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A biofilm is a microbial city. It consists of bacteria embedded in an extracellular polymeric substance (EPS) that functions as a protective barrier. Quorum sensing (QS) is a method of bacterial communication, where autoinducers (AIs) propagate via diffusion through the EPS and water channels within the biofilm. This diffusion process is anisotropic due to varying densities between the EPS and water channels. This study introduces a 2D anisotropic diffusion model for molecular communication (MC) within biofilms, analyzing information propagation between a point-to-point transmitter (TX) and receiver (RX) in bounded space. The channel impulse response is derived using Green's function for concentration (GFC) and is validated with particle-based simulation (PBS). The outcomes reveal similar results for both isotropic and anisotropic diffusion when the TX is centrally located due to symmetry. However, anisotropic conditions lead to greater diffusion peaks when the TX is positioned off-center. Additionally, the propagation of AIs is inversely proportional to both overall biofilm size and and diffusion coefficient values. It is hypothesized that anisotropic diffusion supports faster responses to hostile environmental changes because signals can propagate faster from the edge of the biofilm to the center.

Recent molecular communication (MC) research has integrated more detailed computational models to capture the dynamics of practical biophysical systems. This research focuses on developing realistic models for MC transceivers inspired by spheroids - three-dimensional cell aggregates commonly used in organ-on-chip experimental systems. Potential applications that can be used or modeled with spheroids include nutrient transport in an organ-on-chip system, the release of biomarkers or reception of drug molecules by a cancerous tumor site, or transceiver nanomachines participating in information exchange. In this paper, a simple diffusive MC system is considered where a spheroidal transmitter and receiver are in an unbounded fluid environment. These spheroidal antennas are modeled as porous media for diffusive signaling molecules, then their boundary conditions and effective diffusion coefficients are characterized. Further, for either a point source or spheroidal transmitter, Green's function for concentration (GFC) outside and inside the receiving spheroid is analytically derived and formulated in terms of an infinite series and confirmed by a particle-based simulator (PBS). The provided GFCs enable computation of the transmitted and received signals in the spheroidal communication system. This study shows that the porous structure of the receiving spheroid amplifies diffusion signals but also disperses them, thus there is a trade-off between porosity and information transmission rate. Also, the results reveal that the porous arrangement of the transmitting spheroid not only disperses the received signal but also attenuates it. System performance is also evaluated in terms of bit error rate (BER). Decreasing the porosity of the receiving spheroid is shown to enhance system performance. Conversely, reducing the porosity of the transmitting spheroid can adversely affect system performance., Comment: 14 pages; 10 figures; accepted to appear in IEEE Transactions on Molecular, Biological, and Multi-Scale Communications. This work was presented in part at the 2023 IEEE International Conference on Communication arXiv:2302.09265

Using agar plates hosting a 2D cell population stimulated with signaling molecules is crucial for experiments such as gene regulation and drug discovery in a wide range of biological studies. In this paper, a biophysical model is proposed that incorporates droplet soaking, diffusion of molecules within agar, cell growth over an agar surface, and absorption of signaling molecules by cells. The proposed model describes the channel response and provides valuable insights for designing experiments more efficiently and accurately. The molecule release rate due to droplet soaking into agar, which is characterized and modeled as the source term for the diffusion model, is derived. Furthermore, cell growth is considered over the surface, which dictates the dynamics of signaling molecule reactions and leads to a variable boundary condition. As a case study, genetically-modified $E.\,coli$ bacteria are spread over the surface of agar and Isopropyl-beta-D thiogalactopyranoside (IPTG) is considered as a signaling molecule. IPTG droplets are dropped onto the bacteria-covered agar surface. The parameters for the IPTG molecule release rate as a diffusion source into the agar are estimated from this experiment. Then, a particle-based simulator is used to obtain the spatio-temporal profile of the signaling molecules received by the surface bacteria. The results indicate that the number of molecules reacting with or absorbed by bacteria at different locations on the surface could be widely different, which highlights the importance of taking this variation into account for biological inferences., Comment: Submitted to ACM Nanocom 2023 conference

