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

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

Nanoprogrammed Cross-Kingdom Communication Between Living Microorganisms

[EN] The engineering of chemical communication at the micro/nanoscale is a key emergent topic in micro/nanotechnology, synthetic biology, and related areas. However, the field is still in its infancy; previous advances, although scarce, have mainly focused on communication between abiotic micro/nanosystems or between microvesicles and living cells. Here, we have implemented a nanoprogrammed cross-kingdom communication involving two different microorganisms and tailor-made nanodevices acting as "nanotranslators". Information flows from the sender cells (bacteria) to the nanodevice and from the nanodevice to receiver cells (yeasts) in a hierarchical way, allowing communication between two microorganisms that otherwise would not interact.B.d.L. is grateful to the Spanish Government for her FPU Ph.D. fellowship. The authors wish to thank the Spanish Government (projects RTI2018-100910-B-C41 and RTI2018101599-B-C22 (MCUI/FEDER, EU)) and the Generalitat Valenciana (project PROMETEO 2018/024) for support. Part of this work was included in the Ph.D. thesis of B.d.L.De Luis-Fernández, B.; Morella-Aucejo, Á.; Llopis-Lorente, A.; Martínez-Latorre, J.; Sancenón Galarza, F.; López Del Rincón, C.; Murguía, JR.... (2022). Nanoprogrammed Cross-Kingdom Communication Between Living Microorganisms. Nano Letters. 22(5):1836-1844. https://doi.org/10.1021/acs.nanolett.1c024351836184422

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

Security and Privacy in Molecular Communication and Networking: Opportunities and Challenges

International audienceMolecular Communication (MC) is an emerging andpromising communication paradigm for several multi-disciplinarydomains like bio-medical, industry and military. Differently to thetraditional communication paradigm, the information is encodedon the molecules, that are then used as carriers of information.Novel approaches related to this new communication paradigmhave been proposed, mainly focusing on architectural aspects andcategorization of potential applications. So far, security and privacyaspects related to the molecular communication systems havenot been investigated at all and represent an open question thatneed to be addressed. The main motivation of this paper lies onproviding some first insights about security and privacy aspects ofMC systems, by highlighting the open issues and challenges andabove all by outlining some specific directions of potential solutions.Existing cryptographicmethods and security approaches arenot suitable for MC systems since do not consider the pecific issuesand challenges, that need ad-hoc solutions.We will discuss directionsin terms of potential solutions by trying to highlight themain advantages and potential drawbacks for each direction considered.We will try to answer to the main questions: 1) why thissolution can be exploited in the MC field to safeguard the systemand its reliability? 2) which are the main issues related to the specificapproach

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

Bioengineered conduits for directing digitized molecular-based information

Molecular recognition is a prevalent quality in natural biological environments: molecules- small as well as macro- enable dynamic response by instilling functionality and communicating information about the system. The accession and interpretation of this rich molecular information leads to context about the system. Moreover, molecular complexity, both in terms of chemical structure and diversity, permits information to be represented with high capacity. Thus, an opportunity exists to assign molecules as chemical portrayals of natural, non-natural, and even non-biological data. Further, their associated upstream, downstream, and regulatory pathways could be commandeered for the purpose of data processing and transmission. This thesis emphasizes molecules that serve as units of information, the processing of which elucidates context. The project first strategizes a biocompatible assembly process that integrates biological componentry in an organized configuration for molecular transfer (e.g. from a cell to a receptor). Next, we have explored the use of DNA for its potential to store data in richer, digital forms. Binary data is embedded within a gene for storage inside a cell carrier and is selectively conveyed. Successively, a catalytic relay is developed to transduce similar data from sequence-based DNA storage to a delineated chemical cue that programs cellular phenotype. Finally, these cell populations are used as mobile information processing units that independently seek and collectively categorize the information, which is fed back as fluorescently ‘binned’ output. Every development demonstrates a transduction process of molecular data that involves input acquisition, refinement, and output interpretation. Overall, by equipping biomimetic networks with molecular-driven performance, their interactions serve as conduits of information flow

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