Molecular Communication Research Articles

Markov Chain Modeling of the End-to-End Molecular Communication System Using Ligand Receiver

Molecular communication (MC) makes use of molecules as information carriers for nanoscale and macroscale applications. In this paper, an end-to-end biochemical communication modeling of an MC system is presented. The transmitter is assumed to be a point source, and the receiver is embedded with finite ligand receptors. The inherent memory in the fluid channel is represented by a Markov chain and additionally a novel Markov chain is proposed which takes into effect the aggregated decision of the receiver corresponding to the number of molecules received on the finite individual receptors. The proposed discrete-time Markov chain can potentially replace the block of the finite number of Markov chains for different ligand receptors followed by a threshold comparator. Moreover, the capacity of the ligand channel is analyzed for independent and identically distributed (IID) binary source and upper and lower bounds on the mutual information (MI) rate are derived for the Markov inputs to the ligand channel. The performance analysis for the end-to-end MC system is done by deriving the analytical expressions of the bit error rate for both IID and Markov inputs. Finally, we find the simulated probability of error and observe that the analytical results are corroborated by the simulated ones.

Mobile human ad hoc networks: A communication engineering viewpoint on interhuman airborne pathogen transmission

A number of transmission models for airborne pathogens transmission, as required to understand airborne infectious diseases such as COVID-19, have been proposed independently from each other, at different scales, and by researchers from various disciplines. We propose a communication engineering approach that blends different disciplines such as epidemiology, biology, medicine, and fluid dynamics. The aim is to present a unified framework using communication engineering, and to highlight future research directions for modeling the spread of infectious diseases through airborne transmission. We introduce the concept of mobile human ad hoc networks (MoHANETs), which exploits the similarity of airborne transmission-driven human groups with mobile ad hoc networks and uses molecular communication as the enabling paradigm. In the MoHANET architecture, a layered structure is employed where the infectious human emitting pathogen-laden droplets and the exposed human to these droplets are considered as the transmitter and receiver, respectively. Our proof-of-concept results, which we validated using empirical COVID-19 data, clearly demonstrate the ability of our MoHANET architecture to predict the dynamics of infectious diseases by considering the propagation of pathogen-laden droplets, their reception and mobility of humans.

An Analytical Propagation Model for Diffusion-Based Molecular Communication Systems

A novel analytical propagation model for diffusive molecular communication systems in a three-dimensional fluid environment is derived. The model takes into account the geometry of a spherical receiver, the inclination angle, and the reaction rate of the receiver to accurately model the time-varying distribution and the number of absorbed information molecules at the receiver over a period of time. Accordingly, we derive an expression for the net number of accumulatively-absorbed information molecules at the surface of the receiver. We also study the bit error rate (BER) performance of diffusion-based molecular communications in the presence of the inter-symbol interference. Simulations based on the developed model show the impact of the transmitter-receiver distance, the reaction rate at the surface of the receiver and the diffusion constant of the environment on the fraction of absorbed molecules and the BER performance. A particle-based simulator is implemented to verify the accuracy of the proposed model. Moreover, our results are compared with that of a conventional model, where the geometry of the receiver and the inclination angle are ignored. It is shown that, especially at small transmitter-receiver separation distances, the proposed model predicts a significantly smaller number of absorbed molecules compared to the conventional models.

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

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

Chemical Communication in Artificial Cells: Basic Concepts, Design and Challenges.

In the past decade, the focus of bottom-up synthetic biology has shifted from the design of complex artificial cell architectures to the design of interactions between artificial cells mediated by physical and chemical cues. Engineering communication between artificial cells is crucial for the realization of coordinated dynamic behaviours in artificial cell populations, which would have implications for biotechnology, advanced colloidal materials and regenerative medicine. In this review, we focus our discussion on molecular communication between artificial cells. We cover basic concepts such as the importance of compartmentalization, the metabolic machinery driving signaling across cell boundaries and the different modes of communication used. The various studies in artificial cell signaling have been classified based on the distance between sender and receiver cells, just like in biology into autocrine, juxtacrine, paracrine and endocrine signaling. Emerging tools available for the design of dynamic and adaptive signaling are highlighted and some recent advances of signaling-enabled collective behaviours, such as quorum sensing, travelling pulses and predator-prey behaviour, are also discussed.

