Molecular Communication Research Articles

Cell signaling error control for reliable molecular communications

Molecular communication (MC) allows implantable devices to communicate using biological data-transmission principles (e.g., molecules as information carriers). However, MC faces significant challenges due to molecular noise, which leads to increased communication errors. Thus, error control techniques become critical for reliable intra-body networks. The noise management and error control in these networks must be based on the characterization of the environment dynamics, i.e., characteristics that increase noise, such as the stochastic behavior of the intercellular channels and the presence of pathologies that affect communication. This work proposes an adaptive error control technique for cell signaling–based MC channels (CELLECs). Using an information-theoretic approach, CELLEC mitigates errors in cellular channels with varying noise conditions. The characteristics of the cellular environment and different noise sources are modeled to evaluate the proposal. The additive white Gaussian tissue noise (AWGTN) produced by stochastic chemical reactions is theorized for healthy cells. The MC model also considers the noise of cells affected by one pathology that disrupts cells’ molecular equilibrium and causes them to become reactive (i.e., Alzheimer’s disease). Analyses show that reactive cells have a higher signal-to-noise ratio (21.4%) and path loss (33.05%) than healthy cells, highlighting the need for an adaptive technique to deal with cellular environment variability. Results show that CELLEC improves communication channel performance by lowering the bit error rate (18%).

Energy Allocation for Multiuser Cooperative Molecular Communication Systems in Internet of Bio-Nano Things

Energy Allocation for Multiuser Cooperative Molecular Communication Systems in Internet of Bio-Nano Things

Optimizations of Multi-hop Cooperative Molecular Communication in Cylindrical Anomalous-Diffusive Channel

Optimizations of Multi-hop Cooperative Molecular Communication in Cylindrical Anomalous-Diffusive Channel

Connexin Gap Junction Channels and Hemichannels: Insights from High-Resolution Structures.

Connexins (Cxs) are a family of integral membrane proteins, which function as both hexameric hemichannels (HCs) and dodecameric gap junction channels (GJCs), behaving as conduits for the electrical and molecular communication between cells and between cells and the extracellular environment, respectively. Their proper functioning is crucial for many processes, including development, physiology, and response to disease and trauma. Abnormal GJC and HC communication can lead to numerous pathological states including inflammation, skin diseases, deafness, nervous system disorders, and cardiac arrhythmias. Over the last 15 years, high-resolution X-ray and electron cryomicroscopy (cryoEM) structures for seven Cx isoforms have revealed conservation in the four-helix transmembrane (TM) bundle of each subunit; an αβ fold in the disulfide-bonded extracellular loops and inter-subunit hydrogen bonding across the extracellular gap that mediates end-to-end docking to form a tight seal between hexamers in the GJC. Tissue injury is associated with cellular Ca2+ overload. Surprisingly, the binding of 12 Ca2+ ions in the Cx26 GJC results in a novel electrostatic gating mechanism that blocks cation permeation. In contrast, acidic pH during tissue injury elicits association of the N-terminal (NT) domains that sterically blocks the pore in a "ball-and-chain" fashion. The NT domains under physiologic conditions display multiple conformational states, stabilized by protein-protein and protein-lipid interactions, which may relate to gating mechanisms. The cryoEM maps also revealed putative lipid densities within the pore, intercalated among transmembrane α-helices and between protomers, the functions of which are unknown. For the future, time-resolved cryoEM of isolated Cx channels as well as cryotomography of GJCs and HCs in cells and tissues will yield a deeper insight into the mechanisms for channel regulation. The cytoplasmic loop (CL) and C-terminal (CT) domains are divergent in sequence and length, are likely involved in channel regulation, but are not visualized in the high-resolution X-ray and cryoEM maps presumably due to conformational flexibility. We expect that the integrated use of synergistic physicochemical, spectroscopic, biophysical, and computational methods will reveal conformational dynamics relevant to functional states. We anticipate that such a wealth of results under different pathologic conditions will accelerate drug discovery related to Cx channel modulation.

Interactive transcriptome analyses of Northern Wild Rice (Zizania palustris L.) and Bipolaris oryzae show convoluted communications during the early stages of fungal brown spot development.

Fungal diseases, caused mainly by Bipolaris spp., are past and current threats to Northern Wild Rice (NWR) grain production and germplasm preservation in both natural and cultivated settings. Genetic resistance against the pathogen is scarce. Toward expanding our understanding of the global gene communications of NWR and Bipolaris oryzae interaction, we designed an RNA sequencing study encompassing the first 12 h and 48 h of their encounter. NWR activated numerous plant recognition receptors after pathogen infection, followed by active transcriptional reprogramming of signaling mechanisms driven by Ca2+ and its sensors, mitogen-activated protein kinase cascades, activation of an oxidative burst, and phytohormone signaling-bound mechanisms. Several transcription factors associated with plant defense were found to be expressed. Importantly, evidence of diterpenoid phytoalexins, especially phytocassane biosynthesis, among expression of other defense genes was found. In B. oryzae, predicted genes associated with pathogenicity including secreted effectors that could target plant defense mechanisms were expressed. This study uncovered the early molecular communication between the NWR-B. oryzae pathosystem, which could guide selection for allele-specific genes to boost NWR defenses, and overall aid in the development of more efficient selection methods in NWR breeding through the use of the most virulent fungal isolates.

