Molecular communication (MC) is a promising bio-inspired paradigm for the exchange of information among nanotechnology-enabled devices. These devices, called nanomachines, are expected to have the ability to sense, compute and actuate, and interconnect into networks, called nanonetworks, to overcome their individual limitations and benefit from collaborative efforts. MC realizes the exchange of information through the transmission, propagation, and reception of molecules, and it is proposed as a feasible solution for nanonetworks. This idea is motivated by the observation of nature, where MC is successfully adopted by cells for intracellular and intercellular communication. MC-based nanonetworks have the potential to be the enabling technology for a wide range of applications, mostly in the biomedical, but also in the industrial and surveillance fields. The focus of this Ph.D. thesis is on the most fundamental type of MC, i.e., diffusion-based MC, where the propagation of information-bearing molecules between a transmitter and a receiver is realized through free diffusion in a fluid. The objectives of the research presented in this thesis are to analyze the MC paradigm from the point of view of communication engineering and information theory, and to provide solutions to the modeling and design of MC-based nanonetworks. First, a physical end-to-end model is realized to study each component in a basic diffusion-based MC system design, as well as the overall system, in terms of gain and delay. Second, the noise sources affecting a diffusion-based MC are identified and statistically modeled. Third, upper/lower bounds to the capacity are derived to evaluate the information-theoretic performance of diffusion-based MC. Fourth, a stochastic analysis of the interference when multiple transmitters access the diffusion-based MC channel is provided. Fifth, as a proof of concept, a design of a diffusion-based MC system built upon genetically-engineered biological circuits is analyzed. This research provides fundamental results that establish a basis for the modeling, design, and realization of future MC-based nanonetworks, as novel technologies and tools are being developed.

Nanotechnology is providing a new set of tools to the engineering community to design nanoscale components with unprecedented functionalities. The integration of several nano-components into a single entity will enable the development of advanced nanomachines. Nanonetworks, i.e., networks of nanomachines, will enable a plethora of applications in the biomedical, environmental, industrial and military fields. To date, it is still not clear how nanomachines will communicate. The miniaturization of a classical antenna to meet the size requirements of nanomachines would impose the use of very high radiation frequencies. The available transmission bandwidth increases with the antenna resonant frequency, but so does the propagation loss. Due to the expectedly very limited power of nanomachines, the feasibility of nanonetworks would be compromised if this approach were followed. Therefore, a new wireless technology is needed to enable this paradigm. The objective of this thesis is to establish the foundations of graphene-enabled electromagnetic communication in nanonetworks. First, novel graphene-based plasmonic nano-antennas are proposed, modeled and analyzed. The obtained results point to the Terahertz Band (0.1-10 THz) as the frequency range of operation of novel nano-antennas. For this, the second contribution in this thesis is the development of a novel channel model for Terahertz Band communication. In addition, the channel capacity of the Terahertz Band is numerically investigated to highlight the potential of this still-unregulated frequency band. Third, a novel modulation based on the transmission of femtosecond-long pulses is proposed and its performance is analyzed.% in terms of achievable information rates. Fourth, the use of low-weight codes to prevent channel errors in nanonetworks is proposed and investigated. Fifth, a novel symbol detection scheme at the receiver is developed to support the proposed modulation scheme. Sixth, a new energy model for self-powered nanomachines with piezoelectric nano-generators is developed. Moreover, a new Medium Access Control protocol tailored to the Terahertz Band is developed. Finally, a one-to-one nano-link is emulated to validate the proposed solutions.

Molecular communication (MC) is a new bio-inspired communication paradigm towards realizing the communication and networking at the nanoscale to microscale dimensions among a vast number of engineered natural and/or artificial nanomachines communicating with each other to form a nanonetwork. In this thesis, we investigate a concentration-encoded molecular communication (CEMC) system where the transmitting nanomachine (TN) and the receiving nanomachine (RN) communicate with a single type of information molecules by modulating the transmission rate of information molecules at the TN. The information molecules undergo ideal (i.e. free) diffusion in three dimensions and become available to the RN that observes the concentration of the received molecules at its receptors and thus decodes the message. Our research shows that it is possible to realize complex modulation methods, combat the intersymbol interference (ISI), determine the effective communication ranges based on available signal concentration, develop signal detection schemes, and apply simple channel codes in a CEMC system. It has been found that the performance of the CEMC system is influenced by communication ranges, transmission data rates, ISI, and detection schemes. It is possible to sense the concentration signal intensity and develop optimum receiver structures that can detect the transmitted symbols at the RN. It is also possible to develop optimum signal detection schemes based on the interactions between the information molecules and the receptors using stochastic chemical kinetics (SCK) of the reaction events. Applying simple channel codes at the TN shows that it is possible to increase effective communication range in the CEMC system, however, this increases the complexity of the RN in implementing the detection circuitry. Finally, potential applications of CEMC would be in materializing CEMC-based molecular nanonetworks for emerging areas, e.g. in cancer detection and treatment, targeted drug delivery, and environmental protection and pollution control.

