Molecular Communication System Research Articles

Spatial Frequency-Based Characterization of Disturbance Rejection in Molecular Communication Systems

Spatial Frequency-Based Characterization of Disturbance Rejection in Molecular Communication Systems

A Multiscale Communications System Based on Engineered Bacteria

Although molecular communication systems have been shown to bear great potential for many useful in-body applications, they require the intervention, action, or input of an out-of-body actor. From an Internet of Bio-Nano Things perspective, a successful overall network aims to bring together the two links belonging to the in-body and out-of-body networks for end-to-end communications. For most applications, the uplink from the in-body sensor is more significant since it provides the multi-scalar connection required to relay the information sensed and carried by the molecular communication system to a macro-scale smart terminal. This article proposes two different mechanisms to sense the output of the molecular communication system and transmit the information to an on-body reader. Each mechanism involves different genetically engineered bacteria and specific antenna designs. An experimental setup is provided to demonstrate each proposed concept. The results constitute a proof of concept to detect the in-body bacterial activity from the on-body reader.

Toward Reliable Intra-Body Molecular Communication: An Error Control Perspective

Progress in bioengineering and nanotechnology has led to advances in implantable nanoscale devices. Providing synthetic molecular communication among these devices is an ongoing unsolved challenge. Biological systems inspire promising approaches for engineering data communication in molecular communication, but noises from dynamic tissue signaling result in low data rate and high latency. Thus, error control techniques become critical for reliable communication. This article contributes to a detailed and precise view of existing methods for error control in in-body molecular communication. It classifies the free-diffusion and cell signaling sources of noises. The article presents an error prevention technique, encoding multiple molecular information carriers for cell-signaling-based molecular communication systems. It highlights open research opportunities.

A Molecular Communications System for the Detection of Inflammatory Levels Related to COVID-19 Disease.

A recent and extensive research activity highlighted the process behind the attack and spread of COVID-19 in the human body. What emerged is that the SARS-CoV-2 virus makes use of both the ACE2 receptor, expressed by pneumocytes in the ephitelial alveolar lining, and by the endothelium to spread the disease and to replicate itself. Since the endothelium is an extended tissue lying in the circulatory system, this may lead to a large state of diffuse endothelial inflammation with serious clinical consequences. This situation may be further compromised by the immune system, that may generate pro-inflammatory cytokines (IL-6) as a consequence of the infection. In this paper we propose and analyze a molecular communication system, designed for the detection of excessive IL-6 level, that allows monitoring its evolution in the blood vessels. The proposed analysis was performed by using the BiNS2 simulator, which is suitable for the numerical analysis of flow-based molecular communications in blood vessels, as well as Markov models of the endothelium.

Transmit Signal Shaping for Molecular Communication

The nano size of the molecular transmitter limits it from storing or releasing a large number of molecules instantaneously. This physical constraint makes instantaneous release of molecules from the transmitter infeasible. In this letter, we model the molecule emission process more accurately using rectangular and exponential transmit signals and derive closed form expressions for the number of molecules that are absorbed by the receiver in a Diffusion-Based Molecular Communication (DBMC) system. We show that the effect of inter symbol interference (ISI) depends on the shape of the transmit signal. Also, we design an optimal transmit signal with minimum inter symbol interference effect using the least squares approach. Moreover, the bit error rate performance of the DBMC system is analyzed for different transmit signals compared to that of the ideal system with instantaneous release of molecules. The match between analytical expressions and particle-based simulations is shown.

