Fundamentals of diffusion-based molecular communication in nanonetworks

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.Ph.D

Молекулярні антени на основі силікатів кальцію для біотехніки

Роботу викладено на 93 сторінках, вона містить 5 розділів, 25 ілюстрацій, 26 таблиць і 70 джерел в переліку посилань. Об’єктом дослідження є пластини кремнія n-типу провідності для виготовлення композитної біосумісної структури. Предметом дослідження є силікат кальцію на підкладинці кремнію для створення молекулярних антен. Метою роботи є створення сенсорів біологічних речовин на основі кремнієвого польового транзистора (BioFET). Отримана композитна структура Si/SiO2/(CaO-SiO2), яка демонструє властивість біосумісності, що підтверджено утворенням гідроксиапатиту на поверхні Si після зберігання в розчині, що імітує плазму крові людини. У першому інформаційно-аналітичному розділі роботи визначено необхідність вивчення та удосконалення комунікації і взаємодії на базі обмінюваної інформації елементів Інтернету біо- наноречей. У другому інформаційно- аналітичному розділі роботи наведено сучасний стан розвитку біотехнології та зокрема біопольових транзисторів. У третьому розділі наведена теоретична модель роботи молекулярної антени на основі біопольового транзистора. У четвертому розділі вивчається композитна структура Si/SiO2/(CaOSiO2) на поверхні кремнію, яка була синтезована методом сонохімічного синтезу та подальшим утворенням гідроксиапатиту при вимочуванні зразка в рідині, що симулює плазму людської крові. У п'ятому розділі представлений розроблений стартап-проект на основі досліджень по виконаній роботі.The work was found on 93 pages, it contained 5 sections, 25 images, 26 persons and 70 sources in translation. The object of the study is n-type silicon wafers for the manufacture of composite biocompatible structures. The subject of the study is calcium silicate on a silicon substrate to create molecular antennas. The method of operation creates a sensitive biological potential on a large silicon transistor (BioFET). The obtained Si/SiO2/(CaO-SiO2) composite structure demonstrates the power of biological ability, which confirms the formation of hydroxyapatite at the level of Si after being preserved in the section requiring human creep. In the first information and analytical section of the work, the reliability and improvement of communications were achieved, and we see information from the Internet of bio-things on the basis of exchange data. In another information and analytical section are the current state of development of biotechnology and such biofield transistors. The third section deals with the analytical model of the operation of a molecular antenna on a biological transistor. The fourth section examines the composite structure of Si/SiO2/(CaOSiO2) on the silicon surface, which was synthesized by sonochemical synthesis and the subsequent formation of hydroxyapatite when soaking the sample in a fluid simulating human blood plasma. The fifth section presents a developed startup project based on research on the work done

Channel Modelling of Blood Capillary-based Molecular Communication

Molecular communication (MC) is a new and promising interdisciplinary bio-inspired communication paradigm, which uses molecules as information carriers. Differing from traditional communication, MC is proposed as a feasible solution for nanoscale communication with the help of biological scenarios to overcome the communication limitations. Meanwhile, it is inspired by intracellular and intercellular communication, which involves exchange of information through the transmission, propagation, and reception of molecules. Blood capillaries, extensively distributed in the human body and mutually connected with tissues, are potentially applied to MC, which is the major motivation of this thesis. The focus of this PhD thesis is on the channel modelling of blood capillaries or blood vessels. The objectives of the research are to provide solutions to the modelling of blood capillary-based MC from a communication engineering and information theory perspective. The relationship of the biological scenario in blood capillaries to a communication system is studied. After demonstrating the mapping from biological phenomenon to emission, propagation and reception processes, system models are established. There are three models of blood capillaries behind different biological scenarios. Firstly, the thesis establishes a basic model of vesicle release, vesicle diffusion through blood capillary and ligand reception processes within the endocrine phenomenon. Moreover, differing from previous research in macroscopic Fick's diffusion, this work involves microscopic Langevin diffusion to describe the propagation process with a frequency domain method being proposed to calculate the information-theoretical performance channel capacity. Secondly, a much more realistic blood capillary model with blood flow drift which matches a laminar flow regime is presented, where a generalised Langevin equation is used to model the drift force exerted by blood flow. Finally, the thesis establishes a single input and multiple output MC model with hierarchical levels of Y-shaped bifurcation of blood capillaries, then BER, SNR, and channel capacity performance are analysed

Error control in bacterial quorum communications

Quorum sensing (QS) is used to describe the communication between bacterial cells, whereby a coordinated population response is controlled through the synthesis, accumulation and subsequent sensing of specific diffusible chemical signals called autoinducers, enabling a cluster of bacteria to regulate gene expression and behavior collectively and synchronously, and assess their own population. As a promising method of molecular communication (MC), bacterial populations can be programmed as bio-transceivers to establish information transmission using molecules. In this work, to investigate the key features for MC, a bacterial QS system is introduced, which contains two clusters of bacteria, specifically Vibrio fischeri, as the transmitter node and receiver node, and the diffusive channel. The transmitted information is represented by the concentration of autoinducers with on-off keying (OOK) modulation. In addition, to achieve better reliability and energy efficiency, different error control techniques, including forward error correction (FEC) and Automatic Repeat reQuest (ARQ) are taken into consideration. For FEC, this work presents a comparison of the performance of traditional Hamming codes, Minimum Energy Codes (MEC) and Luby Transform (LT) codes over the channel. In addition, it applied several ARQ protocols, namely Stop-N-Wait (SW-ARQ), Go-Back-N (GBN-ARQ), and Selective-Repeat (SR-ARQ) combined with error detection codes to achieve better reliability. Results show that both the FEC and ARQ techniques can enhance the channel reliability, and that ARQ can resolve the issue of out-of-sequence and duplicate packet delivery. Moreover, this work further addresses the question of optimal frame size for data communication in this channel capacity and energy constrained bacterial quorum communication system. A novel energy model which is constructed using the experimental validated synthetic logic gates has been proposed to help with the optimization process. The optimal fixed frame length is determined for a set of channel parameters by maximizing the throughput and energy efficiency matrix