Pub Date : 2023-07-20DOI: 10.1109/TMBMC.2023.3297135
Jorge Torres Gómez;Pit Hofmann;Frank H. P. Fitzek;Falko Dressler
Recent molecular communication (MC) research suggests machine learning (ML) models for symbol detection, avoiding the unfeasibility of end-to-end channel models. However, ML models are applied as black boxes, lacking proof of correctness of the underlying neural networks (NNs) to detect incoming symbols. This paper studies approaches to the explainability of NNs for symbol detection in MC channels. Based on MC channel models and real testbed measurements, we generate synthesized data and train a NN model to detect of binary transmissions in MC channels. Using the local interpretable model-agnostic explanation (LIME) method and the individual conditional expectation (ICE), the findings in this paper demonstrate the analogy between the trained NN and the standard peak and slope detectors.
{"title":"Explainability of Neural Networks for Symbol Detection in Molecular Communication Channels","authors":"Jorge Torres Gómez;Pit Hofmann;Frank H. P. Fitzek;Falko Dressler","doi":"10.1109/TMBMC.2023.3297135","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3297135","url":null,"abstract":"Recent molecular communication (MC) research suggests machine learning (ML) models for symbol detection, avoiding the unfeasibility of end-to-end channel models. However, ML models are applied as black boxes, lacking proof of correctness of the underlying neural networks (NNs) to detect incoming symbols. This paper studies approaches to the explainability of NNs for symbol detection in MC channels. Based on MC channel models and real testbed measurements, we generate synthesized data and train a NN model to detect of binary transmissions in MC channels. Using the local interpretable model-agnostic explanation (LIME) method and the individual conditional expectation (ICE), the findings in this paper demonstrate the analogy between the trained NN and the standard peak and slope detectors.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"323-328"},"PeriodicalIF":2.2,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982989","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}
Pub Date : 2023-07-19DOI: 10.1109/TMBMC.2023.3296828
Angelika S. Thalmayer;Alisa Ladebeck;Samuel Zeising;Georg Fischer
In molecular communications, magnetic nanoparticles, which are injected into a pipe flow, are used as information carriers. Due to the parabolic shape of the velocity profile in laminar flow regimes, the speed of one particle depends on its radial position in the tube. This results in an unwanted extension of a particle pulse over the propagation time. Potential overlapping of subsequent pulses induces intersymbol interference. Only few research of the current state of the art reduces velocity dispersion directly within the propagation channel. To the best of the authors’ knowledge, this is the first paper that numerically investigates different passive obstacles which are placed directly in the channel for non-turbulent flow regimes to address the dispersion effects. These obstacles serve as decelerators, as they decelerate the fastest particles while at the same time accelerating slower particles. The results reveal that a passive decelerator can reduce the velocity dispersion in molecular communications and, thus, guarantee a more packetized pulse shortly behind the decelerator but also after some distance. Compared with different decelerators, an elliptical-shaped one showed the best results, as it inverts the velocity profile.
{"title":"Reducing Dispersion in Molecular Communications by Placing Decelerators in the Propagation Channel","authors":"Angelika S. Thalmayer;Alisa Ladebeck;Samuel Zeising;Georg Fischer","doi":"10.1109/TMBMC.2023.3296828","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3296828","url":null,"abstract":"In molecular communications, magnetic nanoparticles, which are injected into a pipe flow, are used as information carriers. Due to the parabolic shape of the velocity profile in laminar flow regimes, the speed of one particle depends on its radial position in the tube. This results in an unwanted extension of a particle pulse over the propagation time. Potential overlapping of subsequent pulses induces intersymbol interference. Only few research of the current state of the art reduces velocity dispersion directly within the propagation channel. To the best of the authors’ knowledge, this is the first paper that numerically investigates different passive obstacles which are placed directly in the channel for non-turbulent flow regimes to address the dispersion effects. These obstacles serve as decelerators, as they decelerate the fastest particles while at the same time accelerating slower particles. The results reveal that a passive decelerator can reduce the velocity dispersion in molecular communications and, thus, guarantee a more packetized pulse shortly behind the decelerator but also after some distance. Compared with different decelerators, an elliptical-shaped one showed the best results, as it inverts the velocity profile.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"334-339"},"PeriodicalIF":2.2,"publicationDate":"2023-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982991","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}
Pub Date : 2023-07-18DOI: 10.1109/TMBMC.2023.3296430
Saswati Pal;Sudip Misra;Nabiul Islam
COVID-19-induced cytokine storm, which is formed due to the excessive secretion of cytokine molecules, causes multi-organ damage and subsequently, the death of COVID-19 patients. Mesenchymal Stem Cells (MSCs) are regarded as cellular vaccines to combat the hyper-inflammatory response to cytokine storms. However, determining the required dose of MSCs to be infused within a certain time period is challenging due to the complex vascular networks and varying individual immune responses. In this work, we propose a molecular communication-based system to model the transmission, propagation, and immuno-modulatory response of MSCs to the cytokine storm. The proposed analytical model provides valuable insights into the behavior of the system and can be used as a framework for further experimental-based studies to estimate the required dose of MSCs. We analyze the varying shapes and geometries of the vascular channel on the propagation of the MSCs. We observe that the higher shear stress hinders MSC signal propagation, while lower shear stress induces propagation along the channel. Simulation results show that the MSC signal peaks in four simulation days upon administering the MSCs. Further, the results reveal that repeating the MSC infusion on alternate days is required to maintain a prolonged immuno-modulating effect on the cytokine storm.