A Semi-Analytical Method for Channel Modeling in Diffusion-Based Molecular Communication Networks

Channel modeling is a challenging vital step towards the development of diffusion-based molecular communication networks (DMCNs). Analytical approaches for diffusion channel modeling are limited to simple and specific geometries and boundary conditions. Also, simulation- and experiment-driven methods are very time-consuming and computationally complex. In this paper, the channel model for DMCN employing the fundamental concentration Green's function (CGF) is characterized. A general homogeneous boundary condition framework is considered that includes any linear reaction systems at the boundaries in the environment. To obtain the CGF for a general DMCN including multiple transmitters, receivers, and other objects with arbitrary geometries and boundary conditions, a semi-analytical method (SAM) is proposed. The CGF linear integral equation (CLIE) is analytically derived. By employing the numerical method of moments, the problem of CGF derivation from CLIE is transformed into an inverse matrix problem. Moreover, a sequential SAM is proposed that converts the inversion problem of a large matrix into multiple smaller matrices reducing the computational complexity. Particle-based simulator confirms the results obtained from the proposed SAM. The convergence and run time for the proposed method are examined. Further, the error probability of a simple diffusion-based molecular communication system is analyzed and examined using the proposed method.

A Molecular Communication Detection Method for the Deformability of Erythrocyte Membrane in Blood Vessels.

Molecular communication (MC) inspired drug delivery holds considerable promise as a new design for targeted therapy with high efficiency and minimal toxicity. The process of drug delivery can be modelled in a blood flow-based MC system, where nanoparticles (NPs) carry therapeutic agents through the blood vessel channels to the targeted diseased tissue. Most previous studies in the flow-based MC consider a Newtonian fluid with a laminar flow, which ignores the influence of red blood cells (RBCs). However, the nature of blood flow is a complex and non-Newtonian fluid composed of proteins, platelets, plasma and deformable cells, especially RBCs. The ability to change their shapes is essential to the proper functioning of RBCs in the microvasculature. Different shapes of RBCs have a great impact on the performance of blood flow. Changes in the properties and shapes of RBCs are often associated with different diseases, such as sickle cell anemia, diabetes, and malaria. Thus, it is highly important to establish a more realistic blood flow MC model considering the deformable cells. According to our previous study, the motion and adhesion of individual NPs are modelled through the Brownian adhesion dynamics. Subsequently, this paper establishes a particle-cell hybrid model in the flow-based MC, which focuses on the RBC deformation, aggregation, and dispersion in the blood suspension. Based on the state of the RBC deformation and aggregation in the vessels with different flow rates, this paper proposes a novel methodology for detecting the deformability of the cells. The blood state in terms of RBC deformability is determined by the difference in NPs' concentration at the receiving end., this paper sheds some light on the influence of RBCs on the motion of NPs, which provides new insights on the design of targeted drug delivery and the detection of vascular diseases.

Design Methodology of Passive In-Line Relays for Molecular Communication in Flow-Induced Microfluidic Channel.

Molecular communication is a bioinspired communication that enables macro-scale, micro-scale and nano-scale devices to communicate with each other. The molecular communication system is prone to severe signal attenuation, dispersion and delay, which leads to performance degradation as the distance between two communicating devices increases. To mitigate these challenges, relays are used to establish reliable communication in microfluidic channels. Relay assisted molecular communication systems can also enable interconnection among various entities of the lab-on-chip for sharing information. Various relaying schemes have been proposed for reliable molecular communication systems, most of which lack practical feasibility. Thus, it is essential to design and develop relays that can be practically incorporated into the microfluidic channel. This paper presents a novel design of passive in-line relay for molecular communication system that can be easily embedded in the microfluidic channel and operate without external energy. Results show that geometric modification in the microfluidic channel can act as a relay and restore the degraded signal up-to 28%.

Fluid dynamics-based distance estimation algorithm for macroscale molecular communication

