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

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

Minimum energy channel codes for molecular communications

Owing to the limitations of molecular nanomachines, it is essential to develop reliable, yet energy-efficient communication techniques. Two error correction coding techniques are compared under a diffusive molecular communication mechanism, namely, Hamming codes and minimum energy codes (MECs). MECs, which previously have not been investigated in a diffusive channel, maintain the desired code distance to keep reliability while minimising energy. Results show that MECs outperform the Hamming codes, both in aspects of bit error rate and energy consumption

Throughput and energy efficiency based packet size optimization of ARQ protocols in bacterial quorum communications

The discovery that bacteria use signalling molecules, which are released into the environment, to communicate with each other changed our general perception of organisms inhabiting the world. Nowadays, the term quorum sensing is used to describe the phenomenon whereby a coordinated population response is controlled by exchanging specific diffusible chemical signals called autoinducers, enabling a cluster of bacteria to regulate their gene expression and behaviour collectively and synchronously. Bacteria assess their own population and coordinate their actions through the synthesis, accumulation and subsequent sensing of autoinducers. In this work, a bacterial quorum communication system is introduced, which contains two clusters of bacteria, specifically Vibrio fischeri, a gram-negative marine bacterium, as the transmitter node and receiver node, and the diffusive channel. The transmitted information is encoded into the concentration of autoinducers, with binary representation, and then, it is divided into frames for transmission. Automatic Repeat reQuest protocols are applied to achieve better reliability. In addition, this paper addresses the question of optimal frame size for data communication in this channel capacity and energy constrained bacterial quorum communication system. The optimal fixed frame length is determined for a set of channel parameters by maximising the throughput and energy efficiency matrix

Analysis of In-to-Out Wireless Body Area Network Systems: Towards QoS-Aware Health Internet of Things Applications

In this paper, an analytical and accurate in-to-out (I2O) human body path loss (PL) model at 2.45 GHz is derived based on a 3D heterogeneous human body model under safety constraints. The bit error rate (BER) performance for this channel using multiple efficient modulation schemes is investigated and the link budget is analyzed based on a predetermined satisfactory BER of 10−3. In addition, an incremental relay-based cooperative quality of service-aware (QoS-aware) routing protocol for the proposed I2O WBAN is presented and compared with an existing scheme. Linear programming QoS metric expressions are derived and employed to maximize the network lifetime, throughput, minimizing delay. Results show that binary phase-shift keying (BPSK) outperforms other modulation techniques for the proposed I2O WBAN systems, enabling the support of a 30 Mbps data transmission rate up to 1.6 m and affording more reliable communication links when the transmitter power is increased. Moreover, the proposed incremental cooperative routing protocol outperforms the existing two-relay technique in terms of energy efficiency. Open issues and on-going research within the I2O WBAN area are presented and discussed as an inspiration towards developments in health IoT applications