{"title":"m-MSC: Molecular Communication-Based Analysis for Controlled MSC Treatment of Cytokine Storm","authors":"Saswati Pal;Sudip Misra;Nabiul Islam","doi":"10.1109/TMBMC.2023.3296430","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3296430","url":null,"abstract":"COVID-19-induced cytokine storm, which is formed due to the excessive secretion of cytokine molecules, causes multi-organ damage and subsequently, the death of COVID-19 patients. Mesenchymal Stem Cells (MSCs) are regarded as cellular vaccines to combat the hyper-inflammatory response to cytokine storms. However, determining the required dose of MSCs to be infused within a certain time period is challenging due to the complex vascular networks and varying individual immune responses. In this work, we propose a molecular communication-based system to model the transmission, propagation, and immuno-modulatory response of MSCs to the cytokine storm. The proposed analytical model provides valuable insights into the behavior of the system and can be used as a framework for further experimental-based studies to estimate the required dose of MSCs. We analyze the varying shapes and geometries of the vascular channel on the propagation of the MSCs. We observe that the higher shear stress hinders MSC signal propagation, while lower shear stress induces propagation along the channel. Simulation results show that the MSC signal peaks in four simulation days upon administering the MSCs. Further, the results reveal that repeating the MSC infusion on alternate days is required to maintain a prolonged immuno-modulating effect on the cytokine storm.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"286-294"},"PeriodicalIF":2.2,"publicationDate":"2023-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982984","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}
Pub Date : 2023-07-13DOI: 10.1109/TMBMC.2023.3295338
Ahmet R. Emirdagi;M. Serkan Kopuzlu;M. Okan Araz;Murat Kuscu
A key challenge in Molecular Communications (MC) is low data transmission rates, which can be addressed by channel multiplexing techniques. One way to achieve channel multiplexing in MC is to leverage the diversity of different molecule types with respect to their receptor binding characteristics, such as affinity and kinetic binding/unbinding rates. In this study, we propose a practical multiplexing scheme for MC, which is based on the diversity of ligand-receptor binding affinities. This method requires only a single type of promiscuous receptor on the receiver side, capable of interacting with multiple ligand types. We analytically derive the mean Bit Error Probability (BEP) over all multiplexed MC channels as a function of similarity among ligands in terms of their receptor affinities, the number of receptors, the number of multiplexed channels, and the ratio of concentrations encoding bit-1 and bit-0. We investigate the impact of each design parameter on the performance of multiplexed MC system.
