Pub Date : 2024-09-19DOI: 10.1109/TMBMC.2024.3464415
Emily Frede;Hadi Zadeh-Haghighi;Christoph Simon
In neuroscience, it is of interest to consider all possible modes of information transfer between neurons in order to fully understand processing in the brain. It has been suggested that photonic communication may be possible along axonal connections, especially through the myelin sheath as a waveguide, due to its high refractive index. There is already a good deal of theoretical and experimental evidence for light guidance in the myelin sheath; however, the question of how the polarization of light is transmitted remains largely unexplored. It is presently unclear whether polarization-encoded information could be preserved within the myelin sheath. We simulate guided mode propagation through a myelinated axon structure with multiple Ranvier nodes. This allows both to observe polarization change and to test the assumption of exponentiated transmission loss through multiple Ranvier nodes for guided light in myelin sheath waveguides. We find that the polarization can be well preserved through multiple nodes and that transmission losses through multiple nodes are approximately multiplicative. These results provide an important context for the hypothesis of neural information transmission facilitated by biophotons, strengthening the possibility of both classical and quantum photonic communication within the brain.
{"title":"Optical Polarization Evolution and Transmission in Multi-Ranvier-Node Axonal Myelin-Sheath Waveguides","authors":"Emily Frede;Hadi Zadeh-Haghighi;Christoph Simon","doi":"10.1109/TMBMC.2024.3464415","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3464415","url":null,"abstract":"In neuroscience, it is of interest to consider all possible modes of information transfer between neurons in order to fully understand processing in the brain. It has been suggested that photonic communication may be possible along axonal connections, especially through the myelin sheath as a waveguide, due to its high refractive index. There is already a good deal of theoretical and experimental evidence for light guidance in the myelin sheath; however, the question of how the polarization of light is transmitted remains largely unexplored. It is presently unclear whether polarization-encoded information could be preserved within the myelin sheath. We simulate guided mode propagation through a myelinated axon structure with multiple Ranvier nodes. This allows both to observe polarization change and to test the assumption of exponentiated transmission loss through multiple Ranvier nodes for guided light in myelin sheath waveguides. We find that the polarization can be well preserved through multiple nodes and that transmission losses through multiple nodes are approximately multiplicative. These results provide an important context for the hypothesis of neural information transmission facilitated by biophotons, strengthening the possibility of both classical and quantum photonic communication within the brain.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 4","pages":"613-622"},"PeriodicalIF":2.4,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844592","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 : 2024-09-17DOI: 10.1109/TMBMC.2024.3462727
Bitop Maitra;Ozgur B. Akan
The gut-brain axis is the communication link between the gut and the brain. Although it is known that the gut-brain axis plays a pivotal role in homeostasis, its overall mechanism is still not known. However, for neural synapses, classical molecular communication is described by the formation of ligand-receptor complexes, which leads to the opening of ion channels. Moreover, there are some conditions that need to be fulfilled before the opening of the ion channel. In this study, we consider the gut-brain axis, where neurotransmitters diffuse through the synaptic cleft, considering molecular communication. On the vagus nerve (VN) membrane, i.e., the post-synaptic membrane of the synapse, it undergoes a quantum communication (QC), which initiates the opening of the ion channel, thus initiating the communication signal from the gut to the brain. It evolves a new paradigm of communication approach, Molecular Quantum (MolQ) communication. Based on the QC model, we theoretically analyze the output states, and QC is simulated considering the incoming neurotransmitter’s concentration and validated by analyzing the entropy and the mutual information of the input, i.e., neurotransmitter’s concentration, and output, i.e., ion channel opening.
