Fundamentals of bacteria-based molecular communication for Internet of Bio-Nanothings

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Unluturk, Bige Deniz Deniz
Akyildiz, Ian F.
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Today, thanks to synthetic biology, we can engineer living cells as biosensor devices and thanks to MEMS & nanotechnology, we can manufacture electronic devices at nanoscale. Molecular communication (MC), a novel communication technique where information transfer is based on exchange of molecules, emerges as a solution to establish communication among these natural and man-made biological and electronic devices at nanoscale. When complemented with existing wireless communications technologies, MC will enable a network of these devices, called Internet of Bio-NanoThings (IoBNT). The focus of this PhD thesis is on the bacteria-based MC for IoBNT, where bacteria populations are considered both as devices generating MC signals and information carriers actively delivering molecules via chemotaxis. The objectives of the research presented in this thesis are to model and analyze bacteria-based MC from the point of communication engineering to provide solutions for the creation of artificial MC systems for IoBNT applications. First, a genetically engineered bacteria-based biotransceiver that can send and receive MC signals is designed. The principles of biological circuits for MC are illustrated. Second, the bacterial chemotaxis channels where bacteria actively carry information in its plasmid and move towards the nutrient gradient are modelled using Keller-Segel models. The impact of social behavior of cooperation, competition, and cheating among the microbial society is incorporated in the models. Third, three modulation schemes are proposed for the bacterial chemotaxis channels and their performance is compared in terms of probability of error. Fourth, to leverage natural bacteria-based MC in the body, Microbiome- Gut-Brain Axis is investigated as an infrastructure for IoBNT. Fifth, an IoBNT application for early detection of infections using bacteria-based MC concept is developed. This research provides fundamental results that establish the use of bacteria for various MC functions, push the envelope towards the realization of MC networks by proposing design solutions, and developing specific applications of IoBNT for healthcare.
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