Simulating the performance of SW-ARQ schemes within molecular communications

This paper provides results on an investigation concerning the application of five tailored Stop-and-Wait Automatic Repeat reQuest (SW-ARQ) schemes to a diffusion based molecular communication system. Each scheme is numerically simulated and evaluated to determine its performance with regards to average time cost and energy consumption. It is shown that all five schemes are beneficial depending upon the application scenario. Scheme 1 is the best choice for adjacent communications although, if a slightly higher energy budget can be afforded, schemes 2 and 3 will provide better performance than scheme 1 as the communication distance increases. Schemes 4 and 5 are designed to benefit scenarios with either a varying channel or for a channel with unknown parameters although will also benefit a static channel if again, further system energy can be utilised. This optimisation and trade-off between time and energy requirement for a complete successful transmission will become more important in future applications involving molecular communications where energy efficiency is a design consideration

The design and performance analysis of diffusive molecular communication systems

Molecular Communications (MC) is an increasingly attractive technique to enable the networking of nano-machines by utilising molecules as the information carrier. The molecular diffusion can be described by either the movement of individual molecules or the molecular concentration. Accordingly, two kinds of diffusive MC systems have been modelled in previous literature. On the basis of these studies, the aim of this Ph.D. is to refine these two models, to implement functional transmission techniques and technologies, and to investigate the corresponding system performance. To fulfil this target, the whole Ph.D. is divided into two stages. During each stage, specific tasks have been accomplished, each contributing to the overarching research field of diffusive MC systems. In the first stage, an MC system model, named as the Model-I, is established and enhanced by focusing on the motion of individual molecules. The performance has been evaluated by both deriving mathematical expressions and implementing MATLAB simulations. Based on the Model-I, a distance estimation scheme has been proposed. Compared with existing methods, this new scheme is more accurate and less time-consuming. Moreover, five Stop-and-Wait Automatic Repeat reQuest (SW-AQR) protocols have been implemented on the Model-I. Results reveal that all these SW-ARQ schemes work well and can be beneficial under different circumstances. In the second stage, another MC system model, named as the Model-II, is established and refined with information conveyed by the molecular concentration. Both theoretical derivations and MATLAB simulations are provided to analyse the system reliability. Laid on this foundation, two distance measurement methods have been proposed and shown to be suitable for the Model-II. Additionally, to solve the long-range MC problem, relaying schemes have been applied by deploying a relay node between the source and target nano-machines. The performance improvement of each scheme is also illustrated respectively

Analysis of ARQ protocols for 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 behaviour collectively and synchronously, and assess their own population. As a promising method of molecular communication, bacterial populations can be programmed as bio-transceivers to establish information transmission using molecules. In this work, to investigate the key features for molecular communication, 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, transmission efficiency and channel throughput performance, different Automatic Repeat reQuest (ARQ) protocols are taken into consideration. This configuration is investigated via simulation and the consequent results discussed. The performance of the system is evaluated in terms of transmission time, efficiency, bit error rate (BER) and channel throughput. Results show that Selective-Repeat (SR-ARQ) performs better than Go-Back-N (GBN-ARQ), while the performance of Stop-N-Wait (SW-ARQ) varies for different channel conditions, which is quite different from the performance of ARQ schemes in traditional networking areas

Performance of SW-ARQ in bacterial quorum communications

Bacteria communicate with one another by exchanging specific chemical signals called autoinducers. This process, also called quorum sensing, enables a cluster of bacteria to regulate their gene expression and behaviour collectively and synchronously, such as bioluminescence, virulence, sporulation and conjugation. Bacteria assess their population density by detecting the concentration of autoinducers. In Vibrio fischeri, which is a heterotrophic Gram-negative marine bacterium, quorum sensing relies on the synthesis, accumulation and subsequent sensing of a signalling molecule (3-oxo-C6-HSL, an N-acyl homoserine lactone or AHL). In this work, a data link layer protocol for a bacterial communication paradigm based on diffusion is introduced, considering two populations of bacteria as the transmitter node and the receiver node, instead of employing two individual bacteria. Moreover, some initial results are provided, which concern the application of the Stop-N-Wait Automatic Repeat reQuest (SW-ARQ) schemes to the proposed model. The performances of the system are later evaluated, in terms of the transmission time, frame error rate, energy consumption and transmission efficiency

