{"title":"Toward Standardized Performance Evaluation of Flow-Guided Nanoscale Localization","authors":"Arnau Brosa López;Filip Lemic;Gerard Calvo Bartra;Aina Pérez;Jakob Struye;Jorge Torres Gómez;Esteban Municio;Carmen Delgado;Falko Dressler;Eduard Alarcón;Jeroen Famaey;Sergi Abadal;Xavier Costa Pérez","doi":"10.1109/TMBMC.2024.3523428","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3523428","url":null,"abstract":"Nanoscale devices with Terahertz (THz) communication capabilities are envisioned to be deployed within human bloodstreams. Such devices will enable fine-grained sensing-based applications for detecting early indications (i.e., biomarkers) of various health conditions, as well as actuation-based ones such as targeted drug delivery. Associating the locations of such events with the events themselves would provide an additional utility for precision diagnostics and treatment. This vision yielded a new class of in-body localization coined under the term “flow-guided nanoscale localization”. Such localization can be piggybacked on THz communication for detecting body regions in which biological events were localized with the traveling time reported by nanodevices flowing with the bloodstream. From decades of research on objective benchmarking of “traditional” indoor localization and its eventual standardization (e.g., ISO/IEC18305:2016), we know that in early stages, the reported performance results were often incomplete (e.g., targeting a subset of relevant performance metrics). Reported results in the literature carried out benchmarking experiments in different evaluation environments and scenarios and utilized inconsistent performance indicators. To avoid such a “lock-in” in flowguided localization, we propose a workflow for standardized performance evaluation of such approaches. The workflow is implemented in the form of an open-source simulation framework that is able to jointly account for the mobility of the nanodevices, in-body THz communication with on-body anchors, and energy-related and other technological constraints (e.g., pulsebased modulation) at the nanodevice level. Accounting for these constraints, the framework can generate raw data to streamline into different flow-guided localization solutions for generating standardized performance benchmarks.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 1","pages":"116-127"},"PeriodicalIF":2.4,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143645239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Single Input Multi Output Model of Molecular Communication via Diffusion With Spheroidal Receivers","authors":"Ibrahim Isik;Mitra Rezaei;Adam Noel","doi":"10.1109/TMBMC.2024.3521984","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3521984","url":null,"abstract":"Spheroids are aggregates of cells that can mimic the cellular organization often found in tissues. Spheroids can be created from various cell types, including cancer cells, stem cells, and primary cells, and they serve as valuable tools in biological research. Although there are initial results on how a molecular signal can propagate between a pair of spheroids, practical experiments typically use clusters of spheroids and there isn’t a good understanding of how neighboring spheroids impact the spatiotemporal dynamics of local molecule propagation. This paper simulates a series of scenarios to gain intuition about propagation in such multi-spheroid systems for applications such as transport and drug delivery. The spheroids are modeled as porous media with a corresponding effective diffusion coefficient. System variations are considered with a higher spheroid porosity (i.e., with a higher effective diffusion coefficient) and molecule uptake by the spheroid cells (approximated as a first-order degradation reaction while molecules diffuse within the spheroid). Results show that a local crowd of spheroids will eventually slow overall propagation, such that molecules stay in the vicinity of the transmitter for longer. The results demonstrate that a single-spheroid receiver model is insufficient to accurately model propagation under these conditions.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 1","pages":"101-106"},"PeriodicalIF":2.4,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143637887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"On Error Rate Reduction in Sub-Diffusion-Based Mobile Molecular Communication","authors":"Nadezhda Briantceva;Lokendra Chouhan;Matteo Parsani;Mohamed-Slim Alouini","doi":"10.1109/TMBMC.2024.3522010","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3522010","url":null,"abstract":"This work considers the sub-diffusive dynamics of information-carrying molecules (IM) within a molecular communication (MC) channel, focusing on the implementation of mobility at both the transmitter (TX) and receiver (RX) system components. To capture the essence of these complex movements, we derive the closed-form expressions for the absorption probability (AP), the first-passage-time density (FPTD), and the Cumulative Density Function (CDF). We also incorporate the Reed-Solomon (RS) coding technique to enhance communication performance. Through this integration, we analyze communication metrics such as mutual information and channel capacity. Moreover, we compare the bit error probability (BEP) with and without RS coding. The results provide a comprehensive view of the performance enhancements achieved by coding techniques in MC systems, leading to a more robust and efficient MC system.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 1","pages":"107-115"},"PeriodicalIF":2.4,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143637863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"3D Receiver for Molecular Communications in Internet of Organoids","authors":"Shaojie Zhang;Ozgur B. Akan","doi":"10.1109/TMBMC.2024.3522004","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3522004","url":null,"abstract":"Organoids have garnered attention due to their effectiveness in modeling the 3D structure of organ interactions. However, the communication engineering perspective has received relatively little attention. One way to achieve organoids communication is molecular communication (MC). MC is a bio-inspired communication paradigm that uses molecules as information carriers. It is considered one of the most promising methods for enabling the Internet of Nano-Things (IoNT) and nanonetworks. BioFETs are commonly used to implement practical MC receivers. However, most previous analysis have focused on a planar device, neglecting considerations like the threshold voltage, inter-symbol interference (ISI) and its potential 3D structure. This paper introduces the first FinFET-based MC receiver that covers both the top and side gates with receptors. Both binding noise and flicker noise are considered in the analysis. The performance, in terms of signal-to-noise ratio (SNR) and symbol error probability (SEP), is compared with that of the 2D receiver.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 1","pages":"91-100"},"PeriodicalIF":2.4,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143637890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"IEEE Communications Society Information","authors":"","doi":"10.1109/TMBMC.2024.3507633","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3507633","url":null,"abstract":"","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 4","pages":"C3-C3"},"PeriodicalIF":2.4,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10805221","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Guest Editorial Special Feature on Quantum Biology: Series II","authors":"Harun Šiljak","doi":"10.1109/TMBMC.2024.3509092","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3509092","url":null,"abstract":"","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 4","pages":"602-603"},"PeriodicalIF":2.4,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10805228","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Publication Information","authors":"","doi":"10.1109/TMBMC.2024.3475159","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3475159","url":null,"abstract":"","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 4","pages":"C2-C2"},"PeriodicalIF":2.4,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10805217","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bat-Ider Tumenbayar;Khanh Pham;John C. Biber;Rhonda Drewes;Yongho Bae