Realistic models of the components and processes are required for molecular communication (MC) systems. In this paper, a spheroidal receiver structure is proposed for MC that is inspired by the 3D cell cultures known as spheroids being widely used in organ-on-chip systems. A simple diffusive MC system is considered where the spheroidal receiver and a point source transmitter are in an unbounded fluid environment. The spheroidal receiver is modeled as a porous medium for diffusive signaling molecules, then its boundary conditions and effective diffusion coefficient are characterized. It is revealed that the spheroid amplifies the diffusion signal, but also disperses the signal which reduces the information communication rate. Furthermore, we analytically formulate and derive the concentration Green's function inside and outside the spheroid in terms of infinite series-forms that are confirmed by a particle-based simulator (PBS).

Abnormality detection and localization (ADL) have been studied widely in wireless sensor networks (WSNs) literature, where the sensors use electromagnetic waves for communication. Molecular communication (MC) has been introduced as an alternative approach for ADL in particular areas such as healthcare, being able to tackle the shortcomings of conventional WSNs, such as invasiveness, bio-incompatibility, and high energy consumption. In this paper, we introduce a general framework for MC-based ADL, which consists of multiple tiers for sensing the abnormality and communication between different agents, including the sensors, the fusion center (FC), the gateway (GW), and the external node (e.g., a local cloud), and describe each tier and the agents in this framework. We classify and explain different abnormality recognition methods, the functional units of the sensors, and different sensor features. Further, we describe different types of interfaces required for converting the internal and external signals at the FC and GW. Moreover, we present a unified channel model for the sensing and communication links. We categorize the MC-based abnormality detection schemes based on the sensor mobility, cooperative detection, and cooperative sensing/activation. We also classify the localization approaches based on the sensor mobility and propulsion mechanisms and present a general framework for the externally-controllable localization systems. Finally, we present some challenges and future research directions to realize and develop MC-based systems for ADL. The important challenges in the MC-based systems lie in four main directions as implementation, system design, modeling, and methods, which need considerable attention from multidisciplinary perspectives., Comment: *Ali Etemadi and Maryam Farahnak-Ghazani are co-first authors

Diffusive molecular communication (DMC) is envisioned as a promising approach to help realize healthcare applications within bounded biological environments. In this paper, a DMC system within a biological spherical environment is considered, inspired by bounded biological sphere-like structures throughout the body. As a biological environment, it is assumed that the inner surface of the sphere's boundary is fully covered by biological receptors that may irreversibly react with hitting molecules. Moreover, information molecules diffusing in the sphere may undergo a degradation reaction and be transformed to another molecule type. Concentration Green's function (CGF) of diffusion inside this environment is analytically obtained in terms of a convergent infinite series. By employing the obtained CGF, the information channel between transmitter and transparent receiver of DMC in this environment is characterized. Interestingly, it is revealed that the information channel is reciprocal, i.e., interchanging the position of receiver and transmitter does not change the information channel. Our results indicate that the conventional simplifying assumption that the environment is unbounded may lead to an inaccurate characterization in such biological environments., Comment: arXiv admin note: text overlap with arXiv:1807.02683

Diffusion-based molecular communication (DMC) is one of the most promising approaches for realizing nano-scale communications for healthcare applications. The DMC systems in in-vivo environments may encounter biological entities that release molecules identical to the molecules used for signaling as part of their functionality. Such entities in the environment act as external noise sources from the DMC system's perspective. In this paper, the release of molecules by biological external noise sources is particularly modeled as a compound Poisson process. The impact of compound Poisson noise sources (CPNSs) on the performance of a point-to-point DMC system is investigated. To this end, the noise from the CPNS observed at the receiver is characterized. Considering a simple on-off keying (OOK) modulation and formulating symbol-by-symbol maximum likelihood (ML) detector, the performance of DMC system in the presence of the CPNS is analyzed. For special case of CPNS in high-rate regime, the noise received from the CPNS is approximated as a Poisson process whose rate is normally distributed. In this case, it is proved that a simple single-threshold detector (STD) is an optimal ML detector. Our results reveal that in general, adopting the conventional simple homogeneous Poisson noise model may lead to overly optimistic performance predictions, if a CPNS is present.