{"title":"Molecular Quantum (MolQ) Communication Channel in the Gut-Brain Axis Synapse","authors":"Bitop Maitra;Ozgur B. Akan","doi":"10.1109/TMBMC.2024.3462727","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3462727","url":null,"abstract":"The gut-brain axis is the communication link between the gut and the brain. Although it is known that the gut-brain axis plays a pivotal role in homeostasis, its overall mechanism is still not known. However, for neural synapses, classical molecular communication is described by the formation of ligand-receptor complexes, which leads to the opening of ion channels. Moreover, there are some conditions that need to be fulfilled before the opening of the ion channel. In this study, we consider the gut-brain axis, where neurotransmitters diffuse through the synaptic cleft, considering molecular communication. On the vagus nerve (VN) membrane, i.e., the post-synaptic membrane of the synapse, it undergoes a quantum communication (QC), which initiates the opening of the ion channel, thus initiating the communication signal from the gut to the brain. It evolves a new paradigm of communication approach, Molecular Quantum (MolQ) communication. Based on the QC model, we theoretically analyze the output states, and QC is simulated considering the incoming neurotransmitter’s concentration and validated by analyzing the entropy and the mutual information of the input, i.e., neurotransmitter’s concentration, and output, i.e., ion channel opening.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 4","pages":"604-612"},"PeriodicalIF":2.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844593","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 : 2024-09-02DOI: 10.1109/TMBMC.2024.3453808
Fardad Vakilipoor;Abdulhamid N. M. Ansari;Luca Barletta;Gian Guido Gentili;Maurizio Magarini
This paper presents an approach to address the diffusion equation in scenarios involving multiple absorbing boundary conditions, commonly found in diffusive molecular communication (MC) channels. Instead of using multiple mirror images of the source, fictitious sources with time-varying release rates are introduced to replace the boundaries. This transformation enables the calculation of the expected cumulative number of absorbed particles (CNAP) by multiple absorbing boundaries with finite volume. To compute the expected CNAP, the concept of barycenter, which represents the spatial mean of particles the receiver absorbs is introduced. Substituting absorbing objects with their barycenters leads to model the CNAP in scenarios with convex geometry of absorbers. In a one-dimensional (1D) space, the proposed approach yields the same expression as the method of images for describing the expected CNAP by an absorber. However, in three-dimensional (3D) space, where using the method of images is challenging or even impossible, the proposed approach enables substituting the objects with fictitious sources and compute the expected CNAP. In 1D, an extension of this approach to the case in which one boundary exhibits an absorption characteristic while the other has zero-flux characteristic is demonstrated. This research direction is valuable for modeling channels where not all objects are particle receptors.
{"title":"The Method of Fictitious Negative Sources to Model Diffusive Channels With Absorbing Boundaries","authors":"Fardad Vakilipoor;Abdulhamid N. M. Ansari;Luca Barletta;Gian Guido Gentili;Maurizio Magarini","doi":"10.1109/TMBMC.2024.3453808","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3453808","url":null,"abstract":"This paper presents an approach to address the diffusion equation in scenarios involving multiple absorbing boundary conditions, commonly found in diffusive molecular communication (MC) channels. Instead of using multiple mirror images of the source, fictitious sources with time-varying release rates are introduced to replace the boundaries. This transformation enables the calculation of the expected cumulative number of absorbed particles (CNAP) by multiple absorbing boundaries with finite volume. To compute the expected CNAP, the concept of barycenter, which represents the spatial mean of particles the receiver absorbs is introduced. Substituting absorbing objects with their barycenters leads to model the CNAP in scenarios with convex geometry of absorbers. In a one-dimensional (1D) space, the proposed approach yields the same expression as the method of images for describing the expected CNAP by an absorber. However, in three-dimensional (3D) space, where using the method of images is challenging or even impossible, the proposed approach enables substituting the objects with fictitious sources and compute the expected CNAP. In 1D, an extension of this approach to the case in which one boundary exhibits an absorption characteristic while the other has zero-flux characteristic is demonstrated. This research direction is valuable for modeling channels where not all objects are particle receptors.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 3","pages":"442-454"},"PeriodicalIF":2.4,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10663575","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142320395","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}
Bacterial sensor systems can be used for the detection and measurement of molecular signal concentrations. The dynamics of the sensor directly depend on the biological properties of the bacterial sensor cells; manipulation of these features in the wet lab enables the engineering and optimization of the bacterial sensor kinetics. This necessitates the development of biologically meaningful computational models for bacterial sensors comprising a variety of different molecular mechanisms, which further facilitates a systematic and quantitative evaluation of optimization strategies. In this work, we dissect the detection chain of bacterial sensors, focusing on computational aspects. As a case example, we derive, supported by wet-lab data, a complete computational model for a Streptococcus mutans-based bacterial sensor. We address the engineering of bacterial sensors by mathematically investigating the impact of altered bacterial cell properties on the sensor response characteristics, specifically sensor sensitivity and response signal intensity. This is achieved through a sensitivity analysis targeting both the steady-state and transient sensor response characteristics. Alongside the demonstration of the suitability of our methodological approach, our analysis shows that an increase in sensor sensitivity through targeted manipulation of bacterial physiology often comes at the cost of generally diminished sensor response intensity.