Molecular communication network and its applications in crop sciences

Plant molecular biology and bacterial behaviour research in the future could focus on using genetically engineered bacteria as a sensor, hormonal/disease detector, and target gene expression, as well as establishing a bioluminescence feedback communication system. Over the last two decades, understanding plant signal transduction pathways of plant hormones has become an active research field to understand plant behavior better. To accomplish signal transduction, plants use a variety of hormones for inter- and intra-communication, and biotic or abiotic stressors activate those. Signal transduction pathways refer to the use of various communication methods by effectors to elicit a response at the molecular level. Research methodologies such as inter-kingdom signaling have been introduced to study signal transduction and communication pathways, or what we can term plant molecular communication. However, stochastic qualities are inherent in most technologies used to monitor these biological processes. Molecular communication (MC) is a new research topic that uses the natural features of biological organisms to communicate and aims to manipulate their stochastic nature to achieve the desired results. MC is a multidisciplinary research field inspired by the use of molecules to store, spread, and receive information between biological organisms known as "Biological Nanomachines." It has been used to demonstrate how biological entities may be characterised, modelled, and engineered as communication devices in the same manner as traditional communication technologies are. We attempted to link MC and PLANT'S MC in this studyand we believe that reasonable combined efforts may be made to use the functional applications of MC for detecting and understanding molecular-level activities such as signaling transduction pathways in crops.

Embedded Nano Relay for Intra-Body Network-Based Molecular Communications

We propose an embedded synthetic relay transport protein (RTP) approach for communication between the external environment (blood vessels) and internal targeted nanonetworks (cells/tissues) within the intra-body network. In fact, we designed a bioengineered relay protein-based facilitated diffusing to be an alternative protein in the case of biological transport proteins (such as protein channels, e.g. Pores) failing. The proposed approach is inspired by the traditional wireless communication system-based relay concept, in which embedded nanodevices known as donor, relay, and acceptor bionanomachine construct a molecular communication system. Fluorescence resonance energy transfer nanocommunications are used to connect the embedded bionanomachines, and the therapeutic drug is transferred in the form of exciton. The performance analysis of the proposed approach is evaluated in terms of channel capacity of RTP as function of intrinsic environmental parameters and the location of the relay between the donor, and acceptor bionanomachines. The numerical results show that the proposed approach improves channel capacity by 16.7% over previous work.

What Is the Trait d’Union between Retroactivity and Molecular Communication Performance Limits?

Information exchange is a critical process in all communication systems, including biological ones. Retroactivity describes the load that downstream modules apply to their upstream systems in biological circuits. The motivation behind this work is that of integrating retroactivity, a concept proper of biochemical circuits, with the metrics defined in Information Theory and Digital Communications. This paper focuses on studying the impact of retroactivity on different biological signaling system models, which present analogies with well-known telecommunication systems. The mathematical analysis is performed both in the high and low molecular counts regime, by mean of the Chemical Master Equation and the Linear Noise Approximation, respectively. The main goal of this work is to provide analytical tools to maximize the reliable information exchange across different biomolecular circuit models. Results highlight how, in general, retroactivity harms communication performance. This negative effect can be mitigated by adding to the signaling circuit an independent upstream system that connects with the same pool of downstream circuits.

MO365: Single-Cell Profiling Analysis Reveals the Transcriptomic Landscape Of Kidneys in Patients With Acute Kidney Injury

Abstract BACKGROUND AND AIMS Acute kidney injury (AKI) is a common clinical syndrome associated with considerable mortality and healthcare costs. Up to now, the underlying pathological mechanisms of AKI are still unclear, and specific strategies for early diagnosis and treatment of AKI are lacking. In this research, single-cell RNA sequencing (scRNA-seq) was applied to kidney biopsies of patients with AKI to elucidate novel molecular mechanisms and intercellular communications. METHOD The transcriptomes of human kidney specimens obtained from subjects with AKI and renal transplant healthy living donors were defined by scRNA-seq technology. Differentially expressed genes (DEGs) and cell clusters of the kidney were determined. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed, and cell–cell crosstalk communication analysis among distince cell subtypes were conducted. RESULTS A total of 16 distinct cell clusters were determined in kidney from subjects of AKI and control. Proximal tubule cells of AKI had up-regulation of novel pro-apoptotic genes including USP47, RASSF4, EBAG9, IER3 and NUB1, which have not been reported previously. Further, proximal tubule cells highly expressed endoplasmic reticulum stress related genes (PDIA6, ATF6, HSPA5 and DNAJC3), autophagy related genes (S100A11, CLDN1, TMBIM6, RB1CC1 and VMP1) and genes enriched in RIG-1 signaling. PALM3 was overexpressed in proximal tubule cells of AKI at both mRNA and protein levels, which is involved in cell adhesion, TLR4 signaling and infammation response. DEGs overexpressed in other tubular cells were primarily enriched in NOD-like receptor signaling, estrogen signaling, interleukin-12-mediated signaling and IL-17 signaling. Glomerular cells such as EC upregulated DEGs participating in cell adhesion, apoptosis and chemotaxis. Overexpressed genes in kidney-resident immune cells including macrophages, NK-T cells, monocytes and dendritic cells suggested abnormal regulation related with leukocyte activation, chemotaxis, cell adhesion and complement activation. In addition, the ligand-receptor interactions analysis revealed cell–cell communication contributing to adhesion, recruitment and infiltration of inflammatory cells into the kidneys, and cytokine production in the process of AKI. CONCLUSION Together, this study reveals distinct cell-specific transcriptional landscapes of kidney in AKI patients, also altered signaling pathways and potential cell-cell crosstalk in development of AKI. These data may provide new insights into the pathogenesis and potential therapeutic strategies of AKI.