{"title":"Affinity-Division Multiplexing for Molecular Communications With Promiscuous Ligand Receptors","authors":"Ahmet R. Emirdagi;M. Serkan Kopuzlu;M. Okan Araz;Murat Kuscu","doi":"10.1109/TMBMC.2023.3295338","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3295338","url":null,"abstract":"A key challenge in Molecular Communications (MC) is low data transmission rates, which can be addressed by channel multiplexing techniques. One way to achieve channel multiplexing in MC is to leverage the diversity of different molecule types with respect to their receptor binding characteristics, such as affinity and kinetic binding/unbinding rates. In this study, we propose a practical multiplexing scheme for MC, which is based on the diversity of ligand-receptor binding affinities. This method requires only a single type of promiscuous receptor on the receiver side, capable of interacting with multiple ligand types. We analytically derive the mean Bit Error Probability (BEP) over all multiplexed MC channels as a function of similarity among ligands in terms of their receptor affinities, the number of receptors, the number of multiplexed channels, and the ratio of concentrations encoding bit-1 and bit-0. We investigate the impact of each design parameter on the performance of multiplexed MC system.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"318-322"},"PeriodicalIF":2.2,"publicationDate":"2023-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982988","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}
Pub Date : 2023-07-05DOI: 10.1109/TMBMC.2023.3292321
Fatih Gulec;Andrew W. Eckford
Quorum sensing (QS) mimickers can be used as an effective tool to disrupt biofilms which consist of communicating bacteria and extracellular polymeric substances (EPS). In this paper, a stochastic biofilm disruption model based on the usage of QS mimickers is proposed. A chemical reaction network (CRN) involving four different states is employed to model the biological processes during the biofilm formation and its disruption via QS mimickers. In addition, a state-based stochastic simulation algorithm is proposed to simulate this CRN. The proposed model is validated by the in vitro experimental results of Pseudomonas aeruginosa biofilm and its disruption by rosmarinic acid as the QS mimicker. Our results show that there is an uncertainty in state transitions due to the effect of the randomness in the CRN. In addition to the QS activation threshold, the presented work demonstrates that there are underlying two more thresholds for the disruption of EPS and bacteria, which provides a realistic modeling for biofilm disruption with QS mimickers.
{"title":"A Stochastic Biofilm Disruption Model Based on Quorum Sensing Mimickers","authors":"Fatih Gulec;Andrew W. Eckford","doi":"10.1109/TMBMC.2023.3292321","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3292321","url":null,"abstract":"Quorum sensing (QS) mimickers can be used as an effective tool to disrupt biofilms which consist of communicating bacteria and extracellular polymeric substances (EPS). In this paper, a stochastic biofilm disruption model based on the usage of QS mimickers is proposed. A chemical reaction network (CRN) involving four different states is employed to model the biological processes during the biofilm formation and its disruption via QS mimickers. In addition, a state-based stochastic simulation algorithm is proposed to simulate this CRN. The proposed model is validated by the in vitro experimental results of Pseudomonas aeruginosa biofilm and its disruption by rosmarinic acid as the QS mimicker. Our results show that there is an uncertainty in state transitions due to the effect of the randomness in the CRN. In addition to the QS activation threshold, the presented work demonstrates that there are underlying two more thresholds for the disruption of EPS and bacteria, which provides a realistic modeling for biofilm disruption with QS mimickers.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"346-350"},"PeriodicalIF":2.2,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982994","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}
Pub Date : 2023-06-27DOI: 10.1109/TMBMC.2023.3290076
Federico Calì;Giovanni Li-Destri;Nunzio Tuccitto
This study reports a method for molecular communication in fluids and provides a detailed description of the testbed and numerous experimental data. The prototype involves information being carried by fluorescent carbon nanoparticles. The details of the synthesis and fluorescence properties are also described. Signal modulation was achieved by exploiting the instability effect of an interfacial phenomenon known as viscosity fingering, which occurs when two miscible liquids with different viscosities or strong density variations contact one another. This modulation is called interfacial shift keying. The data confirm the reproducibility of the method. A new approach based on the deliberate superposition of two consecutive close releases is described in detail, and data from several experimental replicas are provided.
