Transmitter and Receiver Architectures for Molecular Communications: A Survey on Physical Design with Modulation, Coding, and Detection Techniques

Inspired by nature, molecular communications (MC), i.e., the use of molecules to encode, transmit, and receive information, stands as the most promising communication paradigm to realize the nanonetworks. Even though there has been extensive theoretical research toward nanoscale MC, there are no examples of implemented nanoscale MC networks. The main reason for this lies in the peculiarities of nanoscale physics, challenges in nanoscale fabrication, and highly stochastic nature of the biochemical domain of envisioned nanonetwork applications. This mandates developing novel device architectures and communication methods compatible with MC constraints. To that end, various transmitter and receiver designs for MC have been proposed in the literature together with numerable modulation, coding, and detection techniques. However, these works fall into domains of a very wide spectrum of disciplines, including, but not limited to, information and communication theory, quantum physics, materials science, nanofabrication, physiology, and synthetic biology. Therefore, we believe it is imperative for the progress of the field that an organized exposition of cumulative knowledge on the subject matter can be compiled. Thus, to fill this gap, in this comprehensive survey, we review the existing literature on transmitter and receiver architectures toward realizing MC among nanomaterial-based nanomachines and/or biological entities and provide a complete overview of modulation, coding, and detection techniques employed for MC. Moreover, we identify the most significant shortcomings and challenges in all these research areas and propose potential solutions to overcome some of them.This work was supported in part by the European Research Council (ERC) Projects MINERVA under Grant ERC-2013-CoG #616922 and MINERGRACE under Grant ERC-2017-PoC #780645

On the development of slime mould morphological, intracellular and heterotic computing devices

The use of live biological substrates in the fabrication of unconventional computing (UC) devices is steadily transcending the barriers between science fiction and reality, but efforts in this direction are impeded by ethical considerations, the field’s restrictively broad multidisciplinarity and our incomplete knowledge of fundamental biological processes. As such, very few functional prototypes of biological UC devices have been produced to date. This thesis aims to demonstrate the computational polymorphism and polyfunctionality of a chosen biological substrate — slime mould Physarum polycephalum, an arguably ‘simple’ single-celled organism — and how these properties can be harnessed to create laboratory experimental prototypes of functionally-useful biological UC prototypes. Computing devices utilising live slime mould as their key constituent element can be developed into a) heterotic, or hybrid devices, which are based on electrical recognition of slime mould behaviour via machine-organism interfaces, b) whole-organism-scale morphological processors, whose output is the organism’s morphological adaptation to environmental stimuli (input) and c) intracellular processors wherein data are represented by energetic signalling events mediated by the cytoskeleton, a nano-scale protein network. It is demonstrated that each category of device is capable of implementing logic and furthermore, specific applications for each class may be engineered, such as image processing applications for morphological processors and biosensors in the case of heterotic devices. The results presented are supported by a range of computer modelling experiments using cellular automata and multi-agent modelling. We conclude that P. polycephalum is a polymorphic UC substrate insofar as it can process multimodal sensory input and polyfunctional in its demonstrable ability to undertake a variety of computing problems. Furthermore, our results are highly applicable to the study of other living UC substrates and will inform future work in UC, biosensing, and biomedicine

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

Characterisation of Skin-based THz Communication Channel for Nano-scale Body-centric Wireless Networks

PhDIn 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 analysi