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.

The concept of communication via breath is introduced under the molecular com munication system, where data can be exchanged through inhalation and exhalation. Those data are carried by volatile organic compounds (VOCs) or pathogens and transferred through an aerosol channel. In this thesis, we propose a molecular com munication model for an instantaneous source in a bounded indoor environment. The walls of this environment could be reflectors and/or absorbers by adjusting the value of deposition velocity. We assume a puff source in a given location and study the per formance of a point source since it is the basic element that can be used to derive the concentration of breath, cough, and sneezing, where the concentration of continuous source can be found by integrating a point source over space and time domains. Also, we show some numerical results to visualize the performance of these mathematical models and evaluate them. As a case study, we consider a real-life scenario of detecting a virus from an exhaled breath of a person standing in an indoor bounded room with reflective and absorptive walls. We derive the spatial-temporal concentration of an exhaled virus at the molecules source and the receiver in the room. Finally, we study the probability of misdetection using a suitable bio-sensor.

Recent technological advances have opened many new possibilities for health appli- cations. Next generation of networks allows real-time monitoring, collaboration, and diagnosis. Machine Learning and Deep Learning enable modeling and understanding complex and enormous datasets. Yet all the innovations also pose new challenges to application designers and maintainers. To deliver high standard e-health services while following regulations, Quality of Service requirements need to be fulfilled, high accuracy needs to be archived, let along all the security defenses to protect sensitive data from leaking. In this thesis, we present a collection of works towards a progressive framework for building secure, responsive, and intelligent e-health applications, focusing on three major components, Analyze, Acquire, and Authenticate. The framework is progres- sive, as it can be applied to various architectures, growing with the project and adapting to its needs. For newer decentralized applications that perform data anal- ysis locally on users’ devices, powerful models outperforming existing solutions can be built using Deep Learning, while Federated Learning provides further privacy guarantee against data leakage, as shown in the case of sleep stage prediction task using smart watch data. For traditional centralized applications performing com- plex computations on the cloud or on-premise clusters, to provide Quality of Service guarantees for the data acquisition process in a sensor network, a delay estimation model based on queueing theory is proposed and verified using simulation. We also explore the novel idea of using molecular communication for authentication, named Molecular Key, enabling the incorporation of environmental information into security policy. We envision this framework can provide stepping stones for future e-health applications.

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.

A number of nanomachines that cooperatively communicate and share information in order to achieve specific tasks is envisioned as a nanonetwork. Due to size and capabilities of nanomachines, the traditional communication paradigms cannot be used for nanonetworks in which network nodes may be composed of just several atoms or molecules and scale on the orders of few nanometers. Instead, the molecular communication is a promising solution approach for nanoscale communication paradigm. However, molecular communication must be thoroughly investigated to realize the nanoscale communication and nanonetworks for many envisioned applications such as nanoscale body area networks, nanoscale molecular computers. In this thesis, a simulation framework (NanoSim) for nanoscale molecular communication networks is presented. The objective of the framework is to provide a simulation experimental tool in order to create a better understanding of nanonetworks and facilitate the development of new communication techniques and validation of theoretical results. The NanoSim framework is built on top of core components of widely used network simulator (ns-2). It incorporates the simulation modules for various nanoscale communication paradigms based on diffusive molecular, motor-based and gap junction-based molecular communication channels. The details of NanoSim are discussed and some functional scenarios are defined to validate NanoSim. In addition to this, the numerical analyses of these functional scenarios and the experimental results for them are presented. The validation of NanoSim is done by comparing these experimental and numerical results.

