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Thesis Overview

1.1 Introduction

T he need to convey messages has always been an important aspect of our society and the ability to send information across vast distances has allowed our cities to grow, our connections to widen and turned our civilisation into a global entity. Nowadays, communication systems provide a constant information access through the use of Electromagnetic (EM) signals. Even though, the benefits brought by EM are too numerous to count, there are still environments where the communication may not be reliable or even feasible. Examples of environments hostile towards EM waves are pipelines, tunnels or salt-water environments. The uneven salinity of the water can make connection unpredictable and the pipelines can absorb the energy of the waves, causing high attenuation. The drawbacks of EM are not limited in macro-scale ( $cm-m$ ), as limitations also exist in small scales, especially in the micro-scale ( $nm-\mu m$ ) where EM is physically limited due to the ratio of the antenna size to the wavelength of the EM signal [1].

An approach that shows promise in overcoming the problems EM faces in both scales is the use of molecular communications. Molecular communications is an approach to transmit information where the transmitter releases to the environment particles (i.e., molecules, gas, pheromones etc.) that are encoded with information and are propagated through the environment until it is detected by a receiver. A diagram that represents a molecular communications process can be seen in Figure 1.1 .

The applications of molecular communication in the macro-scale can be realised in fields such as robotics and infrastructure monitoring (e.g., pipes). It has been proposed that molecular communications can be used as a communication link for monitoring confined environments when the environment cannot act as a waveguide for EM Qiu, S., Guo, W., Wang, S., Farsad, N., and Eckford, A. A molecular communications link for monitoring in confined environments in 2014 IEEE International Conference on Communications Workshops (ICC) IEEE, 2014 . For robotics, molecular communication has been proposed to be used for distress signalling by defective robots Purnamadjaja AH, Russell RA. "Pheromone Communication in a Robot Swarm: Necrophoric Bee Behaviour and its Replication" Robotica vol. 23 pp. 731-742 and for chemical trails for robot guidance Sousa P, Marques L, De Almeida A Toward chemical-trail following robots. In, Seventh International Conference on Machine Learning and Applications (ICMLA08). pp. 489494. doi: 10.1109/ICMLA.2008.133 . There molecular communications can also benefit in environments where search and rescue operations can be harsh to EM waves and in infrastructure monitoring the same can be said of the pipelines in buildings that need to be monitored.

Nature, unlike our society, prefers the use of molecular communication over EM communication. Various examples can be seen in the animal kingdom, where communication is via the use of pheromones between the same species to convey information. The use of molecular communication is not bounded to macro-scale as the use of chemical communication can also be observed in bacteria, especially in quorum sensing B. L. Bassler, How Bacteria Talk to Each Other: Regulation of Gene Expression by Quorum Sensing Current Opinion in Microbiology , vol. 2, no. 6, pp. 582587, 1999, doi:10.1016/S1369-5274(99)00025-9. . Quorum sensing is a bacteria-to-bacteria chemical communication mechanism whereby bacteria share information it gathers (e.g., chemical concentration) and shares this information with surrounding bacteria Tissera, P. S. S., and S. Choe. "Brownian-motion-based molecular communication network using quorum sensing mechanism" in International Conference on Information and Communication Technology Convergence (ICTC) IEEE, 2017, doi:10.1109/ICTC.2017.8190938. . Another benefit of using molecular commmunication over EM is its energy efficiency in the propagation of the chemical, where under some circumstances (i.e., diffusion), the system can be completely independent from external energy sources. The scale in which it can operate and its ability to be energy independent makes molecular communication a possible alternative to EM for harsh environments.

However, there are drawbacks to this novel communication paradigm. The biggest one being the propagation speed and the maximum achievable throughput. The low speed also increases the diffusion time, which decreases the signal amplitude, and generates more errors in the communication system. The system, therefore, may not be suitable for long range communication and EM is the better alternative.

