Modeling convection-diffusion-reaction systems for microfluidic molecular communications with surface-based receivers in Internet of Bio-Nano Things.

We consider a microfluidic molecular communication (MC) system, where the concentration-encoded molecular messages are transported via fluid flow-induced convection and diffusion, and detected by a surface-based MC receiver with ligand receptors placed at the bottom of the microfluidic channel. The overall system is a convection-diffusion-reaction system that can only be solved by numerical methods, e.g., finite element analysis (FEA). However, analytical models are key for the information and communication technology (ICT), as they enable an optimisation framework to develop advanced communication techniques, such as optimum detection methods and reliable transmission schemes. In this direction, we develop an analytical model to approximate the expected time course of bound receptor concentration, i.e., the received signal used to decode the transmitted messages. The model obviates the need for computationally expensive numerical methods by capturing the nonlinearities caused by laminar flow resulting in parabolic velocity profile, and finite number of ligand receptors leading to receiver saturation. The model also captures the effects of reactive surface depletion layer resulting from the mass transport limitations and moving reaction boundary originated from the passage of finite-duration molecular concentration pulse over the receiver surface. Based on the proposed model, we derive closed form analytical expressions that approximate the received pulse width, pulse delay and pulse amplitude, which can be used to optimize the system from an ICT perspective. We evaluate the accuracy of the proposed model by comparing model-based analytical results to the numerical results obtained by solving the exact system model with COMSOL Multiphysics

Signal generation and storage in FRET-based nanocommunications

The paper is concerned with Forster Resonance Energy Transfer (FRET) considered as a mechanism for communication between nanodevices. Two solved issues are reported in the paper, namely: signal generation and signal storage in FRET-based nanonetworks. First, luciferase molecules as FRET transmitters which are able to generate FRET signals themselves, taking energy from chemical reactions without any external light exposure, are proposed. Second, channelrhodopsins as FRET receivers, as they can convert FRET signals into voltage, are suggested. Further, medical in-body systems where both molecule types might be successfully applied, are discussed. Luciferase-channelrhodopsin communication is modeled and its performance is numerically validated, reporting on its throughput, bit error rate, propagation delay and energy consumption

Nano-networks communication architecture: Modeling and functions

Nano-network is a communication network at the Nano-scale between Nano-devices. Nano-devices face certain challenges in functionalities, because of limitations in their processing capabilities and power management. Hence, these devices are expected to perform simple tasks, which require different and novel approaches. In order to exploit different functionalities of Nano-machines, we need to manage and control a set of Nano-devices in a full Nano-network using an appropriate architecture. This step will enable unrivaled applications in the biomedical, environmental and industrial fields. By the arrival of Internet of Things (IoT) the use of the Internet has transformed, where various types of objects, sensors and devices can interact making our future networks connect nearly everything from traditional network devices to people. In this paper, we provide an unified architectural model of Nano-network communication with a layered approach combining Software Defined Network (SDN), Network Function Virtualization (NFV) and IoT technologies and present how this combination can help in Nano-networks’ context. Consequently, we propose a set of functions and use cases that can be implemented by Nano-devices and discuss the significant challenges in implementing these functions with Nano-technology paradigm and the open research issues that need to be addressed.Peer ReviewedPostprint (published version

Internet of Bio Nano Things-based FRET nanocommunications for eHealth

The integration of the Internet of Bio Nano Things (IoBNT) with artificial intelligence (AI) and molecular communications technology is now required to achieve eHealth, specifically in the targeted drug delivery system (TDDS). In this work, we investigate an analytical framework for IoBNT with Forster resonance energy transfer (FRET) nanocommunication to enable intelligent bio nano thing (BNT) machine to accurately deliver therapeutic drug to the diseased cells. The FRET nanocommunication is accomplished by using the well-known pair of fluorescent proteins, EYFP and ECFP. Furthermore, the proposed IoBNT monitors drug transmission by using the quenching process in order to reduce side effects in healthy cells. We investigate the IoBNT framework by driving diffusional rate models in the presence of a quenching process. We evaluate the performance of the proposed framework in terms of the energy transfer efficiency, diffusion-controlled rate and drug loss rate. According to the simulation results, the proposed IoBNT with the intelligent bio nano thing for monitoring the quenching process can significantly achieve high energy transfer efficiency and low drug delivery loss rate, i.e., accurately delivering the desired therapeutic drugs to the diseased cell

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

Cyber physical approach and framework for micro devices assembly

The emergence of Cyber Physical Systems (CPS) and Internet-of-Things (IoT) based principles and technologies holds the potential to facilitate global collaboration in various fields of engineering. Micro Devices Assembly (MDA) is an emerging domain involving the assembly of micron sized objects and devices. In this dissertation, the focus of the research is the design of a Cyber Physical approach for the assembly of micro devices. A collaborative framework comprising of cyber and physical components linked using the Internet has been developed to accomplish a targeted set of MDA life cycle activities which include assembly planning, path planning, Virtual Reality (VR) based assembly analysis, command generation and physical assembly. Genetic algorithm and modified insertion algorithm based methods have been proposed to support assembly planning activities. Advanced VR based environments have been designed to support assembly analysis where plans can be proposed, compared and validated. The potential of next generation Global Environment for Network Innovation (GENI) networking technologies has also been explored to support distributed collaborations involving VR-based environments. The feasibility of the cyber physical approach has been demonstrated by implementing the cyber physical components which collaborate to assemble micro designs. The case studies conducted underscore the ability of the developed Cyber Physical approach and framework to support distributed collaborative activities for MDA process contexts

Nano/Bio-Receiver Architectures and Detection Methods for Molecular Communications

Internet of Nano Things (IoNT) is an emerging technology, which aims at extending the connectivity into nanoscale and biological environments with collaborative networks of artificial nanomachines and biological entities integrated into the Internet. To enable the IoNT and its groundbreaking applications, such as real-time intrabody health monitoring, it is imperative to devise nanoscale communication techniques with low-complexity transceiver architectures. Bio-inspired molecular communications (MC), which uses molecules to transfer information, is the most promising technique to realise IoNT due to its inherent biocompatibility and reliability in physiologically-relevant environments. Despite the substantial body of work concerning MC, the implications of an interface between MC channel and practical MC transceiver architectures are largely neglected, leading to a major gap between theory and practice. As the first step to remove this discrepancy, in this thesis, I develop a realistic analytical ICT model for microfluidic MC with surface-based receivers as a convection-diffusion-reaction system. In the second part, I focus on biological MC receivers, which can be implemented in living cells using synthetic biology tools. In this direction, I theoretically develop low-complexity and reliable MC detection methods exploiting the various statistics of the stochastic ligand-receptor interactions at the membrane of biological MC receivers. The estimation and detection theoretical analysis of these detection methods demonstrate that even single type of receptors can provide sufficient statistics to overcome the receptor saturation problem, cope with the interference of non-cognate molecules, and simultaneously sense the concentration of multiple types of ligands. I also propose synthetic receptor designs for the transduction of decision statistics into a representation by concentration of intracellular molecules, and design chemical reaction networks performing decoding with intracellular reactions. Finally, I fabricate a micro/nanoscale MC receiver based on graphene field-effect transistor biosensors and perform its ICT characterisation in a custom-designed microfluidic MC system with the information encoded into the concentration of DNAs. This experimental platform is the first practical demonstration of micro/nanoscale MC, and can serve as a testbed for developing realistic MC methods