Biyo-nano nesnelerin interneti için nano-ölçekli ve biyolojik-esinli haberleşme teknikleri

Internet of Bio-Nano Things (IoBNT) is a novel ICT framework, in which nanomachines and biological entities, such as nanobiosensors, living cells, engineered bacteria, are connected with each other and with conventional macroscale networks to cooperatively perform sensing, actuation and processing. The framework has an enormous potential to transform the way we connect with and understand the world "at the bottom" by enabling new methods of interfering with the processes inside living organisms at the single-molecular level, and extending the human consciousness and control with bio-nano things collaboratively sensing and acting upon the environments never explored by any other paradigm before. Realization of IoBNT, however, demands novel engineering solutions to overcome unique challenges regarding miniaturization and connectivity subject to peculiarities of nanoscale-physics and limited capabilities of bio-nano things. These challenges call for novel approaches to devise solutions for a set of modeling, analysis and implementation problems on a highly interdisciplinary domain covering engineering, nanotechnology and biophysics. This thesis is focused on the challenges regarding the physical layer of IoBNT. To this end, communication techniques that can enable high-speed and reliable wireless communication in nanonetworks and at the same time provide a seamless interface between the nanonetworks and the macroscale cyber networks are investigated. The first part of the thesis is concentrated on the use of fluorescent molecules, i.e., fluorophores, to enable wireless communication at nanoscale through a quantum mechanical phenomenon, which is F\"orster Resonance Energy Transfer (FRET). Communication and information theoretical models for FRET-based, graphene plasmon-assisted FRET-based and multi-step FRET-based propagation channels are developed. Accounting for the natural optical interface between the nanoscale and macroscale worlds provided by the intrinsic characteristics of fluorophores, the novel concept of Internet of Molecular Things is introduced to further extend the coverage of IoBNT with networks of sub-100nm primitive molecular devices, such as fluorophore-based molecular logic gates, sensors and actuators. Moreover, the first practical realization of a wireless nanoscale communication network is achieved with a network of single molecular fluorescent transceivers. The second part is focused on molecular communications, which has been extensively studied from various aspects including channel and noise models. Different from the existing literature, the feasibility of designing a molecular receiver, in a physical domain other than synthetic biology, meeting the basic requirements of nanonetwork applications and also serving the needs of an electromagnetic nano-macro interface between the chemical domain of nanonetworks and the electrical domain of the cyber networks is thoroughly examined. Based on the advancements in the biosensing literature, Field Effect Transistor-based Biosensors (BioFETs) is proposed as the most viable solution to design a molecular receiver, which can transduce molecular messages into electrical signals. A communication theoretical model for Silicon Nanowire (SiNW) bioFET-based MC receiver is developed and the noise statistics at the receiver output is derived. The performance of this receiver is evaluated with common ICT metrics such as Signal to Noise Ratio (SNR), Symbol Error Probability (SEP) and information theoretical capacity.