Due to the potential of molecular communication at the micro-scale (i.e., drug delivery, in-vivo communication), research efforts have predominantly been focused on understanding the underlying principles of micro-scale molecular communication, leaving the macro-scale communication, ranging from cm to meters , mostly uninvestigated. Hence, there are still many problems needed to be solved and principles to be understood in the large-scale counterpart of molecular communication. In addition, while the mathematical definitions are well defined for micro-scale, macro-scale has different dominant aspects (i.e., advection, dimensional diffusivity) that change the behaviour of the communication. Micro-scale communication, due to its scale, relies on diffusion to transmit the particles. In describing the diffusion element, it is generally modelled as Brownian motion (i.e., random walk) and is unbiased towards any dimension where the diffusion action takes place. In macro-scale, however, diffusion alone is not sufficient to carry out reliable transmission. Therefore, advection element is required. The presence of the advection element changes the behaviour of the diffusive element as diffusion in which advection takes place (i.e., transverse) is significantly higher than dimensions perpendicular to the advection (i.e., radial) . Therefore, the study presented in this thesis approaches molecular communications with a heavy emphasis on understanding the principles of macro-scale communication. The research plan of the study can be categorised into two major aspects. The first aspect of the study is to establish a mathematical model that is able to accurately correlate with experimental data and to be able to predict the communication with different parameters. The second major aspect is the emphasis of experimental study of macro-scale molecular communication. As mentioned previously, molecular communication is currently a research field dominated by theoretical studies, with only a few experimental test beds designed. Therefore, this study is heavily focused on the experimental analysis of macro-scale molecular communications.

1.2 Contributions

The contributions of the thesis are as follows;

• Review on Molecular Communications: A literature survey on the topic of molecular communication was carried out focusing on the numerous topics of communication properties: modulation, channel capacity, error correction, propagation methodologies etc. Additional research was undertaken regarding the simulation frameworks designed to study the various aspects and scales of molecular communication, as well as the application prospect of this novel communication method.

  A diagram showing the various aspects of molecular communication given in the survey is presented in Figure 1.2 .

• Simulation Framework [2], [3], [4]: To analyse the communication system and generate accurate predictions of macro-scale molecular communication behaviour, a simulation framework was developed based on the Advection-Diffusion Equation (ADE). The developed simulation was used to describe the numerous aspects of molecular communication in 3D macro-scale environments.

• Parameter analysis of Molecular Communications [2]: Macro-scale molecular communication is still in its infancy compared to micro-scale molecular communication. The parameters that govern the macro-scale molecular communication were analysed. These include, the signal flow, carrier flow and the bit duration. To further increase understanding a mathematical model of molecular communication propagation is developed and compared with experimental results.

• Distance Analysis of Molecular Communications [3]: Unlike signal flow, carrier flow and bit duration, distance plays a significantly different role due to the method of propagation. Based on the communication in question, there are two types of communication medium; open space (i.e., no boundary) and closed space (i.e., boundary). Experiments were done to analyse both communication mediums and mathematical models were developed to explain these effects.

• Modulation Analysis [4]: An important aspect of any communication method is its ability to convey information, making modulation an essential part of molecular communication. Based on traditional modulation methods for EM transmission, experiments were analysed on $M_C$ -ary modulation and its Symbol Error Rate (SER) with different levels of modulation ( $M_C$ = 2, $M_C$ = 4, $M_C$ = 8). In addition, experimental analysis was carried out on the leftover chemicals lingering in the medium to better understand the effect of inter-symbol interference (ISI) on the communication and based on experimental studies, mathematical descriptions were derived to explain and predict the residual chemicals in the channel. The channel where the transmission occurs is described and mutual information (MI) of the communication is measured. Theoretical comparisons for SER , MI and symbol distribution are carried out for four key parameters in molecular communication: advection, distance, coefficient of diffusivity and symbol period.

• Multi-Chemical Analysis of Molecular Communications: One of the defining aspects of molecular communication, and its possible advantage over EM -based communications, is its use of chemical species to convey information. This prospect opens up new possibilities of increasing the throughput of the communication. To understand this behaviour and to increase the throughput, experimental studies were carried out. Noise caused by multiple chemical species present in the transmission medium is investigated also. Finally, modulation methods were developed to take advantage of the multi-channel transmission by mathematically defining the four modulation methods.

1.3 Organisation of the Thesis

The organisation of the thesis is as follows;

• Chapter 2 presents an overview of numerous aspects of molecular communication. These includes the differences of approach for two types of molecular communications scale; micro ( $nm$ - $\mu m$ ) and macro scale ( $cm$ - $m$ ). The proposed propagation methods used in the literature are reviewed in addition to other aspects of the communications paradigm. These include; modulation methods, ISI mitigation techniques, error correction, simulation frameworks, proposed applications and possible standardisations.

• Chapter 3 focuses on the experimental approach of macro-scale molecular communication. The approach to the problem is described and a detailed description of the various parts of the experimental setup is given. A section is also dedicated to the theory of the detector used in the experiments: quadrupole mass analyser (QMA).

• Chapter 4 is the main mathematical chapter of the thesis where the model used in Chapters 5, 6 and 7 is described. To model the communication system a modified version of the mass transport equation, Advective-Diffusion Equation (ADE) is used as the basis.