{"title":"Quantitative Aspects, Engineering and Optimization of Bacterial Sensor Systems","authors":"Florian Anderl;Gabriela Salvadori;Mladen Veletic;Fernanda Cristina Petersen;Ilangko Balasingham","doi":"10.1109/TMBMC.2024.3452066","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3452066","url":null,"abstract":"Bacterial sensor systems can be used for the detection and measurement of molecular signal concentrations. The dynamics of the sensor directly depend on the biological properties of the bacterial sensor cells; manipulation of these features in the wet lab enables the engineering and optimization of the bacterial sensor kinetics. This necessitates the development of biologically meaningful computational models for bacterial sensors comprising a variety of different molecular mechanisms, which further facilitates a systematic and quantitative evaluation of optimization strategies. In this work, we dissect the detection chain of bacterial sensors, focusing on computational aspects. As a case example, we derive, supported by wet-lab data, a complete computational model for a Streptococcus mutans-based bacterial sensor. We address the engineering of bacterial sensors by mathematically investigating the impact of altered bacterial cell properties on the sensor response characteristics, specifically sensor sensitivity and response signal intensity. This is achieved through a sensitivity analysis targeting both the steady-state and transient sensor response characteristics. Alongside the demonstration of the suitability of our methodological approach, our analysis shows that an increase in sensor sensitivity through targeted manipulation of bacterial physiology often comes at the cost of generally diminished sensor response intensity.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 4","pages":"517-533"},"PeriodicalIF":2.4,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844191","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 : 2024-08-23DOI: 10.1109/TMBMC.2024.3448353
Anil Kamber;H. Birkan Yilmaz;Ali E. Pusane;Tuna Tugcu
In molecular communication via diffusion (MCvD), messenger molecules are emitted by a transmitter and propagate randomly through the fluidic environment. In biological systems, the environment can be considered a bounded space, surrounded by various structures such as tissues and organs. The propagation of molecules is affected by these structures, which reflect the molecules upon collision. Deriving the channel response of MCvD systems with an absorbing spherical receiver requires solving the 3-D diffusion equation in the presence of reflecting and absorbing boundary conditions, which is extremely challenging. In this paper, the method of images is brought to molecular communication (MC) realm to find a closed-form solution to the channel response of a single-input single-output (SISO) system near an infinite reflecting surface. It is shown that a molecular SISO system in a 3-D half-space with an infinite reflecting surface could be approximated as a molecular single-input multiple-output (SIMO) system in a 3-D space, which consists of two symmetrically located, with respect to the reflecting surface, identical absorbing spherical receivers.
{"title":"Half-Space Modeling With Reflecting Surface in Molecular Communication","authors":"Anil Kamber;H. Birkan Yilmaz;Ali E. Pusane;Tuna Tugcu","doi":"10.1109/TMBMC.2024.3448353","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3448353","url":null,"abstract":"In molecular communication via diffusion (MCvD), messenger molecules are emitted by a transmitter and propagate randomly through the fluidic environment. In biological systems, the environment can be considered a bounded space, surrounded by various structures such as tissues and organs. The propagation of molecules is affected by these structures, which reflect the molecules upon collision. Deriving the channel response of MCvD systems with an absorbing spherical receiver requires solving the 3-D diffusion equation in the presence of reflecting and absorbing boundary conditions, which is extremely challenging. In this paper, the method of images is brought to molecular communication (MC) realm to find a closed-form solution to the channel response of a single-input single-output (SISO) system near an infinite reflecting surface. It is shown that a molecular SISO system in a 3-D half-space with an infinite reflecting surface could be approximated as a molecular single-input multiple-output (SIMO) system in a 3-D space, which consists of two symmetrically located, with respect to the reflecting surface, identical absorbing spherical receivers.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 3","pages":"433-441"},"PeriodicalIF":2.4,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142320515","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 : 2024-08-12DOI: 10.1109/TMBMC.2024.3442083
Michael Taynnan Barros;Michelangelo Paci;Aapo Tervonen;Elisa Passini;Jussi T. Koivumäki;Jari A. K. Hyttinen;Kerstin Lenk
With many advancements in in silico multiscale biology in recent years, the paramount challenge is to translate the accumulated knowledge into exciting industry partnerships and clinical applications. Historically, the pharmaceutical industry has worked well with in silico models by leveraging their prediction capabilities for drug testing. However, the needed higher fidelity and higher resolution of models for efficient prediction of pharmacological phenomenon dictates that in silico approaches must account for the verifiable multiscale biophysical phenomena, as a spatial and temporal dimension variation for different processes and models. Our paper has two main goals: 1) To clarify to what extent detailed single- and multiscale modeling has been accomplished thus far, we provide a review on this topic focusing on the biophysics of epithelial, cardiac, and brain tissues; 2) To discuss the present and future role of multiscale biophysics in in silico pharmacology as a digital twin solution by defining a roadmap from simple biophysical models to powerful prediction tools. Digital twins have the potential to pave the way for extensive clinical and pharmaceutical usage of multiscale models, and our paper shows the fundamentals and opportunities for their accurate development, enabling the quantum leaps of future precise and personalized medical software.
