Diffusion-based Molecular Communication System Research Articles

Assessing Molecular Throughput and Efficiency through Simulation in Diffusion-Based Molecular Communication

Objectives: This study investigates the correlation of critical factors influencing throughput and efficiency in diffusion-based molecular communication systems. Method: The study presents a simulation model for 3-D diffusion-based molecular communication, incorporating essential parameters such as molecule size, transmission rate, diffusion rate, and transmitter-receiver distance. Findings: Through comprehensive simulations, the study reveals the effects of different parameters on throughput and efficiency in diffusion-based molecular communication. It highlights the critical trade-offs associated with system design and optimization. The study reveals the key factors influencing the transmission capabilities, the receiver congestion, and the overall efficiency of the communication system. Novelty: In this study, we give a study overview of the latest work of performance metrics in the field of molecular communication. A novel algorithm is proposed to find the throughput and efficiency of molecular communication. The proposed framework analyzes the intricate relationship between system parameters and performance metrics, emphasizing the potential for system optimization. Our simulation work demonstrates how the model parameters influence the performance of the molecular communication system, providing insights for enhancing the system's performance in applications such as targeted drug delivery in the future. Keywords: Molecular Communication, Diffusion, Transmission Rate, Throughput, Efficiency

An Optimized Energy-Harvesting Transmission Scheme for Diffusion-Based Molecular Communications.

In this paper, we propose an optimized transmission scheme with energy-harvesting for a diffusion-based molecular communication system composed by nano-devices fed by piezoelectric nanogenerators. To this end, we firstly derive a system model that analytically describes the mean and the variance of the aggregated noise at the output of the receiver and the achievable Bit Error Rate. Then, we formulate an optimization problem that minimizes an objective function defined as a linear combination of the probability that the voltage across the ultra-nanocapacitor of the transmitter goes under a target value and the number of enqueued packets. We solve this problem by considering the actual energy budget, a target Bit Error Rate, and the need to achieve the simplicity of the transmitter as constraints. Finally, we use computer simulations to validate the formulated analytical models and demonstrate the unique ability of the proposed approach to guarantee BER = 5% and BER = 10% for communication distances up to 47μm and 50μm, respectively, while registering better results against baseline scenarios.

Feedback-Controlled Adaptive Signal Detection Scheme for Diffusion-Based Molecular Communication Systems

This paper proposes a feedback-controlled adaptive method for detecting signals in diffusion-based molecular communication (MC) systems. Signal detection via a receiver nanomachine is a critical challenge for the exchange of information in MC systems. Incorrect estimations or small errors in signal detection can lead to high data detection errors. Existing methods for improving detection performance require high time costs or computational complexity. This paper proposes a simple and practical method that enables receiver nanomachines to automatically estimate signal detection times according to the measured molecular concentrations and weighted feedback errors. The proposed method adjusts the detection time even when the initial parameter values of the system are unknown to the receiver nanomachines. Simulations were performed to evaluate the bit error rate performance of the proposed and existing methods in terms of different data rates, transmission distances, and estimation error lengths under different initial conditions. The simulation results reveal that the implementation of the proposed method is simpler and demonstrates superior performance compared with that of existing methods.

Channel Characterization and Performance of a 3-D Molecular Communication System With Multiple Fully-Absorbing Receivers

Molecular communication (MC) can enable the transfer of information between nanomachines using molecules as the information carrier. In MC systems, multiple receiver nanomachines often co-exist in the same communication channel to serve common or different purposes. However, the analytical channel model for a system with multiple fully absorbing receivers (FARs), which is significantly different from the single FAR system due to the mutual influence of FARs, does not exist in the literature. The analytical channel model is essential in analyzing systems with multiple FARs, including MIMO, SIMO, and cognitive molecular communication systems. In this work, we derive an analytical expression for the hitting probability of a molecule emitted from a point source on each FAR in a diffusion-based MC system with <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$N$ </tex-math></inline-formula> FARs. Using these expressions, we derive the channel model for a SIMO system with a single transmitter and multiple FARs arranged in a uniform circular array (UCA). We then analyze the communication performance of this SIMO system under different cooperative detection schemes and develop several interesting insights.