{"title":"Interfacial Shift Keying Allows a High Information Rate in Molecular Communication: Methods and Data","authors":"Federico Calì;Giovanni Li-Destri;Nunzio Tuccitto","doi":"10.1109/TMBMC.2023.3290076","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3290076","url":null,"abstract":"This study reports a method for molecular communication in fluids and provides a detailed description of the testbed and numerous experimental data. The prototype involves information being carried by fluorescent carbon nanoparticles. The details of the synthesis and fluorescence properties are also described. Signal modulation was achieved by exploiting the instability effect of an interfacial phenomenon known as viscosity fingering, which occurs when two miscible liquids with different viscosities or strong density variations contact one another. This modulation is called interfacial shift keying. The data confirm the reproducibility of the method. A new approach based on the deliberate superposition of two consecutive close releases is described in detail, and data from several experimental replicas are provided.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"300-307"},"PeriodicalIF":2.2,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67823226","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}
Pub Date : 2023-06-27DOI: 10.1109/TMBMC.2023.3290077
Taishi Kotsuka;Yutaka Hori
Molecular communication (MC) enables cooperation of spatially dispersed molecular robots through the feedback control mediated by diffusing signal molecules. However, conventional analysis frameworks for the MC channels mostly consider the dynamics of unidirectional communication, lacking the effect of feedback interactions. In this paper, we propose a general control-theoretic modeling framework for bidirectional MC systems capable of capturing the dynamics of feedback control via MC in a systematic manner. The proposed framework considers not only the dynamics of molecular diffusion but also the boundary dynamics at the molecular robots that captures the lag due to the molecular transmission/reception process affecting the performance of the entire feedback system. Thus, methods in control theory can be applied to systematically analyze various dynamical properties of the feedback system. We perform a frequency response analysis based on the proposed framework to show a general design guideline for MC channels to transfer signal with desired control bandwidth. Finally, these results are demonstrated by showing the step-by-step design procedure of a specific MC channel satisfying a given specification.
{"title":"A Control-Theoretic Model for Bidirectional Molecular Communication Systems","authors":"Taishi Kotsuka;Yutaka Hori","doi":"10.1109/TMBMC.2023.3290077","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3290077","url":null,"abstract":"Molecular communication (MC) enables cooperation of spatially dispersed molecular robots through the feedback control mediated by diffusing signal molecules. However, conventional analysis frameworks for the MC channels mostly consider the dynamics of unidirectional communication, lacking the effect of feedback interactions. In this paper, we propose a general control-theoretic modeling framework for bidirectional MC systems capable of capturing the dynamics of feedback control via MC in a systematic manner. The proposed framework considers not only the dynamics of molecular diffusion but also the boundary dynamics at the molecular robots that captures the lag due to the molecular transmission/reception process affecting the performance of the entire feedback system. Thus, methods in control theory can be applied to systematically analyze various dynamical properties of the feedback system. We perform a frequency response analysis based on the proposed framework to show a general design guideline for MC channels to transfer signal with desired control bandwidth. Finally, these results are demonstrated by showing the step-by-step design procedure of a specific MC channel satisfying a given specification.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"274-285"},"PeriodicalIF":2.2,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982996","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}
Pub Date : 2023-06-20DOI: 10.1109/TMBMC.2023.3274026
{"title":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Publication Information","authors":"","doi":"10.1109/TMBMC.2023.3274026","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3274026","url":null,"abstract":"","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 2","pages":"C2-C2"},"PeriodicalIF":2.2,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/iel7/6687308/10157988/10158296.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68020453","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}
Pub Date : 2023-06-20DOI: 10.1109/TMBMC.2023.3274028
{"title":"IEEE Communications Society Information","authors":"","doi":"10.1109/TMBMC.2023.3274028","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3274028","url":null,"abstract":"","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 2","pages":"C3-C3"},"PeriodicalIF":2.2,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/iel7/6687308/10157988/10157989.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68018593","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}
Pub Date : 2023-06-20DOI: 10.1109/TMBMC.2023.3278539
Harun Šiljak
Quantum biology is not a new field of study: as the physicists’ work on foundations of quantum theory matured, the question of linking it with the secrets of living organisms drew more and more attention. It was posed as a natural philosophy question as well, exploring the link of quantum randomness with the competing perceptions of the world, idealist and materialist. It also posed a question to what will later become known as systems theory: is reductionism ever warranted in complex systems? These first thoughts on quantum effects as underlying mechanisms of living organisms predate the modern molecular biology revolution.
{"title":"Guest Editorial Special Feature on Quantum Biology","authors":"Harun Šiljak","doi":"10.1109/TMBMC.2023.3278539","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3278539","url":null,"abstract":"Quantum biology is not a new field of study: as the physicists’ work on foundations of quantum theory matured, the question of linking it with the secrets of living organisms drew more and more attention. It was posed as a natural philosophy question as well, exploring the link of quantum randomness with the competing perceptions of the world, idealist and materialist. It also posed a question to what will later become known as systems theory: is reductionism ever warranted in complex systems? These first thoughts on quantum effects as underlying mechanisms of living organisms predate the modern molecular biology revolution.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 2","pages":"233-234"},"PeriodicalIF":2.2,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/iel7/6687308/10157988/10158274.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68018597","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}
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