Defense Date

2015

Document Type

Dissertation

Degree Name

Doctor of Philosophy

Department

Computer Science

First Advisor

Preetam Ghosh

Second Advisor

Michael L. Mayo

Third Advisor

Thang Dinh

Fourth Advisor

Wei Cheng

Fifth Advisor

Kevin R. Pilkiewicz

Sixth Advisor

Danail Bonchev

Abstract

Understanding the role of structural patterns within complex networks is essential to establish the governing principles of such networks. Social networks, biological networks, technological networks etc. can be considered as complex networks where information processing and transport plays a central role. Complexity in these net works can be due to abstraction, scale, functionality and structure. Depending on the abstraction each of these can be categorized further. Gene regulatory networks are one such category of biological networks. Gene regulatory networks (GRNs) are assumed to be robust under internal and external perturbations. Network motifs such as feed-forward loop motif and bifan motif are believed to play a central role functionally in retaining GRN behavior under lossy conditions. While the role of static characteristics like average shortest path, density, degree centrality among other topological features is well documented by the research community, the structural role of motifs and their dynamic characteristics are not xiii well understood. Wireless sensor networks in the last decade were intensively studied using network simulators. Can we use in-silico experiments to understand biological network topologies better? Does the structure of these motifs have any role to play in ensuring robust information transport in such networks? How do their static and dynamic roles differ? To understand these questions, we use in-silico network models to capture the dynamic characteristics of complex network topologies. Developing these models involve network mapping, sink selection strategies and identifying metrics to capture robust system behavior. Further, I studied the dynamic aspect of network characteristics using variation in network information flow under perturbations defined by lossy conditions and channel capacity. We use machine learning techniques to identify significant features that contribute to robust network performance. Our work demonstrates that although the structural role of feed-forward loop motif in signal transduction within GRNs is minimal, these motifs stand out under heavy perturbations.

Rights

© The Author

Is Part Of

VCU University Archives

Is Part Of

VCU Theses and Dissertations

Date of Submission

12-2-2015

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