Molecular communication between Apelin-13, Apelin-36, Elabela, and nitric oxide in gestational diabetes mellitus.

Gestational diabetes mellitus (GDM) is a type of diabetes that affects from 3.8% to 6.9% of pregnancies worldwide, causing significant mortality and unfavorable obstetric outcomes, such as delivery trauma and macrosomia risk. The fundamental processes of this metabolic disorder that first appeared during pregnancy are still unknown. Tissue hormones, particularly adipokines, have aided in understanding the pathophysiology of numerous disorders in recent years. This study aims to determine if Apelin-13 (APLN-13), Apelin-36 (APLN-36), Elabela (ELA), and nitric oxide (NO) molecules have all a part in the pathophysiology of GDM. The study included 30 pregnant control women and 30 pregnant women who had been diagnosed with GDM in the second trimester and whose body mass index and age were compatible with each other. Blood samples were collected from 60 participants during the second trimester (30 control pregnant women and 30 GDM pregnant women) and postpartum (17 controls vs. 14 GDM). In these blood samples, the amounts of APLN-13, APLN-36, ELA, and NO were studied using the ELISA method. In addition, the participants' glucose, lipid profiles, and other parameters were obtained from the hospital record files. At postpartum, 29 pregnant women (13 control and 16 pregnant women with GDM) dropped out of the study without explanation. In the second trimester and postpartum plasma of mothers with GDM, APLN-13, APLN-36, NO, and ELA molecules were found to be significantly higher (< 0.05), compared to those of the control mothers, while APLN-13, APLN-36, NO values were significantly lower (0.05). While APLN-13, APLN-36, NO amounts in mothers with GDM were positively correlated with glucose amounts, they were negatively correlated with ELA amounts. Similarly, the triglyceride amounts in mothers with GDM were positively correlated with APLN-13, APLN-36 and NO, while they were negatively correlated with the ELA amounts. Due to gestational diabetes, APLN-13, APLN-36, NO, glucose, and triglyceride increased, and ELA decreased. It is predicted that the glucose increase in GDM is because Apelins reduce glucose transport to erythrocytes by inhibiting the sodium-dependent glucose transporter (SGLT) and that the increase in triglyceride and NO may be associated with high glucose levels in GDM. As a result, we believe that the above-mentioned chemicals may cause GDM Pathology by triggering one another.

Channel Characterization of Diffusion-Based Molecular Communication With Multiple Fully-Absorbing Receivers

In this paper an analytical model is introduced to describe the impulse response of the diffusive channel between a pointwise transmitter and a given fully-absorbing (FA) receiver in a molecular communication (MC) system. The presence of neighbouring FA nanomachines in the environment is taken into account by describing them as sources of negative molecules. The channel impulse responses of all the receivers are linked in a system of integral equations. The solution of the system with two receivers is obtained analytically. For a higher number of receivers the system of integral equations is solved numerically. It is also shown that the channel impulse response shape is distorted by the presence of the neighbouring FA interferers. For instance, there is a time shift of the peak in the number of absorbed molecules compared to the case without interference, as predicted by the proposed model. The analytical derivations are validated by means of particle based simulations.

Retraction Note: Molecular communication networks: drug target scalability based on artificial intelligence prediction techniques

Retraction Note: Molecular communication networks: drug target scalability based on artificial intelligence prediction techniques

New Insights on Molecular Communication in Nano Communication Networks and their Applications

The advancement in nanotechnology has carved out a way to establish a powerful base to fall on for implementation of nanoscale machines having the capability to carry out significant yet trivial tasks. This impetus has led the researchers to continually bring up various solutions for implementing and executing nanoscale communications taking into consideration of biological as well as electromagnetic communication. The primary aims are expanding the abilities of nanoscale devices to integrated multiple composite tasks by reciprocated coordination, which can be carried out through this communication type. This paper describes the current research developments in nano communication networks, focusing on molecular communication (MC). MC makes use of molecules as an information transporter between nanoscale machines. Molecules help in enciphering messages to send between a sender and a receiver. MC has, thereby, become an inseparable part of the IoNT (Internet of Nano-Things) as a communication model among nanoscale machines. This paper also gives a description of the design of MC systems and various channelling models used to address the various challenges and opportunities in this new upcoming and developing field. In addition, this review article is also inclusive of an investigative survey on the recent developments in this field.