Distance estimation schemes for diffusion based molecular communication systems

Molecule concentration is often used as the information carrier to accomplish diffusion-based molecular communications (DMC) among nano-machines. To achieve the optimal functionality, knowing the distance between the transmitter nano-machine (TN) and the receiver nano-machine (RN) is of high importance. In this paper, two distance estimation schemes are proposed based upon the RN-sensed concentration which changes with regards to the time and distance. The RN estimates the distance by means of measuring either the concentration-peak time or received concentration energy. Simulations are performed to compare the accuracy of each scheme and to discover how the diffusion channel and noise may influence the accuracy. Results show that both schemes will provide a beneficial enhancement to molecular communication systems

Nano-Communication for Biomedical Applications: A Review on the State-of-the-Art From Physical Layers to Novel Networking Concepts

We review EM modeling of the human body, which is essential for in vivo wireless communication channel characterization; discuss EM wave propagation through human tissues; present the choice of operational frequencies based on current standards and examine their effects on communication system performance; discuss the challenges of in vivo antenna design, as the antenna is generally considered to be an integral part of the in vivo channel; review the propagation models for the in vivo wireless communication channel and discuss the main differences relative to the ex vivo channel; and address several open research problems and future research directions

Network coding for computer networking

Conventional communication networks route data packets in a store-and-forward mode. A router buffers received packets and forwards them intact towards their intended destination. Network Coding (NC), however, generalises this method by allowing the router to perform algebraic operations on the packets before forwarding them. The purpose of NC is to improve the network performance to achieve its maximum capacity also known as max-flow min-cut bound. NC has become very well established in the field of information theory, however, practical implementations in real-world networks is yet to be explored. In this thesis, new implementations of NC are brought forward. The effect of NC on flow error control protocols and queuing over computer networks is investigated by establishing and designing a mathematical and simulation framework. One goal of such investigation is to understand how NC technique can reduce the number of packets required to acknowledge the reception of those sent over the network while error-control schemes are employed. Another goal is to control the network queuing stability by reducing the number of packets required to convey a set of information. A custom-built simulator based on SimEvents® has been developed in order to model several scenarios within this approach. The work in this thesis is divided into two key parts. The objective of the first part is to study the performance of communication networks employing error control protocols when NC is adopted. In particular, two main Automatic Repeat reQuest (ARQ) schemes are invoked, namely the Stop-and-Wait (SW) and Selective Repeat (SR) ARQ. Results show that in unicast point-to point communication, the proposed NC scheme offers an increase in the throughput over traditional SW ARQ between 2.5% and 50.5% at each link, with negligible decoding delay. Additionally, in a Butterfly network, SR ARQ employing NC achieves a throughput gain between 22% and 44% over traditional SR ARQ when the number of incoming links to the intermediate node varies between 2 and 5. Moreover, in an extended Butterfly network, NC offered a throughput increase of up to 48% under an error-free scenario and 50% in the presence of errors. Despite the extensive research on synchronous NC performance in various fields, little has been said about its queuing behaviour. One assumption is that packets are served following a Poisson distribution. The packets from different streams are coded prior to being served and then exit through only one stream. This study determines the arrival distribution that coded packets follow at the serving node. In general this leads to study general queuing systems of type G/M/1. Hence, the objective of the second part of this study is twofold. The study aims to determine the distribution of the coded packets and estimate the waiting time faced by coded packets before their complete serving process. Results show that NC brings a new solution for queuing stability as evidenced by the small waiting time the coded packets spend in the intermediate node queue before serving. This work is further enhanced by studying the server utilization in traditional routing and NC scenarios. NC-based M/M/1 with finite capacity K is also analysed to investigate packet loss probability for both scenarios. Based on the results achieved, the utilization of NC in error-prone and long propagation delay networks is recommended. Additionally, since the work provides an insightful prediction of particular networks queuing behaviour, employing synchronous NC can bring a solution for systems’ stability with packet-controlled sources and limited input buffers