Many species, from single-cell bacteria to advanced animals, use molecular communication (MC) to share information with each other via chemical signals. Although MC is mostly studied in microscale, new practical applications emerge in macroscale. It is essential to derive an estimation method for channel parameters such as distance for practical macroscale MC systems which include a sprayer emitting molecules as a transmitter (TX) and a sensor as the receiver (RX). Due to the similarity between sneezing/coughing and spraying mechanisms, these practical systems have the potential to be applied in modeling airborne pathogen (viruses, bacteria, etc.) transmission with a MC perspective where an infected human emitting pathogen-laden droplets is considered as a TX. In this paper, a novel approach based on fluid dynamics is proposed for the derivation of the distance estimation in practical MC systems. According to this approach, transmitted molecules are considered as moving and evaporating droplets in the MC channel. With this approach, the Fluid Dynamics-based Distance Estimation (FDDE) algorithm which predicts the propagation distance of the transmitted droplets by updating the diameter of evaporating droplets at each time step is proposed. FDDE algorithm is validated by experimental data. The results reveal that the distance can be estimated by the fluid dynamics approach which introduces novel parameters such as the volume fraction of droplets in a mixture of air and liquid droplets and the beamwidth of the TX. Furthermore, the effect of the evaporation is shown with the numerical results.

Molecular communication system with non-absorbing receiver

The molecules propagation via the molecular communication channel is governed by Fick’s law that describes movement of molecules based on the difference between concentration levels at the transmitter and at the receiver. If the receiver does not absorb all molecules sent, then the molecules stay in the channel influencing future transmission. This leads to accumulation of molecules meaning the channel has memory. The paper deals with developing the detection method for such a cumulative channel. By mapping the received signals and forming a trellis plot we were able to observe the received signal changes and design a detection method based on the trellis. In the paper, we simulate a molecular transmission, including absorption, inter symbol interference and noise, and their respective effects on the transmitted data.

Transfer Function Models for Cylindrical MC Channels With Diffusion and Laminar Flow

The analysis and design of advection-diffusion based molecular communication (MC) systems in cylindrical environments is of particular interest for applications such as micro-fluidics and targeted drug delivery in blood vessels. Therefore, the accurate modeling of the corresponding MC channel is of high importance. The propagation of particles in these systems is caused by a combination of diffusion and flow with a parabolic velocity profile, i.e., laminar flow. The propagation characteristics of the particles can be categorized into three different regimes: The flow dominant regime where the influence of diffusion on the particle transport is negligible, the dispersive regime where diffusion has a much stronger impact than flow, and the mixed regime where both effects are important. For the limiting regimes, i.e., the flow dominant and dispersive regimes, well-known solutions and approximations for particle transport exist. For the mixed regime, approximations, numerical techniques, and particle based simulations are employed. However, the few analytical models that are applicable in all three regimes impose significant constraints on the possible transmitter locations and particle release profiles. In this paper, we develop a more general analytical model for the advection-diffusion problem in cylindrical environments, which is applicable in all three regimes and accounts for general particle release models. The proposed model exhibits a higher accuracy than existing models and is based on a transfer function approach, where the main challenge is the incorporation of laminar flow. The properties of the proposed model are analyzed by numerical evaluation for different scenarios including the uniform and point release of particles. We provide a comparison with particle based simulations and existing analytical models from the literature to demonstrate the validity of the proposed analytical model.

Secrecy Optimization for Diffusion-Based Molecular Timing Channels

Security in the context of molecular communication systems is an important design aspect that has not attracted much attention till date. This letter analyzes the information-theoretic secrecy of diffusive molecular timing channels when the distance of the eavesdropper is assumed to be random and uniformly distributed. Using an existing upper bound on the timing channel capacity, we calculate the optimal secrecy rate and optimal transmission rate for Bob which would help in achieving an improved secrecy throughput performance. Based on this optimal rate, we calculate the maximum achievable throughput. We then use this formulation to minimize the generalized secrecy outage probability (GSOP) by simultaneously maximizing the average fractional equivocation and minimizing the average information leakage rate. The numerical results show that while choosing the system parameters, there is always a trade-off between different performance metrics like GSOP, average fractional equivocation, and average information leakage rate. The proposed secrecy optimization provides a robust understanding of the physical layer secrecy at the molecular level, enabling the design of secure molecular communication systems.