• Chapter 5 analyses different types of parameters and their effect on the signal. These are: signal flow, carrier flow and bit duration. In addition, two types of distances were studied: open distance and closed distance. All the aforementioned parameters are then compared to the model described in Chapter 4.

• Chapter 6 emphasises the communication characteristics of the novel communication paradigm. These include analysis of $M_C$ -ary modulation and ISI , based on empirical data obtained from experiments and linked to mathematical theory. A theoretical analysis of SER , achievable MI and symbol distribution for four key parameters were analysed. These are: transmission distance, advective flow, coefficient of diffusivity and symbol period. An experimental transmission of a message is conducted and compared with the theoretical model presented in Chapter 4.

• Chapter 7 experiments on multiple chemical transmissions . A proof-of-concept transmission was carried out with multiple chemicals along with noise analysis. Transmission of multiple chemicals opens up new possibilities and, to exploit these, new modulation methods were developed and experimented upon.

• Chapter 8 discusses the implications of the studies done in the thesis and proposes future-work related to the topic.

1.4 Publications

The following are the publications which resulted from this dissertation research and follow up work.

1.4.1 Journal Publications

1.

D. T. McGuiness , S. Giannoukos, A. Marshall and S. Taylor “Experimental Results on the Open-Air Transmission of Macro-Molecular Communication Using Membrane Inlet Mass Spectrometry” in IEEE Communications Letters , vol. 22, no. 12, pp. 2567 – 2570, 2018. doi: 10.1109/LCOMM.2018.2875445

2.

D. T. McGuiness , S. Giannoukos, A. Marshall and S. Taylor “Parameter Analysis in Macro-Scale Molecular Communications Using Advection-Diffusion” in IEEE Access , vol. 6, pp. 46706 – 46717, 2018. doi: 10.1109/ACCESS.2018.2866679

3.

S. Giannoukos, D. T. McGuiness , A. Marshall, J. Smith and S. Taylor “A Chemical Alphabet for Macromolecular Communications" in Analytical Chemistry , vol. 90, no. 12. pp. 7739 – 7746, 2018. doi: 10.1021/acs.analchem.8b01716

4.

D. T. McGuiness , S. Giannoukos, A. Marshall and S. Taylor “Modulation Analysis in Macro-Molecular Communications” in IEEE Access , vol. 7, pp. 11049 – 11065, 2019. doi: 10.1109/ACCESS.2019.2892850

5.

D. T. McGuiness , V. Selis and A. Marshall “Molecular-Based Nano-Communication Network: a Ring Topology Nano-bots for In-Vivo Drug Delivery System” in IEEE Access , vol. 7, pp. 12901 – 12913, 2019. doi: 10.1109/ACCESS.2019.2892816

6.

D. T. McGuiness , S. Giannoukos, S. Taylor and A. Marshall “Experimental and Analytical analysis of Macro-Scale Molecular Communications in Closed Boundaries” in IEEE Transactions on Molecular, Biological and Multi-Scale Communications , vol. 5, pp. 44 – 55, 2019. doi: 10.1109/TMBMC.2019.2955094

1.4.2 Conference Proceedings

1.

D. T. McGuiness , A. Marshall, S. Taylor and S. Giannoukos “Asymmetrical Inter-Symbol Interference in Macro-Scale Molecular Communications" in $5^{th}$ International Conference on Nanoscale Computing and Communication , ACM, 2018. doi: 10.1145/3233188.3233194

2.

V. Selis, D. T. McGuiness and A. Marshall “Nano-machine to Nano-machine Molecular Communications for Drug Delivery Systems” in $6^{th}$ International Conference on Nanoscale Computing and Communication , ACM, 2019. doi: 10.1145/3345312.3345471

3.

D. T. McGuiness , S. Giannoukos, S. Taylor and A. Marshall “Experimental Study of the Flush Dynamics of Macro-Scale Molecular Communications” in $6^{th}$ International Conference on Nanoscale Computing and Communication , ACM, 2019. doi: 10.1145/3345312.3345489

1.4.3 Poster Presentations

1.

D. T. McGuiness , S. Giannoukos, F. P. M. Jjunju, J. Smith, A. Marshall and S. Taylor “Investigating Mass Spectromic Communication Approaches for Odor Transmission over Data Networks” in ASMS , 2017.

2.

F. P. M. Jjunju, S. Giannoukos, D. T. McGuiness , A. Marshall, V. Selis, J. Smith, S. Maher and S. Taylor “Scent Transmission over the Internet Using Mass Spectrometry” in ASMS , 2017.