Performance Analysis and Receiver Design of Spatio-Temporal Coded Modulation Scheme for Diffusion-Based Molecular MIMO Systems

Diffusion-based molecular communication (DBMC) systems allow messenger molecules to reach the intended receiver using laws of diffusion. The Brownian motion of messenger molecules introduces delay in the system causing the problem of inter-symbol interference (ISI). Along with ISI, the problem of inter-link interference (ILI) comes into picture in the diffusion-based molecular multiple-input multiple-output (DB-MoMIMO) systems. To combat against ISI and ILI issues, index modulation (IM) approaches are recently proposed in the literature for improving the performance of DB-MoMIMO systems. Despite the existence of IM approaches, problems of ISI and ILI still persist due to the slow random motion of molecules in DB-MoMIMO channels. Motivated by this, a novel coded modulation approach called molecular spatio-temporal coded modulation (MSTCM) is proposed in this paper which shows promising improvement in the performance of DB-MoMIMO systems by encoding the information both in space and time axes. Further, if system has access to two types of molecules, the dual-type modulation schemes are discussed for the same. Moreover, the encoder and decoder designs for the proposed mapping strategy are provided. In addition, a theoretical bit error rate expression for the MSTCM scheme is derived and simulation results are shown to corroborate the theoretical ones.

Wiener and Kalman Detection Methods for Molecular Communications.

Diffusion-based molecular communication system (DBMC) is a system in which information-carrying molecules are sent from the transmitter and passively transported to the receiver in a fluid environment. Nanomachines, which are the main part of this system, have limited processing capacity. Besides, at the receiver, high inter-symbol interference (ISI) occurs due to free movement of molecules and the variance of the observation noise is signal dependent. Hence, it is important to design high-performance and low complexity receiver detection methods. In this paper, finite impulse response (FIR) Wiener filter is introduced for the first time, which has considerably less computational complexity compared to the minimum mean square error (MMSE) algorithm proposed in the literature. Moreover, extended Kalman filter is introduced for the first time to DBMC as a receiver detection method. Finally, Viterbi algorithm is modified and used as a benchmark for performance evaluation.

A Simple Queuing Model for Molecular Communications Receivers.

The complexity of molecular communications system, involving a massive number of interacting entities, makes scalability a fundamental property of simulators and modeling tools. A typical scenario is that of targeted drug delivery systems, which makes use of biological nanomachines close to a biological target, able to release molecules in the diseased area. In this paper, we propose a simple but reliable receiver model for diffusion-based molecular communication systems tackling the time needed for analyzing such a system. The proposed model consists of using an equivalent markovian queuing model, which reproduces the aggregate behavior of thousands of receptors spread over the receiver surface. It takes into account not only the fact that the absorption of molecules can occur only through receptors, but also that absorption is not an instantaneous process and may require a significant time during which the receptor is not available to bind to other molecules. Our results, expressed in terms of number of absorbed molecules and average number of busy receptors, demonstrate that the proposed approach is in good agreement with results obtained through particle-based simulations of a large number of receptors, although the time taken for obtaining the results with the proposed model is an order of magnitudes lower than the simulation time. We believe that this model can be the precursor of novel class of models based on similar principles that allow realizing reliable simulations of much larger systems.

Low complexity receiver design for time-varying Poisson molecular communication channels with memory

This paper introduces novel approaches for the design of the linear filter and the detection algorithms in unbounded advection diffusion-based molecular communication systems affected by inter-symbol interference. The received signal samples are modeled as Poisson random variables with memory where the effect of enzymatic reactions is also included. A main characteristic of the new filter design is to allow for a real-time computation of the filter's coefficients. For the detection of the transmitted symbols, we define an averaging method suitable for time-varying channels with finite memory length. In this paper the mean value of the Poisson channel is varying with time and we quantify the memory length with a finite number, from receiver point of view. The computational burden of the proposed approaches is evaluated in terms of number of required operations and their performance is evaluated in terms of bit error rate for different sets of parameters. We show that the proposed design of the filter and of the detection algorithms enables us to achieve a performance comparable to that of the state of the art approaches in relation to their simplicity.

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.

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.

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.

Iterative Signal Detection for Diffusion-Based Molecular Communications

Inter-symbol interference (ISI) due to slow-moving molecules is one of the key limitations affecting throughput of a diffusion based molecular communication (MC). In this paper, we propose novel ISI mitigation approaches for diffusion based MC systems. The first approach uses weighted sum (WS) to enhance the received signal-to-ISI plus noise ratio (SINR) by exploiting the apriori characteristics of the diffusion channel impulse response. In the second approach, an iterative method estimates the ISI in a frame using the block-wise data symbol detection and subtracts this estimated ISI before the signal detection. Both the proposed methods improve the MC system’s performance as compared to the conventional signal detection method. Further, we have analyzed the combined WS and iterative method, resulting in further improvement in the performance. Furthermore, the effect of various system parameters such as frame duration, diffusion coefficient, and the distance between transmitter and receiver is analyzed.