Bounds on the Constrained Capacity for the Diffusive Poisson Molecular Channel With Memory

This letter focuses on the analysis of a diffusion-based molecular communication (MC) system where the received signal is approximated as a Poisson random variable. Concentration shift keying (CSK) is used as the modulation technique for encoding information in the system. In particular, this work aims to study the performance of the MC system in terms of reliable information exchange for the channel with finite-state memory, which introduces intersymbol interference (ISI). The main objective is the derivation of analytical expressions for the upper and the lower bound of the constrained channel capacity for a range of values of the modulated symbols, i.e., for a number of different sets of amplitude levels of CSK modulation, and for various levels of ISI. In addition, the numerical evaluation of the derived expressions is presented. Results allow discussing the relationship between ISI level and achievable channel capacity. Moreover, numerical outcomes highlight how the estimation of the bounds is not affected by the presence of ISI in the case of binary CSK modulation, as the bounds remain quite tight.

Low Complex Receiver Design for Modified Inverse Source Coded Diffusion-Based Molecular Communication Systems

Diffusion Based Molecular Communication (DBMC) uses messenger molecules to transfer information between nanomachines. A major challenge for DBMC is Inter Symbol Interference (ISI), which is due to the diffusive nature of the molecular channel. By computing lower and upper bounds for the number of received molecules, in this letter we prove that ISI and Bit Error Rate (BER) of a DBMC system depend on a-priori probability of transmitted data. We derive the optimal value of the a-priori probability for which ISI and BER are minimized. A coding technique, called Modified Inverse Source Coding (MISC), is proposed to control the a-priori probability of the transmitted data. We also propose two low complexity receivers for MISC-DBMC. The first is a low complexity Reduced State Sequence Detector (RSSD) based on the Viterbi algorithm. The second is a computationally less intensive Decision Feedback based Maximum A-Posteriori (DF-MAP) threshold detector. Simulation results demonstrate that the DF-MAP receiver has a similar BER performance as that of the RSSD receiver in the ideal scenario, but practically it is limited by error propagation. Also, we show that the MISC-DBMC system using RSSD or DF-MAP receiver has better BER performance, increased range, and lower complexity compared to uncoded DBMC system.

Resource Allocation for Multiuser Molecular Communication Systems Oriented to the Internet of Medical Things.

Communication between nanomachines is still an important topic in the construction of the Internet of Bio-Nano Things (IoBNT). Currently, molecular communication (MC) is expected to be a promising technology to realize IoBNT. To effectively serve the IoBNT composed of multiple nanomachine clusters, it is imperative to study multiple-access MC. In this article, based on the molecular division multiple access technology, we propose a novel multiuser MC system, where information molecules with different diffusion coefficients are first employed. Aiming at the user fairness in the considered system, we investigate the optimization of molecular resource allocation, including the assignment of the types of molecules and the number of molecules of a type. Specifically, three performance metrics are considered, namely, min–max fairness for error probability, max–min fairness for achievable rate, and weighted sum-rate maximization. Moreover, we propose two assignment strategies for types of molecules, i.e., best-to-best (BTB) and best-to-worst (BTW). Subsequently, for a two-user scenario, we analytically derive the optimal allocation for the number of molecules when types of molecules are fixed for all users. In contrast, for a three-user scenario, we prove that the BTB and BTW schemes with the optimal allocation for the number of molecules can provide the lower and upper bounds on system performance, respectively. Finally, numerical results show that the combination of BTW and the optimal allocation for the number of molecules yields better performance than the benchmarks.

Information rate analysis of ASK-based molecular communication systems with feedback

In this paper we develop lower and upper bounds on the capacity of an amplitude shift keying (ASK)-based molecular communication (MC) system with feedback. Analyzing the effect of feedback on the performance of MC is motivated by the growing use of feedback in controlling drug delivery. Based on causal knowledge of the number of transmitted and received molecules, the input probability of symbols is adapted so as to maximize directed information in the molecular communication channel. We considered one dimensional channel with drift velocity caused by blood flow. In our system, molecules propagate in a fluid with a drift velocity; the receiver absorbs the molecule unless it is saturated (saturation models a limit on ligand binding). The input is limited by a toxicity constraint of injected molecules. We also study the effects of feedback on the achievable information rates in terms of the time delay in receiving the feedback. We show that, especially for higher values of toxicity constraint and sequence length, feedback, in terms of causal knowledge of the number of delivered molecules, improves performance of ASK-based molecular communication.