Molecular communications in complex systems of dynamic supramolecular polymers

Supramolecular polymers are composed of monomers that self-assemble non-covalently, generating distributions of monodimensional fibres in continuous communication with each other and with the surrounding solution. Fibres, exchanging molecular species, and external environment constitute a sole complex system, which intrinsic dynamics is hard to elucidate. Here we report coarse-grained molecular simulations that allow studying supramolecular polymers at the thermodynamic equilibrium, explicitly showing the complex nature of these systems, which are composed of exquisitely dynamic molecular entities. Detailed studies of molecular exchange provide insights into key factors controlling how assemblies communicate with each other, defining the equilibrium dynamics of the system. Using minimalistic and finer chemically relevant molecular models, we observe that a rich concerted complexity is intrinsic in such self-assembling systems. This offers a new dynamic and probabilistic (rather than structural) picture of supramolecular polymer systems, where the travelling molecular species continuously shape the assemblies that statistically emerge at the equilibrium.

A reflection of life - my tale of microdiversity, equity and inclusion in cell biology (and beyond).

A reflection of life - my tale of microdiversity, equity and inclusion in cell biology (and beyond).

Autoinhibition and regulation by phosphoinositides of ATP8B1, a human lipid flippase associated with intrahepatic cholestatic disorders.

P4-ATPases flip lipids from the exoplasmic to the cytosolic leaflet, thus maintaining lipid asymmetry in eukaryotic cell membranes. Mutations in several human P4-ATPase genes are associated with severe diseases, for example in ATP8B1 causing progressive familial intrahepatic cholestasis, a rare inherited disorder progressing toward liver failure. ATP8B1 forms a binary complex with CDC50A and displays a broad specificity to glycerophospholipids, but regulatory mechanisms are unknown. Here, we report functional studies and the cryo-EM structure of the human lipid flippase ATP8B1-CDC50A at 3.1 Å resolution. We find that ATP8B1 is autoinhibited by its N- and C-terminal tails, which form extensive interactions with the catalytic sites and flexible domain interfaces. Consistently, ATP hydrolysis is unleashed by truncation of the C-terminus, but also requires phosphoinositides, most markedly phosphatidylinositol-3,4,5-phosphate (PI(3,4,5)P3), and removal of both N- and C-termini results in full activation. Restored inhibition of ATP8B1 truncation constructs with a synthetic peptide mimicking the C-terminal segment further suggests molecular communication between N- and C-termini in the autoinhibition and demonstrates that the regulatory mechanism can be interfered with by exogenous compounds. A recurring (G/A)(Y/F)AFS motif of the C-terminal segment suggests that this mechanism is employed widely across P4-ATPase lipid flippases in plasma membrane and endomembranes.

Research data supporting: "Molecular communications in complex systems of dynamic supramolecular polymers"

Research data supporting: "Molecular communications in complex systems of dynamic supramolecular polymers"

Molecular Communications Enhanced by Time-Varying Electric Field.

In this work, we propose applying a time-varying electric field to a time-slotted molecular communication system with ionized message particles to combat inter-symbol interference (ISI) and enhance the transmission performance. Firstly, the solution to the Nernst-Planck equation, which describes the motion of ions under the electric field, is derived. With the derived solution, the bit error probability (BEP) and the receiver operating characteristic (ROC) curve are analyzed. Then, the time-varying electric field is optimized by the proposed algorithms to respectively minimize the error probability (MinEP), maximize the signal-to-interference ratio (MaxSIR), and maximize the sensing probability (MaxSP). For solving the MinEP and MaxSIR problems, algorithms based on the approximate gradient descent method are proposed. In addition, an efficient algorithm is proposed for solving the MaxSP problem. The proposed MinEP and MaxSIR schemes are shown to effectively mitigate ISI, and the proposed MaxSP scheme delivers the near-optimal performance with low complexity, demonstrating that the performance of molecular communications can be significantly enhanced by applying the time-varying electric field.

Relative Localization for Silent Absorbing Target in Diffusive Molecular Communication System

Recently, anomaly detection or localization in molecular communication (MC) system has become a research hot topic that can be used to distinguish the abnormal cells in the human body. Due to no or very few molecules the target released, it is difficult to detect the silent target in the MC system. In this article, we construct a three-node MC (TNMC) system, including a point source transmitter, a passive receiver, and a silent absorbing target (SAT), the SAT cannot release but has the ability to absorb the molecules. Based on the above system, we propose a probability equivalent modeling (PEM) method to model the channel of the TNMC system and derive the channel impulse response (CIR) of the receiver. Besides, we propose a localization algorithm based on maximum-likelihood estimation (MLE) and Newton–Raphson method to spot the relative location of the SAT. Simulation results verify the correctness of the PEM method and effectiveness for localizing the target.

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.