Diffusion-based clock synchronization for molecular communication under inverse Gaussian distribution

Nanonetworks are expected to expand the capabilities of individual nanomachines by allowing them to cooperate and share information by molecular communication. The information molecules are released by the transmitter nanomachine and diffuse across the aqueous channel as a Brownian motion holding the feature of a strong random movement with a large propagation delay. In order to ensure an effective real-time cooperation, it is necessary to keep the clock synchronized among the nanomachines in the nanonetwork. This paper proposes a model on a two-way message exchange mechanism with the molecular propagation delay based on the inverse Gaussian distribution. The clock offset and clock skew are estimated by the maximum likelihood estimation (MLE). Simulation results by MATLAB show that the mean square errors (MSE) of the estimated clock offsets and clock skews can be reduced and converge with a number of rounds of message exchanges. The comparison of the proposed scheme with a clock synchronization method based on symmetrical propagation delay demonstrates that our proposed scheme can achieve a better performance in terms of accuracy

Biological Oscillators in Nanonetworks-Opportunities and Challenges.

One of the major issues in molecular communication-based nanonetworks is the provision and maintenance of a common time knowledge. To stay true to the definition of molecular communication, biological oscillators are the potential solutions to achieve that goal as they generate oscillations through periodic fluctuations in the concentrations of molecules. Through the lens of a communication systems engineer, the scope of this survey is to explicitly classify, for the first time, existing biological oscillators based on whether they are found in nature or not, to discuss, in a tutorial fashion, the main principles that govern the oscillations in each oscillator, and to analyze oscillator parameters that are most relevant to communication engineer researchers. In addition, the survey highlights and addresses the key open research issues pertaining to several physical aspects of the oscillators and the adoption and implementation of the oscillators to nanonetworks. Moreover, key research directions are discussed

Cooperative signal amplification for molecular communication in nanonetworks.

English: Nanotechnology is enabling the development of devices in a scale ranging from a few to hundreds of nanometers. Communication between these devices greatly expands the possible applications, increasing the complexity and range of operation of the system. In particular, the resulting nanocommunication networks (or nanonetworks) show great potential for applications in the biomedical field, in which diffusion-based molecular communication is regarded as a promising alternative to electromagnetic-based solutions due to the bio-stability and energy-related requirements of this scenario. In this new paradigm, the information is encoded into pulses of molecules that reach the receiver by means of diffusion. However, molecular signals suffer a significant amount of attenuation as they propagate through the medium, thus limiting the transmission range. In this work we propose, among others, a signal amplification scheme for molecular communication nanonetworks in which a group of emitters jointly transmits a given signal after achieving synchronization by means of Quorum Sensing. By using the proposed methodology, the transmission range is extended proportionally to the number of synchronized emitters. We also provide an analytical model of Quorum Sensing, validated through simulation. This model accounts for the activation threshold (which will eventually determine the resulting amplification level) and the delay of the synchronization process.Castellano: La nanotecnología permite el desarrollo de dispositivos en una escala que va de las unidades a centenares de nanómetros. La comunicación entre estos dispositivos hace aumentar el número de aplicaciones posibles, ya que se mejora la complejidad y el rango de actuación del sistema. En concreto, las redes de nanocomunicaciones (o nanoredes) resultantes muestran un gran potencial cuando se trata de aplicaciones biomédicas, en las cuales la comunicación molecular basada en difusión de partículas supera a las soluciones electromagnéticas clásicas debido a las imposiciones energéticas y de biocompatibilidad de este escenario. En este nuevo paradigma de comunicación, la información se codifica en pulsos de moléculas que llegan al receptor gracias al fenómeno de la difusión. No obstante, las señales moleculares son sometidas a una gran atenuación a medida que se propagan a través del medio, hecho que limita severamente el alcance o rango de transmisión. En esta tesis se propone, entre otros, un esquema de amplificación de la señal para nanoredes de comunicación molecular, en el cual un grupo de emisores transmite una cierta señal de manera conjunta después de haberse sincronizado mediante la ejecución de Quorum Sensing. Con el método que proponemos, el alcance aumenta proporcionalmente al número de transmisores que se sincronizan. Además, proponemos un modelo analítico de Quorum Sensing, el cual se valida mediante simulación. Dicho modelo permite calcular el nivel umbral de activación del conjunto (hecho que determina la amplificación resultante y el rango de transmisión final) y el retardo que el proceso de sincronización introduce.Català: La nanotecnologia permet el desenvolupament de dispositius en una escala de unitats a centenars de nanòmetres. La comunicació entre aquests dispositius fa augmentar el nombre de possibles aplicacions, ja que es millora la complexitat i el rang d'actuació del sistema. En concret, les xarxes de nanocomunicacions (o nanoxarxes) resultants mostren un gran potencial quan ens referim a aplicacions biomèdiques, en les quals la comunicació molecular basada en difusió de partícules supera a les solucions de caire electromagnètic degut a les imposicions energètiques i de biocompatilitat d'aquest escenari. En aquest nou paradigma de comunicació, la informació és codificada en polsos de molècules que arriben al receptor gràcies al fenomen de la difusió. No obstant, els senyals moleculars són sotmesos a una gran atenuació a mesura que es propaguen a través del medi, fet que limita severament el rang de transmissió. En aquesta tesi es proposa, entre d'altres, un esquema d'amplificació del senyal per a nanoxarxes de comunicació molecular, en el qual un grup d'emissors transmet un cert senyal de manera conjunta després d'haver-se sincronitzat executant Quorum Sensing. Amb el mètode que proposem, l'abast o rang de transmissió augmenta proporcionalment al nombre d'emissors que se sincronitzen. A més a més, proposem un model analític de Quorum Sensing, el qual és validat mitjançant simulació. Dit model permet calcular el nivell llindar d'activació del conjunt (que de fet determina l'amplificació resultant i el rang de transmissió final) i el retard que el procés de sincronització introdueix