{"title":"Transcriptomic and Multi-Scale Network Analyses Reveal Key Drivers of Cardiovascular Disease","authors":"Bat-Ider Tumenbayar;Khanh Pham;John C. Biber;Rhonda Drewes;Yongho Bae","doi":"10.1109/TMBMC.2024.3501576","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3501576","url":null,"abstract":"Cardiovascular diseases (CVDs) and pathologies are often driven by changes in molecular signaling and communication, as well as in cellular and tissue components, particularly those involving the extracellular matrix (ECM), cytoskeleton, and immune response. The fine-wire vascular injury model is commonly used to study neointimal hyperplasia and vessel stiffening, but it is not typically considered a model for CVDs. However, applying this model to study CVDs in conjunction with established processes could offer valuable insights. In this paper, we hypothesize that vascular injury induces changes in gene expression, molecular communication, and biological processes similar to those observed in CVDs at both the transcriptome and protein levels. To investigate this, we analyzed gene expression in microarray datasets from injured and uninjured femoral arteries in mice two weeks post-injury, identifying 1,467 significantly and differentially expressed genes involved in several CVDs such as including vaso-occlusion, arrhythmia, and atherosclerosis. We further constructed a protein-protein interaction network with seven functionally distinct clusters, with notable enrichment in ECM, metabolic processes, actin-based process, and immune response. Significant molecular communications were observed between the clusters, most prominently among those involved in ECM and cytoskeleton organizations, inflammation, and cell cycle. Machine Learning Disease pathway analysis revealed that vascular injury-induced crosstalk between ECM remodeling and immune response clusters contributed to aortic aneurysm, neovascularization of choroid, and kidney failure. Additionally, we found that interactions between ECM and actin cytoskeletal reorganization clusters were linked to cardiac damage, carotid artery occlusion, and cardiac lesions. Overall, through multi-scale bioinformatic analyses, we demonstrated the robustness of the vascular injury model in eliciting transcriptomic and molecular network changes associated with CVDs, highlighting its potential for use in cardiovascular research.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 1","pages":"78-90"},"PeriodicalIF":2.4,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143637817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Characterization and Performance Optimization of Heterogeneous Media-Based Mobile Molecular Communication Systems","authors":"Nihit Bhatnagar;Sandeep Joshi","doi":"10.1109/TMBMC.2024.3496000","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3496000","url":null,"abstract":"In this letter, we study a three-dimensional heterogeneous media-based mobile molecular communication (MC) system, with the communicating devices as point transmitters and passive spherical-shaped receiver nano-machines. For the shorter time range, the diffusion process faces internal diffusivity fluctuations, due to which communicating devices and the information-carrying molecule’s diffusivity exhibit stochastic behavior. We propose a stochastic diffusivity-based mobile MC system model, which considers the non-Gaussian Brownian displacement of molecules and characterize it by the channel impulse response, and derive its mean. We consider the molecule’s constrained time-varying Poisson statistical diffusive channel model at a high inter-symbol interference regime and analyze the channel performance in terms of the bit error rate and channel capacity. Furthermore, the numerical results are verified through particle-based simulations.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 1","pages":"128-133"},"PeriodicalIF":2.4,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143637889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Closing the Implementation Gap in MC: Fully Chemical Synchronization and Detection for Cellular Receivers","authors":"Bastian Heinlein;Lukas Brand;Malcolm Egan;Maximilian Schäfer;Robert Schober;Sebastian Lotter","doi":"10.1109/TMBMC.2024.3486190","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3486190","url":null,"abstract":"In the context of the Internet of Bio-Nano Things (IoBNT), nano-devices are envisioned to perform complex tasks collaboratively, i.e., by communicating with each other. One candidate for the implementation of such devices are engineered cells due to their inherent biocompatibility. However, because each engineered cell has only little computational capabilities, transmitter and receiver (RX) functionalities can afford only limited complexity. In this paper, we propose a simple, yet modular, architecture for a cellular RX that is capable of processing a stream of observed symbols using chemical reaction networks. Furthermore, we propose two specific detector implementations for the RX. The first detector is based on a machine learning model that is trained offline, i.e., before the cellular RX is deployed. The second detector utilizes pilot symbol-based training and is therefore able to continuously adapt to changing channel conditions online, i.e., after deployment. To coordinate the different chemical processing steps involved in symbol detection, the proposed cellular RX leverages an internal chemical timer. Furthermore, the RX is synchronized with the transmitter via external, i.e., extracellular, signals. Finally, the proposed architecture is validated using theoretical analysis and stochastic simulations. The presented results confirm the feasibility of both proposed implementations and reveal that the proposed online learning-based RX is able to perform reliable detection even in initially unknown or slowly changing channels. By its modular design and exclusively chemical implementation, the proposed RX contributes towards the realization of versatile and biocompatible nano-scale communication networks for IoBNT applications narrowing the existing implementation gap in cellular molecular communication (MC).","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 1","pages":"30-50"},"PeriodicalIF":2.4,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143637888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}