new conditions are valuable due to their simplicity and scalability to large systems. They concern the positioning of control agents and targets as well as the propagation time of signals through the plant, and they help significantly with design decisions. Various graph structures (such as queues, grids, spiders, rings, etc.) are considered and for each, these conditions are used to develop a control scheme with the minimum number of control agents needed.

One of the most prevalent inherited diseases is cystic fibrosis. This disease is caused by a mutation in a membrane protein, the cystic fibrosis transmembrane conductance regulator (CFTR). CFTR is known to function as a chloride channel that regulates the viscosity of mucus that lines the ducts of a number of organs. Generally, most of the prevalent mutations of CFTR are located in one of two nucleotide binding domains, namely, the nucleotide binding domain 1 (NBD1). However, some mutations in nucleotide binding domain 2 (NBD2) can equally cause cystic fibrosis. In this work, a hierarchical graph is built for NBD2. Using this model for NBD2, we examine the consequence of single point mutations on NBD2. We collate the wildtype structure with eight of the most prevalent mutations and observe how the NBD2 is affected by each of these mutations.

The field of chemical graph theory utilizes simple graphs as models of molecules. These models are called molecular graphs, and quantifiers of molecular graphs are known as molecular descriptors or topological indices. Today's chemists use molecular descriptors to develop algorithms for computer aided drug designs, and computer based searching algorithms of chemical databases and the field is now more commonly known as combinatorial or computational chemistry. With the completion of the human genome project, related fields are emerging such as chemical genomics and pharmacogenomics. Recent advances in molecular biology are driving new methodologies and reshaping existing techniques, which in turn produce novel approaches to nucleic acid modeling and protein structure prediction. The origins of chemical graph theory are revisited and new directions in combinatorial chemistry with a special emphasis on biochemistry are explored. Of particular importance is the extension of the set of molecular descriptors to include graphical invariants. We also describe the use of artificial neural networks (ANNs) in predicting biological functional relationships based on molecular descriptor values. Specifically, a brief discussion of the fundamentals of ANNs together with an example of a graph theoretic model of RNA to illustrate the potential for ANN coupled with graphical invariants to predict function and structure of biomolecules is included.