Automata Modeling of Quorum Sensing for Nanocommunication Networks

Projecte final de carrera realitzat en col.laboració amb Broadband Wireless Networking Lab. Georgia Institute of Technology. AtlantaNanotechnology is enabling the development of devices in a scale ranging one to hundreds of nanometers. Communication between these devices underlying in the nanoscale greatly expands the possible applications, increasing the complexity and range of operation of the system. Several options for nanocommunications have been discovered and studied, and many of them take some natural mechanisms and processes as a model, or directly use di erent elements from nature to serve its purposes. For instance, in molecular communications, the information is encoded in tiny particles secreted by the emitter. In this work, a special case of molecular communications is studied and modeled. Quorum Sensing is a mechanism used by bacteria to sense their own population and coordinate or synchronize their actions, through the emission and sensing of molecules called autoinducers. The behavior of each bacterium involved featuring Quorum Sensing is modeled as an individual nite state automaton, capturing its course of action. Later, the design of a novel nanomachine that will include Quorum Sensing is presented, along with its applications. Mainly, Quorum Sensing will serve to synchronize the processes of a group of nanodevices, and this idea is developed to present \Collective Actuation Synchronization" and \Collective Actuation after Localized Sensing" nanomachines. Finally, these con gurations are implemented and simulated, and the results are later discussed

On the scalability limits of communication networks to the nanoscale

Nanosystems, integrated systems with a total size of a few micrometers, are capable of interacting at the nanoscale, but their short operating range limits their usefulness in practical macro-scale scenarios. Nanonetworks, the interconnection of nanosystems, will extend their range of operation by allowing communication among nanosystems, thereby greatly enhancing their potential applications. In order to integrate communication capabilities into nanosystems, their communication subsystem needs to shrink to a size of a few micrometers. There are doubts about the feasibility of scaling down current metallic antennas to such a small size, mainly because their resonant frequency would be extremely high (in the optical domain) leading to a large free-space attenuation of the radiated EM waves. In consequence, as an alternative to implement wireless communications among nanosystems, two novel paradigms have emerged: molecular communication and graphene-enabled wireless communications. On the one hand, molecular communication is based on the exchange of molecules among nanosystems, inspired by communication among living cells. In Diffusion-based Molecular Communication (DMC), the emitted molecules propagate throughout the environment following a diffusion process until they reach the receiver. On the other hand, graphene, a one-atom-thick sheet of carbon atoms, has been proposed to implement graphene plasmonic RF antennas, or graphennas. Graphennas with a size in the order of a few micrometers show plasmonic effects which allow them to radiate EM waves in the terahertz band. Graphennas are the enabling technology of Graphene-enabled Wireless Communications (GWC). In order to answer the question of how communication networks will scale when their size shrinks, this thesis presents a scalability analysis of the performance metrics of communication networks to the nanoscale, following a general model with as few assumptions as possible. In the case of DMC, two detection schemes are proposed: amplitude detection and energy detection. Key performance metrics are identified and their scalability with respect to the transmission distance is found to differ significantly from the case of traditional wireless communications. These unique scaling trends present novel challenges which require the design of novel networking protocols specially adapted to DMC networks. The analysis of the propagation of plasmonic waves in graphennas allows determining their radiation performance. In particular, the resonant frequency of graphennas is not only lower than in metallic antennas, but it also increases more slowly as their length is reduced to the nanoscale. Moreover, the study of parameters such as the graphenna dimensions, the relaxation time of graphene and the applied chemical potential shows the tunability of graphennas in a wide frequency range. Furthermore, an experimental setup to measure graphennas based on feeding them by means of a photoconductive source is described. The effects of molecular absorption in the short-range terahertz channel, which corresponds to the expected operating scenario of graphennas, are analyzed. Molecular absorption is a process in which molecules present in the atmosphere absorb part of the energy of the terahertz EM waves radiated by graphennas, causing impairments in the performance of GWC. The study of molecular absorption allows quantifying this loss by deriving relevant performance metrics in this scenario, which show novel scalability trends as a function of the transmission distance with respect to the case of free-space propagation. Finally, the channel capacity of GWC is found to scale better as the antenna size is reduced than in traditional wireless communications. In consequence, GWC will require lower transmission power to achieve a given performance target. These results establish a general framework which may serve designers as a guide to implement wireless communication networks among nanosystems

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