A Lean Control Theoretic Approach to Energy-Harvesting in Diffusion-Based Molecular Communications

This letter focuses on a diffusion-based molecular communication system, fed by a nanoscale energy-harvesting mechanism, and conceives a power control mechanism based on feedback control theory. Specifically, the load current drained by the transmitter interface is set proportionally to the available energy harvested from the environment by using a closed-loop control scheme. The resulting system is analytically described through a nonlinear state equation, that jointly considers harvesting and discharging processes. Its asymptotic stability is evaluated around the equilibrium point, while considering some technological constraints. Finally, a numerical example is discussed to clearly show the behavior of the proposed approach in conceivable scenarios.

Equilibrium Signaling: Molecular Communication Robust to Geometry Uncertainties

A basic property of any diffusion-based molecular communication system is the geometry of the enclosing container. In particular, the geometry influences the system's behavior near the boundary and in all existing modulation schemes governs receiver design. However, it is not always straightforward to characterize the geometry of the system. This is particularly the case when the molecular communication system operates in scenarios where the geometry may be complex or dynamic. In this article, we propose a new scheme-called equilibrium signaling-which is robust to uncertainties in the geometry of the fluid boundary. In particular, receiver design only depends on the relative volumes of the transmitter or receiver, and the entire container. Our scheme relies on reversible reactions in the transmitter and the receiver, which ensure the existence of an equilibrium state into which information is encoded. In this case, we derive near optimal detection rules and develop a simple and effective estimation method to obtain the container volume. We also show that equilibrium signaling can outperform classical modulation schemes, such as concentration shift keying, under practical sampling constraints imposed by biological oscillators.

Nanomachine Localization in a Diffusive Molecular Communication System

The information-bearing molecules are used for communication among nanomachines in a diffusion-based molecular communication (DMC) system. The location of the nanomachine is needed for improving the performance of a DMC system. In the literature, only the distance between a transmitter nanomachine (TN) and a receiver nanomachine is estimated. In contrast, an iterative maximum likelihood estimate of the nanomachine location is computed herein. Notably, both the signal-dependent noise and intersymbol interference (ISI) effects are considered for nanomachine localization. Further, the nanomachine localization is performed, when the locations of the receiver nanomachine are both known and unknown. Additionally, the condition for the unique localizability of the TN and the bound of the proposed estimator are obtained. The results illustrate the effectiveness of the proposed method.

Analysis and Design of Two-Hop Diffusion-Based Molecular Communication With Ligand Receptors

This work presents a performance analysis of a decode-and-forward (DF) relay-assisted diffusion-based molecular communication system consisting of one nanotransmitter, one nanoreceiver and one nanotransceiver acting as relay. We consider cases using one molecule in our two-hop relay network (1M2H), and using two molecules (2M2H). Inspired by the biological signal transduction systems, the ligand-receptor binding mechanism is introduced for the receptors on the surface of receiver. Inter-symbol interference (ISI) and self-interference (SI) can be identified as the performance-limiting effects in our relaying network. The number of received molecules can be approximated by the normal distribution, and using this approximation, a closed-form expression of bit error probability for the relay-assisted network is derived. Then, we put forward an optimization problem for minimizing the bit error probability, and solve it using an algorithm based on the gradient descent to find the optimal detection threshold. In addition, the expression of channel capacity is obtained for two-hop molecular communication with ligand receptors. Numerical results show that the 2M2H network has greater capacity than the 1M2H network.

Channel Characterization for 1-D Molecular Communication With Two Absorbing Receivers

This letter develops a one-dimensional (1D) diffusion-based molecular communication system to analyze channel responses between a single transmitter (TX) and two fully-absorbing receivers (RXs). Incorporating molecular degradation in the environment, rigorous analytical formulas for i) the fraction of molecules absorbed, ii) the corresponding hitting rate, and iii) the asymptotic fraction of absorbed molecules as time approaches infinity at each RX are derived when an impulse of molecules are released at the TX. By using particle-based simulations, the derived analytical expressions are validated. Simulations also present the distance ranges of two RXs that do not impact molecular absorption of each other, and demonstrate that the mutual imfluence of two active RXs reduces with the increase in the degradation rate.

A Novel Time-Based Modulation Scheme in Time-Asynchronous Channels for Molecular Communications.

In this paper, a novel time-based modulation scheme is proposed in the time-asynchronous channel for diffusion-based molecular communication systems with drift. Based on this modulation scheme, we demonstrate that the sample variance of information molecules' arrival time approximately follows a noncentral chi-squared distribution. According to its conditional probability density function (PDF), the asynchronous receiver designs are deduced based on the maximum likelihood (ML) detection, with or without background noise in the channel environment. Since the proposed schemes can be applied to the case of transmitting multiple information molecules, simulation results reveal that the bit error ratio (BER) performance improves with the increase of the number of released information molecules per bit. Furthermore, when the background noise is not negligible, our proposed asynchronous scheme outperforms the asynchronous modulation techniques based on encoding information on the time between two consecutive release of information molecules.

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.