{"title":"From Multiscale Biophysics to Digital Twins of Tissues and Organs: Future Opportunities for in-silico Pharmacology","authors":"Michael Taynnan Barros;Michelangelo Paci;Aapo Tervonen;Elisa Passini;Jussi T. Koivumäki;Jari A. K. Hyttinen;Kerstin Lenk","doi":"10.1109/TMBMC.2024.3442083","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3442083","url":null,"abstract":"With many advancements in in silico multiscale biology in recent years, the paramount challenge is to translate the accumulated knowledge into exciting industry partnerships and clinical applications. Historically, the pharmaceutical industry has worked well with in silico models by leveraging their prediction capabilities for drug testing. However, the needed higher fidelity and higher resolution of models for efficient prediction of pharmacological phenomenon dictates that in silico approaches must account for the verifiable multiscale biophysical phenomena, as a spatial and temporal dimension variation for different processes and models. Our paper has two main goals: 1) To clarify to what extent detailed single- and multiscale modeling has been accomplished thus far, we provide a review on this topic focusing on the biophysics of epithelial, cardiac, and brain tissues; 2) To discuss the present and future role of multiscale biophysics in in silico pharmacology as a digital twin solution by defining a roadmap from simple biophysical models to powerful prediction tools. Digital twins have the potential to pave the way for extensive clinical and pharmaceutical usage of multiscale models, and our paper shows the fundamentals and opportunities for their accurate development, enabling the quantum leaps of future precise and personalized medical software.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 4","pages":"576-594"},"PeriodicalIF":2.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844266","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 : 2024-08-01DOI: 10.1109/TMBMC.2024.3436905
Stefan Angerbauer;Nunzio Tuccitto;Giuseppe Trusso Sfrazzetto;Rossella Santonocito;Werner Haselmayr
Intelligent nano-machines are a promising candidate technology for the next generation of health care. The realization of such units relies on novel, unconventional approaches, to navigate the challenges of this particular domain. In this work, we present three chemical processes, that can be used to realize a recently proposed molecular matrix multiplication unit on the lab-scale. The matrix multiplication is the fundamental operation for the realization of neural networks and, therefore, artificial intelligence. Hence, this work presents an important step towards practical realization of intelligent nano-machines for the next generation of health care.
{"title":"Investigation of Different Chemical Realizations for Molecular Matrix Multiplications","authors":"Stefan Angerbauer;Nunzio Tuccitto;Giuseppe Trusso Sfrazzetto;Rossella Santonocito;Werner Haselmayr","doi":"10.1109/TMBMC.2024.3436905","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3436905","url":null,"abstract":"Intelligent nano-machines are a promising candidate technology for the next generation of health care. The realization of such units relies on novel, unconventional approaches, to navigate the challenges of this particular domain. In this work, we present three chemical processes, that can be used to realize a recently proposed molecular matrix multiplication unit on the lab-scale. The matrix multiplication is the fundamental operation for the realization of neural networks and, therefore, artificial intelligence. Hence, this work presents an important step towards practical realization of intelligent nano-machines for the next generation of health care.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 3","pages":"464-469"},"PeriodicalIF":2.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10620232","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142320514","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 : 2024-07-29DOI: 10.1109/TMBMC.2024.3434545
M. Javad Fakhimi;Ozgur B. Akan
Nanoantennas, operating at optical frequencies, are a transformative technology with broad applications in 6G wireless communication, IoT, smart cities, healthcare, and medical imaging. This paper explores their fundamental aspects, applications, and advancements, aiming for a comprehensive understanding of their potential in various applications. It begins by investigating macroscopic and microscopic Maxwell’s equations governing electromagnetic wave propagation at different scales. The study emphasizes the critical role of surface plasmon polariton wave propagation in enhancing light-matter interactions, contributing to high data rates, and enabling miniaturization. Additionally, it explores using two-dimensional materials like graphene for enhanced control in terahertz communication and sensing. The paper also introduces the employment of nanoantennas as the main building blocks of Nano-scale Radar (NR) systems for the first time in the literature. NRs, integrated with communication signals, promise accurate radar sensing for nanoparticles inside a nano-channel, making them a potential future application in integrated sensing and communication (ISAC) systems. These nano-scale radar systems detect and extract physical or electrical properties of nanoparticles through transmitting, receiving, and processing electromagnetic waves at ultra-high frequencies in the optical range. This task requires nanoantennas as transmitters/receivers/transceivers, sharing the same frequency band and hardware for high-performance sensing and resolution.
