Energy requirements of error correction codes in diffusion-based molecular communication systems

Molecular Communications is a promising area with significant potential applications. To enhance the reliability of the transmission process, self-orthogonal convolutional codes (SOCCs) are proposed and investigated with respect to both bit error rate (BER) and energy efficiency. The codes are compared to both an un-coded system and one that employs Hamming codes to show that they can provide a benefit for molecular communication systems. The influence of the channel memory is also analysed in this paper. In addition, taking into account the extra energy required to implement the coding, the critical distance is investigated as another performance metric for nano-to-nano device communication, nano-to-macro device communication and macro-to-nano device communication. Considering the transmission distance and the operating BER of the designed system, the designer can determine whether the use of coding is beneficial or which code better suits the system

Error correction codes for molecular communication systems.

Molecular communications (MC) is a bio-inspired paradigm that aims to utilise molecules to exchange information among nano-machines. Given the tiny devices used in a MC system and the feasibility of MC in biological environments, MC can be applied to many applications ranging from the healthcare to manufacturing fields. In order to better realize these applications in the future, this Ph.D. research is dedicated to the investigation of a more functional, precise and reliable Diffusion-based Molecular Communications (DBMC) system. To achieve this goal, the contributions of this thesis are as follows. Firstly, the point-to-point (PTP) DBMC system with the absorbing receiver model is established and investigated. A study of the accuracy of the analytical channel model is also introduced. Secondly, dependent on different types of the transmitter (TX) and receiver (RX), three different communication scenarios are proposed. Thirdly, to enhance the reliability of the information at RX, the Error Correction Codes (ECCs), as the most prominent technique is employed within the DBMC system to control or correct any errors introduced during the transmission process. Fourthly, due to the limitation of the power budget of the nano-machines, the energy efficiency of the system is also taken into account. Finally, a two-receiver broadcast DBMC system is established with an absorbing interfering receiver (RI) and an absorbing target receiver (RT). By analysing the performance of the communication link between TX and RT (target communication link), the impact of the positions of RI on RT is studied. This study indicates that the application of ECCs does enhance the performance of PTP DBMC systems. In addition, the encoder and decoder design, and the BER performance are shown to be the two primary factors for selecting the most suitable ECC for the application. Finally, considering a two-receiver broadcast DBMC system with absorbing receivers, the existence of RI does affect the performance of the target communication link which is crucial result for the field moving forward

Molecular communications techniques for the internet of bio-nano things

The ”Internet of Bio-Nano Things” (IoBNT) is a new networking paradigm defined as the interconnection of nanoscale devices. IoBNT is a revolutionizing concept that will likely enable a wide range of applications, in particular, it is envisioned that healthcare systems will be transformed with the development and integration of body-centric networks into future generations of communication systems. Within this context, molecular communications (MC) emerge as the most promising way of transmitting information for in-body communications, due to being inherently biocompatible, energy-efficient, and robust in physiological conditions. One of the biggest challenges is how to minimize the effects of environmental noise and reduce intersymbol interference (ISI) which can be very high in an MC via diffusion scenario. Analogous to traditional communications, channel coding is one of the most promising types of techniques for addressing this problem. This work is based on the study and evaluation of novel energy efficient and low complexity coding, modulation and detection schemes for MC. With a special focus on the implementation of Tomlinson, Cercas, Hughes (TCH) codes as a new attractive approach for the MC environment, due to the particular codeword properties which enable simplified detection. Simulation results show that TCH codes are more effective for these scenarios when compared to other existing alternatives, without introducing too much complexity or processing power into the system. Furthermore, an experimental macroscale proof-of-concept is described, which uses pH as the information carrier and demonstrates that the proposed TCH codes can improve the reliability in this type of communication channel.A ”Internet das Coisas” Bio-Nano é um novo paradigma de rede definido como a interconexão de dispositivos nano escala. Este é um conceito revolucionário que espectavelmente permitirá uma vasta gama de aplicações. Em particular, prevê-se que os sistemas de saúde sejam transformados com a integração de redes centradas no corpo, em futuras gerações de sistemas de comunicação. Neste contexto, as comunicações moleculares (CM) emergem como a forma mais promissora de transmitir informação, devido ao facto de serem intrinsecamente biocompatíveis, eficientes em termos energéticos e robustos em condições fisiológicas. Um dos maiores desafios é como minimizar os efeitos do ruído ambiental e reduzir a interferência intersimbólica que pode ser muito elevada num cenário de CM por difusão. A codificação de canal é um dos tipos de técnicas mais promissoras para abordar este problema. Este trabalho baseia-se na avaliação da modulação, da deteção e de novos esquemas de codificação energeticamente eficientes e de baixa complexidade aplicados em CM. Com especial foco, na implementação de códigos Tomlinson, Cercas, Hughes (TCH) como uma nova abordagem para um ambiente de CM, devido às suas particulares propriedades das palavras de código, que permitem uma deteção simplificada. Os resultados das simulações mostram que os códigos TCH são mais eficazes para estes cenários quando comparados com outras alternativas existentes, sem introduzir demasiada complexidade ou poder de processamento no sistema. Adicionalmente, é descrita uma experiência macroscópica, que utiliza o pH como portador de informação, demonstrando que os códigos TCH propostos podem melhorar a fiabilidade para CM

