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

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

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

Sensing and molecular communication using synthetic cells: Theory and algorithms

Molecular communication (MC) is a novel communication paradigm in which molecules are used to encode, transmit and decode information. MC is the primary method by which biological entities exchange information and hence, cooperate with each other. MC is a promising paradigm to enable communication between nano-bio machines, e.g., biosensors with potential applications such as cancer and disease detection, smart drug delivery, toxicity detection etc. The objective of this research is to establish the fundamentals of diffusion-based molecular communication and sensing via biological agents (e.g., synthetic bacteria) from a communication and information theory perspective, and design algorithms for reliable communication and sensing systems. In the first part of the thesis, we develop models for the diffusion channel as well as the molecular sensing at the receiver and obtain the maximum achievable rate for such a communication system. Next, we study reliability in MC. We design practical nodes by employing synthetic bacteria as the basic element of a biologically-compatible communication system and show how reliable nodes can be formed out of the collective behavior of a population of unreliable bio-agents. We model the probabilistic behavior of bacteria, obtain the node sensing capacity and propose a practical modulation scheme. In order to improve the reliability, we also introduce relaying and error-detecting codes for MC. In the second part of the thesis, we study the molecular sensing problem with potential applications in disease detection. We establish the rate-distortion theory for molecular sensing and investigate as to how distortion can be minimized via an optimal quantizer. We also study sensor cell arrays in which sensing redundancy is achieved by using multiple sensors to measure several molecular inputs simultaneously. We study the interference in sensing molecular inputs and propose a probabilistic message passing algorithm to solve the pattern detection over the molecular inputs of interest.Ph.D

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

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

Empleo de bacterias lácticas y sus metabolitos como estrategia de biocontrol para disminuir la incidencia de cepas de <i>Salmonella</i> spp. formadoras de biopelículas en granjas avícolas

Estudio de las propiedades de superficie y la formación de biofilm de cepas de Salmonella aisladas de granjas avícolas de la región en diferentes condiciones de cultivo y superficies. Evaluación de la interacción de bacterias lácticas, sus proteínas de superficie y metabolitos presentes en los sobrenadantes de cultivo con las cepas de Salmonella y estudio de la reducción de biofilm del patógeno. Aplicación de bacterias lácticas y sus metabolitos como estrategia alternativa para la reduccion de la formación de biofilm de Salmonella sobre la superficie de cáscara de huevo.Facultad de Ciencias Exacta

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

Drug Discovery

Natural products are a constant source of potentially active compounds for the treatment of various disorders. The Middle East and tropical regions are believed to have the richest supplies of natural products in the world. Plant derived secondary metabolites have been used by humans to treat acute infections, health disorders and chronic illness for tens of thousands of years. Only during the last 100 years have natural products been largely replaced by synthetic drugs. Estimates of 200 000 natural products in plant species have been revised upward as mass spectrometry techniques have developed. For developing countries the identification and use of endogenous medicinal plants as cures against cancers has become attractive. Books on drug discovery will play vital role in the new era of disease treatment using natural products