Diffusive molecular communication (DMC) is one of the most promising approaches for realizing nano-scale communications in biological environments for healthcare applications. In this paper, a DMC system in biological cylindrical environment is considered, inspired by blood vessel structures in the body. The internal surface of the cylinder boundary is assumed to be covered by the biological receptors which may irreversibly react with hitting molecules. Also, information molecules diffusing in the fluid medium are subject to a degradation reaction and flow. The concentration Green's function of diffusion in this environment is analytically derived which takes into account asymmetry in all radial, axial and azimuthal coordinates. Employing obtained Green's function, information channel between transmitter and transparent receiver of DMC is characterized. To evaluate the DMC system in the biological cylinder, a simple on-off keying modulation scheme is adopted and corresponding error probability is derived. Particle based simulation results confirm the proposed analysis. Also, the effect of different system parameters on the concentration Green's function are examined. Our results reveal that the degradation reaction and the boundary covered by biological receptors may be utilized to mitigate intersymbol interference and outperform corresponding error probability.

This paper studies the problem of receiver modeling in molecular communication systems. We consider the diffusive molecular communication channel between a transmitter nano-machine and a receiver nano-machine in a fluid environment. The information molecules released by the transmitter nano-machine into the environment can degrade in the channel via a first-order degradation reaction and those that reach the receiver nano-machine can participate in a reversible bimolecular reaction with receiver receptor proteins. Thereby, we distinguish between two scenarios. In the first scenario, we assume that the entire surface of the receiver is covered by receptor molecules. We derive a closed-form analytical expression for the expected received signal at the receiver, i.e., the expected number of activated receptors on the surface of the receiver. Then, in the second scenario, we consider the case where the number of receptor molecules is finite and the uniformly distributed receptor molecules cover the receiver surface only partially. We show that the expected received signal for this scenario can be accurately approximated by the expected received signal for the first scenario after appropriately modifying the forward reaction rate constant. The accuracy of the derived analytical results is verified by Brownian motion particle-based simulations of the considered environment, where we also show the impact of the effect of receptor occupancy on the derived analytical results., Comment: 15 pages, 10 figures, 1 appendix. Accepted for publication in IEEE Transactions on NanoBioscience. (Author's comment: Manuscript submitted June 03, 2016; accepted August 23, 2016. This article is the extended version of the conference paper arXiv:1512.06726)

In diffusion-based molecular communication (DMC), one important functionality of a transmitter nano-machine is signal modulation. In particular, the transmitter has to be able to control the release of signaling molecules for modulation of the information bits. An important class of control mechanisms in natural cells for releasing molecules is based on ion channels which are pore-forming proteins across the cell membrane whose opening and closing may be controlled by a gating parameter. In this paper, a modulator for DMC based on ion channels is proposed which controls the rate at which molecules are released from the transmitter by modulating a gating parameter signal. Exploiting the capabilities of the proposed modulator, an on-off keying modulation scheme is introduced and the corresponding average modulated signal, i.e., the average release rate of the molecules from the transmitter, is derived in the Laplace domain. By making a simplifying assumption, a closed-form expression for the average modulated signal in the time domain is obtained which constitutes an upper bound on the total number of released molecules regardless of this assumption. The derived average modulated signal is compared to results obtained with a particle based simulator. The numerical results show that the derived upper bound is tight if the number of ion channels distributed across the transmitter (cell) membrane is small., Comment: This paper is an extended version of a paper submitted to IEEE Globecom 2016