Nous avons proposé nanocode bloc simple pour assurer la fiabilité des communications nano. Nous proposons également la compression d'image simple, efficace de l'énergie pour les communications nano. Nous étudions les performances des méthodes proposées en termes d'efficacité énergétique, le taux d'erreur binaire et de robustesse contre les erreurs de transmission. Dans la compression d'image pour les communications nano, nous comparons notre méthode proposée SEIC avec compression standart images des méthodes telles que JPEG, JPEG 2000, GIF et PNG. Les résultats montrent que notre méthode proposée surpasse les méthodes de compression d'image standard dans la plupart des indicateurs. Dans la compression d'erreur pour les communications nano, nous proposons nanocode de simple bloc (SBN) et comparer la performance avec le code de correction d'erreur existant pour nanocommunication, tels que Canal Minimum Energy (MEC) et le faible poids de la Manche (LWC) codes. Le résultat montre que notre méthode proposée surpasse MEC et LWC en termes de fiabilité et de la complexité du matériel. / We proposed nanocode single block to ensure the reliability of nano communications. We also offer the simple image compression, power efficient for nano communications. We study the performance of the proposed methods in terms of energy efficiency, bit error rate and robustness against transmission errors. In image compression for nanocommunications, we compare our proposed method SEIC with standart compression image methods such as JPEG, JPEG 2000, GIF and PNG. The results show that our proposed method outperforms standard image compression methods in most metrics. In error compression for nanocommunications, we propose simple block nanocode (SBN) and compare the performance with existing error correction code for nanocommunication, such as Minimum Energy Channel (MEC) and Low weight Channel (LWC) codes. The result show that our proposed method outperforms MEC and LWC in terms of reliability and hardware complexity.

In pursuit of enhancing the capabilities of healthcare diagnostics and monitoring, the electromagnetic spectrum has been utilized efficiently from the MHz up to THz and beyond. The era of smart phones, wearable devices and on-body networks have unfolded plethora of health applications with efficient channel communication mechanisms, faster data transfer rates and multi-user functionalities. With the advancement in material fabrication and spectroscopic techniques, a new realm of healthcare nanodevices have emerged with immense potential to garner in-depth information of the human body, real-time of tissue morphology, molecular features, hydration level and atmospheric water vapour on channel parameters. In addition to this, engineered skin substitute models: 2D collagen and 3D organotypics, are investigated to address the importance of individual biological features comprising of water dynamics and cell culture, affecting the channel parameters. The experimental results of various tissue samples, skin substitutes and numerical evalua-tion of channel parameters can be used to further improve the communication capabilities of in-body nanonetworks. The original contributions on characterization of skin substitutes can be applied to study various health conditions, effects of drugs and skin ageing on a molecular level. The results presented in this thesis, foresee an increasing demand in skin substitute models due to their biological flexibility and control according to desired medical applications. monitoring and tackle medical emergencies. A collection of these devices with sensing capabilities together form a nanonetwork performing computing tasks such as storage, actuation, data transfer and communication. The thesis brings forth the analysis and optimization of channel parameters; such as pathloss and molecular noise temperature, when the proposed in-body nanodevices communicate amongst each other in the terahertz (THz) range. The novel contribution of the work is mapping the optical properties of human skin by bringing together the measurement of various skin tissues and its influence on channel parameters. In the later part of the thesis, emphasis is given on the individual biological entities of the tissue contributing to channel parameters, such as collagen as an abundant protein, variation in fibrous extra-cellular matrix due to fibroblast cells and amalgamation of different layers; namely, epidermis and dermis of the skin. Recently proposed graphene-based antennas resolve the cumbersomeness of existing medical devices by drastically reducing its size to a few hundreds of nanometres. These biocompatible nanodevices focus on exchanging the intricate details of the human body via nanoscale electromagnetic communication in the terahertz domain of the spectrum. The thesis aims to investigate the material properties of skin tissues with terahertz time do-main spectroscopy and numerically evaluate the channel parameters for in-body nanoscale networks that potentially would form an essential part of a hierarchical body-centric communication network extending from inside the human body to a wider community network. The results are presented in regards to the complexity of human tissue as a channel medium. The measured refractive index and absorption coefficient data is applied to numerically calculate channel pathloss and molecular noise temperature. The results provide a real-time analysis of tissue morphology, molecular features, hydration level and atmospheric water vapour on channel parameters. In addition to this, engineered skin substitute models: 2D collagen and 3D organotypics, are investigated to address the importance of individual biological features comprising of water dynamics and cell culture, affecting the channel parameters. The experimental results of various tissue samples, skin substitutes and numerical evaluation of channel parameters can be used to further improve the communication capabilities of in-body nanonetworks. The original contributions on characterization of skin substitutes can be applied to study various health conditions, effects of drugs and skin ageing on a molecular level. The results presented in this thesis, foresee an increasing demand in skin substitute models due to their biological flexibility and control according to desired medical applications.

