Structure and topology of transcriptional regulatory networks and their applications in bio-inspired networking

Biological networks carry out vital functions necessary for sustenance despite environmental adversities. Transcriptional Regulatory Network (TRN) is one such biological network that is formed due to the interaction between proteins, called Transcription Factors (TFs), and segments of DNA, called genes. TRNs are known to exhibit functional robustness in the face of perturbation or mutation: a property that is proven to be a result of its underlying network topology. In this thesis, we first propose a three-tier topological characterization of TRN to analyze the interplay between the significant graph-theoretic properties of TRNs such as scale-free out-degree distribution, low graph density, small world property and the abundance of subgraphs called motifs. Specifically, we pinpoint the role of a certain three-node motif, called Feed Forward Loop (FFL) motif in topological robustness as well as information spread in TRNs. With the understanding of the TRN topology, we explore its potential use in design of fault-tolerant communication topologies. To this end, we first propose an edge rewiring mechanism that remedies the vulnerability of TRNs to the failure of well-connected nodes, called hubs, while preserving its other significant graph-theoretic properties. We apply the rewired TRN topologies in the design of wireless sensor networks that are less vulnerable to targeted node failure. Similarly, we apply the TRN topology to address the issues of robustness and energy-efficiency in the following networking paradigms: robust yet energy-efficient delay tolerant network for post disaster scenarios, energy-efficient data-collection framework for smart city applications and a data transfer framework deployed over a fog computing platform for collaborative sensing --Abstract, page iii