New Insights from Network Theory and Analysis: From the Mechanics of Granular Materials to the Robustness of Cellular MetabolismPublic Deposited
Granular matter and living cells represent two extremes of what have come to be regarded as complex systems - systems characterized by a richness in global behavior that is not easily deduced from the interactions of their individual parts, even when those interactions are simple and well understood. On the one hand, granular matter is perhaps the simplest prototype of a complex system, whereas living cells are among the most complex of the complex systems studied in science. Recently, network theory has emerged as a valuable framework for analyzing, classifying, and understanding complex systems. In this dissertation, we use networks - applying established analysis techniques as well as developing new techniques - to investigate specific problems pertaining to granular matter and cellular metabolisms. From network analysis we gain new insights into (1) the distributions of particle pressures in bi-disperse granular packings; (2) the structural evolution of a gradually tilted granular bed; (3) the transport properties of granular media; and (4) the relationship between structure and robustness of cellular metabolisms. The studies on granular systems are supported by particle dynamics simulations; the study on metabolic robustness is supported by genome-scale <em>in silico<\em> reconstructions of <em>Escherichia coli<\em>, <em>Saccharomyces cerevisiae<\em>, <em>Methanosarcina barkeri<\em>, and <em>Staphylococcus aureus<\em>.