Machine-to-Machine (M2M) communications is an emerging communication paradigm that provides ubiquitous connectivity between devices along with an ability to communicate autonomously without human intervention. M2M communications acts as an enabling technology for the practical realization of Internet-of-Things (IoT). However, M2M communications differs from conventional Human-to-Human (H2H) communications due to its unique features such as massive number of connected devices, small data transmissions, little or no mobility, requirements of high energy efficiency and reliability, etc. These features create various challenges for existing communication networks which are primarily optimized for H2H communications. Therefore, novel solutions are required to meet the key requirements of M2M communications. In addition, enhancements are required at different layers of the protocol stack to support co-existence of M2M devices and H2H users. The main objective of this research is to investigate the challenges of M2M communications in two broad types of M2M networks; capillary M2M and cellular M2M networks. The primary focus is on developing novel solutions, algorithms, and protocol enhancements for successfully enabling M2M communications. Since cognitive radio technology is very promising for M2M communications, special emphasis is on capillary M2M networks with cognitive radio based Physical layer. Besides, the focus is also on exploring new frontiers in M2M communications. This thesis covers different aspects of M2M communications. Considering the motivation for cognitive M2M and service requirements of M2M devices, two cognitive MAC protocols have been proposed. The first protocol is centralized in nature and utilizes a specialized frame structure for co-existence with the primary network as well as handling different Quality-of-Service (QoS) requirements of M2M devices. The second protocol is a distributed cognitive MAC protocol, which is specially designed to provide high energy efficiency and reliability for M2M devices operating in challenging wireless environments. Both protocols explicitly account for the peculiarities of cognitive radio environments. The protocols have been evaluated using analytical modeling and simulation studies. Recently IETF has standardized a specially designed routing protocol for capillary M2M networks, known as RPL (Routing for Low Power and Lossy Networks). RPL is emerging as the de facto routing protocol for many M2M applications including the smart grid. On the other hand, the application of cognitive radio for smart grid communication is under active investigation in the research community. Hence, it is important to investigate the applicability and adaptation of RPL in cognitive radio environments. In this regard, an enhanced RPL based routing protocol has been proposed for cognitive radio enabled smart grid networks. The enhanced protocol provides novel modifications to RPL for protecting the primary users along with meeting the utility requirements of the secondary network. An important challenge in LTE-based cellular networks with M2M communications is the uplink radio resource management as available resources are shared between M2M devices and H2H users, having different and often conflicting QoS requirements. Apart from this, energy efficiency requirements become critically important. Further, the specific constraints of Single Carrier Frequency Division Multiple Access (SC-FDMA) complicate the resource allocation problem. In this respect, an energy efficient resource allocation algorithm for the uplink of LTE networks with M2M/H2H co-existence under statistical QoS guarantees has been developed, that is based on canonical duality theory. The proposed algorithm outperforms classical algorithms in terms of energy efficiency while satisfying the QoS requirements of M2M devices and H2H users. A new frontier in M2M communications is the nano-M2M communications, which is envisioned to create the Internet-of-Nano-Things (IoNT). Molecular communication (MC) is a promising communication technique for nano-M2M communications. In literature, no model for error performance of MC exists. Therefore, an error performance model has been developed that explicitly accounts for noise and interference effects. Since relaying and network coding based solutions are gaining popularity for nano-M2M networks, the error performance of a network coded molecular nano-M2M network has been evaluated as well. Finally, the thesis is concluded based on the overall picture of the research conducted. In addition, some directions for future work are included as well.

Recent developments in nanotechnology have enabled the fabrication of nanomachines with very limited sensing, computation, communication, and action capabilities. The network of communicating nanomachines is envisaged as nanonetworks that are designed to accomplish complex tasks such as drug delivery and health monitoring. For the realization of future nanonetworks, it is essential to develop novel and efficient communication and networking paradigms. In this thesis, the first step towards designing a mobile ad hoc molecular nanonetwork (MAMNET) with electrochemical communication is taken. MAMNET consists of mobile nanomachines and infostations that share nanoscale information using electrochemical communication whenever they have a physical contact with each other. In MAMNET, the intermittent connectivity introduced by the mobility of nanomachines and infostations is a critical issue to be addressed. In this thesis, an analytical framework that incorporates the effect of mobility into the performance of electrochemical communication among nanomachines is presented. Using the analytical model, numerical analysis for the performance evaluation of MAMNET is obtained. Results reveal that MAMNET achieves adequately high throughput performance to enable frontier nanonetwork applications with sufficiently low communication delay.