Molecular communication data augmentation and deep learning based detection

This manuscript presents a novel model for generating synthetic data for a biological molecular communication (MC) system to train a Neural Network (NN) for the purpose of discriminating transmitted bits. To achieve this, a deep learning algorithm was trained using the synthetic data and tested against experimentally measured data. The polynomial curve fitting coefficients are chosen as features. The featurization stage is followed by a NN that captures different aspects of the temporal correlation of the received signals. The real data was collected from an MC testbed that employed transfected Escherichia coli (E. coli) bacteria expressing the light-driven proton pump gloeorhodopsin from Gloeobacter violaceus. By stimulating the bacteria with externally controlled light, protons were secreted, which changed the pH level of the environment. A pH detector was then used to measure the pH of the environment. We propose the use of a deep convolutional neural network to detect the transmitted bits. This paper discusses the data augmentation, processing, and NNs that are pertinent to practical MC problems. The trained algorithm demonstrated an accuracy of over 99.9% in detecting transmitted bits from received signals at a bit rate of 1 bit/min, without requiring any specific knowledge of the underlying channel.

Diffusive molecular communication for bacterium propagation over human gut track

Diffusive molecular communication for bacterium propagation over human gut track

Wireless Body Area Nanonetworks via Vascular Molecular Communication.

Advancements in biotechnology and molecular communication have enabled the utilization of nanomachines in Wireless Body Area Networks (WBAN2) for applications such as drug delivery, cancer detection, and emergency rescue services. To study these networks effectively, it is essential to develop an ideal propagation model that includes the channel response between each pair of in-range nanomachines and accounts for the interference received at each receiver node. In this paper, we employ an advection-diffusion equation to obtain a deterministic channel matrix through a vascular WBAN2. Additionally, the closed forms of inter-symbol interference (ISI) and co-channel interference (CCI) are derived for both full duplex (FDX) and half duplex transmission (HDX) modes. By applying these deterministic formulations, we then present the stochastic equivalents of the ideal channel model and interference to provide an innovative communication model by simultaneously incorporating CCI, ISI, and background noise. Finally, we evaluate the results with numerous experiments and use signal-to-interference-plus-noise ratio (SINR) and capacity as metrics.

Fabrication and simulation of a microvalve for molecular communication control on a chip

In recent years, microvalves have become increasingly significant in microfluidic structures. In microfluidic devices, these microvalves are crucial to controlling fluid flow. Due to their ability to precisely manipulate and adjust the fluid, these structures are more efficient in applications, particularly in medicine, drug delivery, protein analysis, microscale communication, and chemical processes. Utilizing a numerical model for the design and fabrication of a microvalve results in the development of a more optimized and efficient structure. Microvalves can be generally divided into active and passive categories. This research focuses on the design and fabrication of a pneumatic microvalve, which falls under the category of active microvalves. This structure has two distinct chambers that allow for microscale communication. The microvalve is constructed using two layers, where the upper layer controls the lower layer, which contains fluid flow through pneumatic pressure. The performance of the system was evaluated through experimental analysis. The microchannel passage remained obstructed when the flow rates were set to 0.2 ml/h and when maintaining a constant pump pressure of 15 psi. However, the fluid flow is connected even when the pressure is cut off. We believe this structure will impact diverse applications, including molecular communication.

A Tutorial on Coding Methods for DNA-Based Molecular Communications and Storage

A Tutorial on Coding Methods for DNA-Based Molecular Communications and Storage

On Secrecy Performance in D-MoSK-Based 3-D Diffusive Molecular Communication System.

This paper studies the secrecy performance in a 3-D diffusive molecular communication system with the general depleted molecule shift keying (D-MoSK) modulation, where a point transmitter Alice transmits through diffusion multiple types of molecules modulation to a legitimate absorbing receiver Bob, suffering the eavesdropping from an absorbing eavesdropper Eve. We first develop a solid theoretical framework to determine the probabilistic distributions for the number of molecules absorbed by Bob and Eve, respectively. Based on the results, we then derive the average symbol error rate (SER) as well as the mutual information of Alice-Bob and Alice-Eve, and further apply the Shannon theory to determine the secrecy capacity of Alice-Bob transmission. We also develop the closed-form results for the optimal detection threshold at Bob to achieve the secrecy capacity, and thus devise a complete algorithm for secrecy capacity maximization. Finally, we provide numerical results to illustrate the secrecy performance in the concerned system.

Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor

•The signaling process during mycorrhiza establishment involves intense molecular communication between symbionts. It has been suggested that a group of protein effectors, the so-called MiSSPs, plays a broader function in the symbiosis metabolism, however, many of these remain uncharacterized structurally and functionally.•Herein we used three-dimensional protein structure modeling methods, ligand analysis, and molecular docking to structurally characterize and describe two protein effectors, MiSSP13 and MiSSP16.5, with enhanced expression during the mycorrhizal process in Laccaria bicolor.•MiSSP13 and MiSSP16.5 show structural homology with the cysteine and aspartate protease inhibitor, cocaprin (CCP1). Through structural analysis, it was observed that MiSSP13 and MiSSP16.5 have an active site similar to that observed in CCP1. The protein-protein docking data showed that MiSSP13 and MiSSP16.5 interact with the papain and pepsin proteases at sites that are near to where CCP1 interacts with these same targets, suggesting a function as inhibitor of cysteine and aspartate proteases. The interaction of MiSSP13 with papain and MiSSP16.5 with pepsin was stronger than the interaction of CCP1 with these proteases, suggesting that the MiSSPs had a greater activity in inhibiting these classes of proteases. Based on the data supplied, a model is proposed for the function of MiSSPs 13 and 16.5 during the symbiosis establishment. Our findings, while derived from in silico analyses, enable us formulate intriguing hypothesis on the function of MiSSPs in ectomycorrhization, which will require experimental validation.

An Effective Constellation Design for Concentration Shift Keying in Molecular Communication Systems

An Effective Constellation Design for Concentration Shift Keying in Molecular Communication Systems

Assessing electrogenetic activation via a network model of biological signal propagation

Introduction: Molecular communication is the transfer of information encoded by molecular structure and activity. We examine molecular communication within bacterial consortia as cells with diverse biosynthetic capabilities can be assembled for enhanced function. Their coordination, both in terms of engineered genetic circuits within individual cells as well as their population-scale functions, is needed to ensure robust performance. We have suggested that “electrogenetics,” the use of electronics to activate specific genetic circuits, is a means by which electronic devices can mediate molecular communication, ultimately enabling programmable control.Methods: Here, we have developed a graphical network model for dynamically assessing electronic and molecular signal propagation schemes wherein nodes represent individual cells, and their edges represent communication channels by which signaling molecules are transferred. We utilize graph properties such as edge dynamics and graph topology to interrogate the signaling dynamics of specific engineered bacterial consortia.Results: We were able to recapitulate previous experimental systems with our model. In addition, we found that networks with more distinct subpopulations (high network modularity) propagated signals more slowly than randomized networks, while strategic arrangement of subpopulations with respect to the inducer source (an electrode) can increase signal output and outperform otherwise homogeneous networks.Discussion: We developed this model to better understand our previous experimental results, but also to enable future designs wherein subpopulation composition, genetic circuits, and spatial configurations can be varied to tune performance. We suggest that this work may provide insight into the signaling which occurs in synthetically assembled systems as well as native microbial communities.

Received Signal and Channel Parameter Estimation in Molecular Communications

Received Signal and Channel Parameter Estimation in Molecular Communications

What Really is “Molecule” in Molecular Communications? The Quest for Physics of Particle-Based Information Carriers

What Really is “Molecule” in Molecular Communications? The Quest for Physics of Particle-Based Information Carriers

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Publication Information

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Publication Information

Microfluidic Molecular Communication Transmitter Based on Hydrodynamic Gating

Microfluidic Molecular Communication Transmitter Based on Hydrodynamic Gating

Guest Editorial Special Issue on Microfluidic Systems for Molecular Communications

Guest Editorial Special Issue on Microfluidic Systems for Molecular Communications

Artificial intelligence empowered physical layer security for 6G: State-of-the-art, challenges, and opportunities

With the commercial deployment of the 5G system, researchers from both academia and industry are moving attention to the blueprint of the 6G system. The space–air–ground–sea integrated 6G system is envisioned to support various new applications with very diverse requirements in terms of quality of service and security. Due to the open nature of the wireless channel, highly dynamic network topology, and mission-critical applications, 6G will face various security threats. The conventional upper-layer cryptography-based security mechanisms face multiple challenges to resist physical layer attacks in the context of large numbers computing, power-limited low-cost Internet of Thing (IoT) devices. The Physical layer security (PLS) mechanisms by exploiting the random nature of the wireless channel and intrinsic hardware imperfection provide complementary approaches to secure the 6G system. Meanwhile, the quick development and successful application of artificial intelligence facilitate the advancement of PLS solutions. In this paper, we make a comprehensive overview of machine learning-empowered PLS techniques toward 6G. We first introduce the vision of the 6G system, typical applications, key enabling radio technologies, security threats, and security requirements to 6G. Then typical machine learning (ML) methods and the driving forces for introducing intelligent PLS in 6G are presented. Afterward, the major academic works on PLS oriented to key 6G radio techniques including cell-free massive MIMO, visible light communication, Terahertz technology, configurable intelligent surfaces, molecular communication, and ambient backscatter communication are discussed. Then, the latest works on ML-enabled PLS solutions including physical layer key generation, secure wireless transmission, physical layer authentication, intelligent anti-jamming, and ML-enabled attack and detection are systematically reviewed. Finally, we identify important open issues and future research opportunities to inspire further studies to realize a more intelligent and secure 6G system.