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The future pervasive communication and computing devices are envisioned to be tightly integrated with biological systems, i.e., the Internet of Bio-Nano Things. In particular, the study and exploitation of existing processes for the biochemical information exchange and elaboration in biological systems are currently at the forefront of this research direction. Molecular Communication (MC), which studies biochemical information systems with theory and tools from computer communication engineering, has been recently proposed to model and characterize the aforementioned processes. Combined with the rapidly growing ﬁeld of bio-informatics, which creates a rich profusion of biological data and tools to mine the underlying information, this investigation direction is set to produce interesting results and methodologies not only for systems engineering but also for novel scientiﬁc discovery. The multidisciplinary nature of this work presents an interesting challenge in terms of creating a structured approach to combine the aforementioned disciplines for the study of information propagation processes in biological organisms, and their relationship with information for their control, optimization, and exploitation. In this thesis, we study a selection of these processes, through diﬀerent and independent contributions, at the system layer, cellular layer and pathway layer. First, we model the overall functionality of a multicellular metabolic system, the human digestion, in terms of energy production from major nutrients in the food. Second, we analyze metabolic processes in a single cell and their adaptability to incoming nutrient availability information from the environment. Third, we model and characterize the processes that enable information to propagate from the external environment and be processed by the cell. Numerical results are presented to provide a ﬁrst proof-of-concept characterization of all these processes in terms of communication theory. While it may be possible to connect each of these layers in future work, this goes beyond the scope of the work reported in this thesis.
Adviser: Massimiliano Pierobon