A Droplet-Based Signal Reconstruction Approach to Channel Modeling in Molecular Communication

In this paper, a novel fluid dynamics-based approach to channel modeling, which considers liquid droplets as information carriers instead of molecules in the molecular communication (MC) channel, is proposed for practical macroscale MC systems. This approach considers a two-phase flow which is generated by the interaction of droplets in liquid phase with air molecules in gas phase. Two-phase flow is combined with the signal reconstruction (SR) of the receiver (RX) to propose a channel model. The SR part of the model quantifies how the accuracy of the sensed molecular signal in its reception volume depends on the sensitivity response of the RX and the adhesion/detachment process of droplets. The proposed channel model is validated by employing experimental data.

On Molecular Flow Velocity Meters

Flow velocity is an important characteristic of the fluidic mediums. In this article, we introduce a molecular based flow velocity meter consisting of a molecule releasing node and a receiver that counts these molecules. We consider both flow velocity detection and estimation problems, which are employed in different applications. For the flow velocity detection, we obtain the maximum a posteriori (MAP) decision rule. To analyze the performance of the proposed flow velocity detector, we obtain the error probability, its Gaussian approximation and Chernoff information (CI) upper bound, and investigate the optimum and sub-optimum sampling times accordingly. We show that, for binary hypothesis, the sub-optimum sampling times using CI upper bound are the same. Further, the sub-optimum sampling times are close to the optimum sampling times. For the flow velocity estimation, we obtain the MAP and minimum mean square error (MMSE) estimators. We consider the mean square error (MSE) to investigate the error performance of the flow velocity estimators and obtain the Bayesian Cramer-Rao (BCR) and expected Cramer-Rao (ECR) lower bounds. Further, we obtain the optimum sampling times for each estimator. It is seen that the optimum sampling times for each estimator are nearly the same. The proposed flow velocity meter can be used to design a new modulation technique in molecular communication (MC), where information is encoded in the flow velocity of the medium instead of the concentration, type, or release time of the molecules. The setup and performance analysis of the proposed flow velocity detector and estimator for molecular communication system need further investigation.

Clock Synchronization for Mobile Molecular Communication Systems.

Molecular communication (MC) is a promising paradigm, which conveys messages at the nano- or micro- scale for information exchange by using molecules or particles as signal carriers. Clock synchronization between transmitters and receivers in MC systems plays an important role in information exchange and nanodevices' collaboration. The current research about the synchronization mainly focuses on fixed MC systems. However, the movements of transmitters and receivers commonly exist in MC systems. In this paper, two clock synchronization schemes, the least square method and the peak time method, are proposed to estimate the clock offset between a mobile transmitter and a mobile receiver in mobile MC systems. The synthesis time of information molecules is also taken into consideration in the proposed schemes, and by using different types of molecules, the influence of the synthesis time of molecules can be solved. The effects of the movement of receiver on the received signal are discussed. The performance of the proposed schemes is evaluated by simulations and discussed.

Optimal Detection Interval for Absorbing Receivers in Molecular Communication Systems With Interference

We consider a molecular communication system comprised of a transmitter, an absorbing receiver, and an interference source. Assuming amplitude modulation, we analyze the dependence of the bit error rate (BER) on the detection interval, which is the time within one transmission symbol interval during which the receiver is active to absorb and detect the number of information-carrying molecules. We then propose efficient algorithms to determine the optimal detection interval that minimizes the BER of the molecular communication system assuming no inter-symbol interference (ISI). Simulation and numerical evaluations are provided to highlight further insights into the optimal results. For example, we demonstrate that the optimal detection interval can be very small compared to the transmission symbol interval. Moreover, our numerical results show that significant BER improvements are achieved by using the optimal detection interval for systems without and with ISI.