Symbol Synchronization for Diffusive Molecular Communication Systems

Symbol synchronization refers to the estimation of the start of a symbol interval and is needed for reliable detection. In this paper, we develop a symbol synchronization framework for molecular communication (MC) systems where we consider some practical challenges which have not been addressed in the literature yet. In particular, we take into account that in MC systems, the transmitter may not be equipped with an internal clock and may not be able to emit molecules with a fixed release frequency. Such restrictions hold for practical nanotransmitters, e.g. modified cells, where the lengths of the symbol intervals may vary due to the inherent randomness in the availability of food and energy for molecule generation, the process for molecule production, and the release process. To address this issue, we propose to employ two types of molecules, one for synchronization and one for data transmission. We derive the optimal maximum likelihood (ML) symbol synchronization scheme as a performance upper bound. Since ML synchronization entails high complexity, we also propose two low-complexity synchronization schemes, namely a peak observation-based scheme and a threshold-trigger scheme, which are suitable for MC systems with limited computational capabilities. Our simulation results reveal the effectiveness of the proposed synchronization~schemes and suggest that the end-to-end performance of MC systems significantly depends on the accuracy of symbol synchronization.Comment: This paper has been accepted for presentation at IEEE International Conference on Communications (ICC) 201

One symbol blind synchronization in SIMO molecular communication systems

Molecular communication offers new possibilities in the micro-and nano-scale application environments. Similar to other communication paradigms, molecular communication also requires clock synchronization between the transmitter and the receiver nanomachine in many time-and control-sensitive applications. This letter presents a novel high-efficiency blind clock synchronization mechanism. Without knowing the channel parameters of the diffusion coefficient and the transmitter-receiver distance, the receiver only requires one symbol to achieve synchronization. The samples are used to estimate the propagation delay by least square method and achieve clock synchronization. Single-input multiple-output (SIMO) diversity design is then proposed to mitigate channel noise and therefore to improve the synchronization accuracy. The simulation results show that the proposed clock synchronization mechanism has a good performance and may help chronopharmaceutical drug delivery applications

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

Molecular information delivery in porous media

Information delivery via molecular signals is abundant in nature and potentially useful for industry sensing. Many propagation channels (e.g., tissue membranes and catalyst beds) contain porous medium materials and the impact this has on communication performance is not well understood. Here, communication through realistic porous channels is investigated for the first time via statistical breakthrough curves. Assuming that the number of arrived molecules can be approximated as a Gaussian random variable and using fully resolved computational fluid dynamics results for the breakthrough curves, the numerical results for the throughput, mutual information, error probability, and information diversity gain are presented. Using these numerical results, the unique characteristics of the porous medium channel are revealed

Symbol-by-Symbol Maximum Likelihood Detection for Cooperative Molecular Communication

In this paper, symbol-by-symbol maximum likelihood (ML) detection is proposed for a cooperative diffusion-based molecular communication (MC) system. In this system, the transmitter (TX) sends a common information symbol to multiple receivers (RXs) and a fusion center (FC) chooses the TX symbol that is more likely, given the likelihood of its observations from all RXs. The transmission of a sequence of binary symbols and the resultant intersymbol interference are considered in the cooperative MC system. Three ML detection variants are proposed according to different RX behaviors and different knowledge at the FC. The system error probabilities for two ML detector variants are derived, one of which is in closed form. The optimal molecule allocation among RXs to minimize the system error probability of one variant is determined by solving a joint optimization problem. Also for this variant, the equal distribution of molecules among two symmetric RXs is analytically shown to achieve the local minimal error probability. Numerical and simulation results show that the ML detection variants provide lower bounds on the error performance of simpler, non-ML cooperative variants and demonstrate that these simpler cooperative variants have error performance comparable to ML detectors.Comment: 15 pages, 7 figures; submission for possible IEEE publication. arXiv admin note: text overlap with arXiv:1704.0562

Characterization of cooperators in Quorum sensing with 2D molecular signal analysis

In quorum sensing (QS), bacteria exchange molecular signals to work together. An analytically-tractable model is presented for characterizing QS signal propagation within a population of bacteria and the number of responsive cooperative bacteria (i.e., cooperators) in a two-dimensional (2D) environment. Unlike prior works with a deterministic topology and a simplified molecular propagation channel, this work considers continuous emission, diffusion, degradation, and reception among randomly-distributed bacteria. Using stochastic geometry, the 2D channel response and the corresponding probability of cooperation at a bacterium are derived. Based on this probability, new expressions are derived for the moment generating function and different orders of moments of the number of cooperators. The analytical results agree with the simulation results obtained by a particle-based method. In addition, the Poisson and Gaussian distributions are compared to approximate the distribution of the number of cooperators and the Poisson distribution provides the best overall approximation. The derived channel response can be generally applied to any molecular communication model where single or multiple transmitters continuously release molecules into a 2D environment. The derived statistics of the number of cooperators can be used to predict and control the QS process, e.g., predicting and decreasing the likelihood of biofilm formation

Convex optimization of distributed cooperative detection in multi-receiver molecular communication

In this paper, the error performance achieved by cooperative detection among K distributed receivers in a diffusion-based molecular communication system is analyzed and optimized. In this system, the receivers first make local hard decisions on the transmitted symbol and then report these decisions to a fusion center (FC). The FC combines the local hard decisions to make a global decision using an N -out-of- K fusion rule. Two reporting scenarios, namely, perfect reporting and noisy reporting, are considered. Closed-form expressions are derived for the expected global error probability of the system for both reporting scenarios. New approximated expressions are also derived for the expected error probability. Convex constraints are then found to make the approximated expressions jointly convex with respect to the decision thresholds at the receivers and the FC. Based on such constraints, suboptimal convex optimization problems are formulated and solved to determine the optimal decision thresholds which minimize the expected error probability of the system. Numerical and simulation results reveal that the system error performance is greatly improved by combining the detection information of distributed receivers. They also reveal that the solutions to the formulated suboptimal convex optimization problems achieve near-optimal global error performance

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