In this thesis, we suggest using nano-relays in a network using molecular com- munication in free space to improve the performance of the system in terms of delay. An approximation method for jump diffusion processes, which is based on Markov chains, is used to model molecular propagation in such scenarios. The model is validated through comparing analytic results with simulation results. The results illustrate the advantage of using nano-relays over diffusion in terms of delay. The proposed model is then used to inves- tigate the effect of different parameters, such as filaments’ length and the number of filaments attached to each nano-relay, on the delay performance of the communication technique. We used transient solution of the model in the first set of results. How- ever, stationary solution of the model can generate useful results, too. In the second set of results, the model is extended for an unbounded scenario. Con- sidering the propagation as a one-sided skip free process and using matrix analytic methods, we find the final distribution for the position of informa- tion molecules. It will be shown that it is possible to keep molecules in a desired region. The effect of different parameters on the final distribution for the position of information molecules is investigated, too. This analysis can be useful in drug delivery applications. / February 2016

As traditional communication technology we use in our day-to-day life reaches its limitations, the international community searches for new methods to communicate information. One such novel approach is the so-called molecular communication system. During the last few decades, molecular communication systems become more and more popular. The main difference between traditional communication and molecular communication systems is that in the latter, information transfer occurs through chemical means, most often between microorganisms. This process already happens all around us naturally, for example, in the human body. Even though the molecular communication topic is attractive to researchers, and a lot of theoretical results are available - one cannot claim the same about the practical use of molecular communication. As for experimental results, a few studies have been done on the macroscale, but investigations at the micro- and nanoscale ranges are still lacking because they are a challenging task. In this work, a self-contained introduction of the underlying theory of molecular communication is provided, which includes knowledge from different areas such as biology, chemistry, communication theory, and applied mathematics. Two numerical methods are implemented for three well-studied partial differential equations of the MC field where advection, diffusion, and the reaction are taken into account. Numerical results for test cases in one and three dimensions are presented and discussed in detail. Conclusions and essential analytical and numerical future directions are then drawn.

Yes / This article examines recent research in molecular communications from a telecommunications system design perspective. In particular, it focuses on channel models and stateof- the-art physical layer techniques. The goal is to provide a foundation for higher layer research and motivation for research and development of functional prototypes. In the first part of the article, we focus on the channel and noise model, comparing molecular and radio-wave pathloss formulae. In the second part, the article examines, equipped with the appropriate channel knowledge, the design of appropriate modulation and error correction coding schemes. The third reviews transmitter and receiver side signal processing methods that suppress intersymbol- interference. Taken together, the three parts present a series of physical layer techniques that are necessary to producing reliable and practical molecular communications. / The work of C.-B. Chae was in part supported by the Basic Science Research Program (2014R1A1A1002186) funded by the Ministry of Science, ICT and Future Planning (MSIP), Korea, through the National Research Foundation of Korea.

The implications of non-Gaussian interference for various communication systemsare explored. The focus is on the Kappa distribution, Generalized Gaussian distribu-tions, and the distribution of the interference in molecular communication systems.A review of how dynamic systems that are not in equilibrium are modeled by theKappa distribution and how this distribution models interference in HF communica-tions systems at sunrise is provided. The channel model, bit error rate for single andmultiple antennas, channel capacity, and polar code performance are shown.<div><br><div>Next, a review of the Generalized Gaussian distribution that has been found tomodel the interference resulting from surface activities is provided. This modeling isextended to find the secrecy capacity so that information cannot be obtained by theeavesdropper.</div><div><br></div><div>Finally, future nanomachnines are examined. The vulnerability to a receptorantagonist of a ligand-based molecule receiver is explored. These effects are consideredto be interference as in other wireless systems and the damage to signal reception isquantified.</div></div>

In this work we consider nano-scale communication using bacterial popula- tions as transceivers. We demonstrate using a microfluidic test-bed and a population of genetically engineered Escherichia coli bacteria serving as the communication re- ceiver that a simple modulation like on-off keying (OOK) is indeed achievable, but suffers from very poor data-rates. We explore an alternative communication strategy called time elapse communication (TEC) that uses the time period between signals to encode information. We identify the severe limitations of TEC under practical non-zero error conditions in the target environment, and propose an advanced communication strategy called smart time elapse communication (TEC-SMART) that achieves over a 10x improvement in data-rate over OOK.