ISI-aware channel code design for molecular communication via diffusion

© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.In molecular communication via diffusion, information molecules diffusing in the environment are subject to Brownian motion. Due to probabilistic propagation, the arrival of the molecules at the receiver is spread in time, leading to the reception of some molecules belonging to the previous symbol(s) during the upcoming symbol duration. Known as inter-symbol interference (ISI), this problem has been extensively studied in the literature by applying a large spectrum of techniques, mostly inspired by approaches in the wireless communication domain, including channel coding techniques. Unfortunately, many known channel codes do not perform well in the molecular communications domain since the diffusion channel features a significant memory component. In this paper, novel methods for channel coding by incorporating the effect of ISI in the design of the channel codes for the molecular diffusion channel are proposed. The results show that the proposed methods provide significant improvements in performance in terms of the codeword error rate.Postprint (author's final draft

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

Channel Coding in Molecular Communication

This dissertation establishes and analyzes a complete molecular transmission system from a communication engineering perspective. Its focus is on diffusion-based molecular communication in an unbounded three-dimensional fluid medium. As a basis for the investigation of transmission algorithms, an equivalent discrete-time channel model (EDTCM) is developed and the characterization of the channel is described by an analytical derivation, a random walk based simulation, a trained artificial neural network (ANN), and a proof of concept testbed setup. The investigated transmission algorithms cover modulation schemes at the transmitter side, as well as channel equalizers and detectors at the receiver side. In addition to the evaluation of state-of-the-art techniques and the introduction of orthogonal frequency-division multiplexing (OFDM), the novel variable concentration shift keying (VCSK) modulation adapted to the diffusion-based transmission channel, the lowcomplex adaptive threshold detector (ATD) working without explicit channel knowledge, the low-complex soft-output piecewise linear detector (PLD), and the optimal a posteriori probability (APP) detector are of particular importance and treated. To improve the error-prone information transmission, block codes, convolutional codes, line codes, spreading codes and spatial codes are investigated. The analysis is carried out under various approaches of normalization and gains or losses compared to the uncoded transmission are highlighted. In addition to state-of-the-art forward error correction (FEC) codes, novel line codes adapted to the error statistics of the diffusion-based channel are proposed. Moreover, the turbo principle is introduced into the field of molecular communication, where extrinsic information is exchanged iteratively between detector and decoder. By means of an extrinsic information transfer (EXIT) chart analysis, the potential of the iterative processing is shown and the communication channel capacity is computed, which represents the theoretical performance limit for the system under investigation. In addition, the construction of an irregular convolutional code (IRCC) using the EXIT chart is presented and its performance capability is demonstrated. For the evaluation of all considered transmission algorithms the bit error rate (BER) performance is chosen. The BER is determined by means of Monte Carlo simulations and for some algorithms by theoretical derivation

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