A diffusion molecular channel is a channel with memory, as molecules released into the medium hit the receptors after a random delay. Coding over the diffusion channel is performed by choosing the type, intensity, or the released time of molecules diffused in the environment over time. To avoid intersymbol interference (ISI), molecules of the same type should be released at time instances that are sufficiently far apart. This ensures that molecules of a previous transmission are faded in the environment, before molecules of the same type are reused for signaling. In this paper, we consider ISI-free time-slotted modulation schemes. The maximum reliable transmission rate for these modulations is given by the constrained coding capacity of the graph that represents the permissible transmission sequences. However, achieving the constrained coding capacity requires long blocklengths and delays at the decoder, making it impractical for simple nanomachines. The main contribution of this paper is to consider modulations with small delay (short blocklength) and show that they get very close to constrained coding capacity.

In this paper, the capacity of a diffusion based molecular communication network under the model of a Linear Time Invarient-Poisson (LTI-Poisson) channel is studied. Introduced in the context of molecular communication, the LTI-Poisson model is a natural extension of the conventional memoryless Poisson channel to include memory. Exploiting prior art on linear ISI channels, a computable finite-letter characterization of the capacity of single-hop LTI-Poisson networks is provided. Then, the problem of finding more explicit bounds on the capacity is examined, where lower and upper bounds for the point to point case are provided. Furthermore, an approach for bounding mutual information in the low SNR regime using the symmetrized KL divergence is introduced and its applicability to Poisson channels is shown. To best of our knowledge, the first non-trivial upper bound on the capacity of Poisson channel with a maximum transmission constraint in the low SNR regime is found. Numerical results show that the proposed upper bound is of the same order as the capacity in the low SNR regime.

A key pre-distribution scheme (KPS) based on multiple codewords of block codes is presented for wireless sensor networks. The connectivity and security of the proposed KPS, quantified in terms of probabilities of sharing common keys for communications of pairs of nodes and their resilience against colluding nodes, are analytically assessed. The analysis is applicable to both linear and nonlinear codes and is simplified in the case of maximum distance separable codes. It is shown that the multiplicity of codes significantly enhances the security and connectivity of KPS at the cost of a modest increase of the nodes storage. Numerical and simulation results are provided, which sheds light on the effect of system parameters of the proposed KPS on its complexity and performance. Specifically, it is shown that the probability of resilience of secure pairs against collusion of other nodes only reduces slowly as the number of colluding nodes increase.

In this paper, a diffusion-based molecular communication channel between two nano-machines is considered. The effect of the amount of memory on performance is characterized, and a simple memory-limited decoder is proposed and its performance is shown to be close to that of the best possible imaginable decoder (without any restriction on the computational complexity or its functional form), using Genie-aided upper bounds. This effect is specialized for the case of Molecular Concentration Shift Keying; it is shown that a four-bits memory achieved nearly the same performance as infinite memory. Then a general class of threshold decoders is considered and shown not to be optimal for Poisson channel with memory, unless SNR is higher than a value specified in the paper. Another contribution is to show that receiver sampling at a rate higher than the transmission rate, i.e., a multi-read system, can significantly improve the performance. The associated decision rule for this system is shown to be a weighted sum of the samples during each symbol interval. The performance of the system is analyzed using the saddle point approximation. The best performance gains are achieved for an oversampling factor of three., Comment: Submitted to JSAC

In this letter, we propose a new molecular modulation scheme for nanonetworks. To evaluate the scheme we introduce a more realistic system model for molecule dissemination and propagation processes based on the Poisson distribution. We derive the probability of error of our proposed scheme as well as the previously introduced schemes, including concentration and molecular shift keying modulations by taking into account the error propagation effect of previously decoded symbols. Since in our scheme the decoding of the current symbol does not depend on the previously transmitted and decoded symbols, we do not encounter error propagation; and so as our numerical results indicate, the proposed scheme outperforms the previously introduced schemes. We then introduce a general molecular communication system and use information theoretic tools to derive fundamental limits on its probability of error.