{"title":"Nanoantennas and Nanoradars: The Future of Integrated Sensing and Communication at the Nanoscale","authors":"M. Javad Fakhimi;Ozgur B. Akan","doi":"10.1109/TMBMC.2024.3434545","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3434545","url":null,"abstract":"Nanoantennas, operating at optical frequencies, are a transformative technology with broad applications in 6G wireless communication, IoT, smart cities, healthcare, and medical imaging. This paper explores their fundamental aspects, applications, and advancements, aiming for a comprehensive understanding of their potential in various applications. It begins by investigating macroscopic and microscopic Maxwell’s equations governing electromagnetic wave propagation at different scales. The study emphasizes the critical role of surface plasmon polariton wave propagation in enhancing light-matter interactions, contributing to high data rates, and enabling miniaturization. Additionally, it explores using two-dimensional materials like graphene for enhanced control in terahertz communication and sensing. The paper also introduces the employment of nanoantennas as the main building blocks of Nano-scale Radar (NR) systems for the first time in the literature. NRs, integrated with communication signals, promise accurate radar sensing for nanoparticles inside a nano-channel, making them a potential future application in integrated sensing and communication (ISAC) systems. These nano-scale radar systems detect and extract physical or electrical properties of nanoparticles through transmitting, receiving, and processing electromagnetic waves at ultra-high frequencies in the optical range. This task requires nanoantennas as transmitters/receivers/transceivers, sharing the same frequency band and hardware for high-performance sensing and resolution.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 4","pages":"493-516"},"PeriodicalIF":2.4,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844374","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}
The sensitivity of many in vivo applications necessitates investigating adversarial activities in micro-scale MC systems. On the other hand, macro-scale applications of MC are easier to launch security attacks on. In this paper, we study the problem of jamming attacks in MC, where a concentration transmitter releases a particular type of molecule to send its message over a diffusive channel to a transparent receiver. A jammer wishes to disrupt the communication either by transmitting the same molecule type or a reacting molecule type. We propose jamming-resistant coding schemes to counteract this attack. For this purpose, three jamming models based on different capabilities of attackers and their possible strategies are introduced. The difference of jamming models relates to existence of sensing and learning capabilities. For two jammer types, our coding approaches are based on splitting each time slot into subslots, where a random pre-shared pattern is used to determine the transmit strategy in these subslots. The coding scheme against the third jammer type, which is the strongest one, is designed based on error correction codes with maximum Hamming distance. To analyse the performances of the proposed schemes, we derive the probability of error at the receiver. The results of the proposed schemes against the first and the second types of jammers confirm their effectiveness in protecting against jamming attacks. For example, in the specific case of the jammer channel and main channel discussed in the results section, we achieve an almost 78% reduction in the probability of errors at the receiver compared to a non-coded system when facing the first type of jammer. The third type of jammer represents the worst-case attack scenario, and its performance can be used as an upper bound for system performance.
{"title":"A Jamming-Resistant Molecular Communication Scheme","authors":"Sahar Shahbaz;Mahtab Mirmohseni;Masoumeh Nasiri-Kenari","doi":"10.1109/TMBMC.2024.3426920","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3426920","url":null,"abstract":"The sensitivity of many in vivo applications necessitates investigating adversarial activities in micro-scale MC systems. On the other hand, macro-scale applications of MC are easier to launch security attacks on. In this paper, we study the problem of jamming attacks in MC, where a concentration transmitter releases a particular type of molecule to send its message over a diffusive channel to a transparent receiver. A jammer wishes to disrupt the communication either by transmitting the same molecule type or a reacting molecule type. We propose jamming-resistant coding schemes to counteract this attack. For this purpose, three jamming models based on different capabilities of attackers and their possible strategies are introduced. The difference of jamming models relates to existence of sensing and learning capabilities. For two jammer types, our coding approaches are based on splitting each time slot into subslots, where a random pre-shared pattern is used to determine the transmit strategy in these subslots. The coding scheme against the third jammer type, which is the strongest one, is designed based on error correction codes with maximum Hamming distance. To analyse the performances of the proposed schemes, we derive the probability of error at the receiver. The results of the proposed schemes against the first and the second types of jammers confirm their effectiveness in protecting against jamming attacks. For example, in the specific case of the jammer channel and main channel discussed in the results section, we achieve an almost 78% reduction in the probability of errors at the receiver compared to a non-coded system when facing the first type of jammer. The third type of jammer represents the worst-case attack scenario, and its performance can be used as an upper bound for system performance.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 4","pages":"534-548"},"PeriodicalIF":2.4,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844508","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 : 2024-07-15DOI: 10.1109/TMBMC.2024.3427660
Taha Sajjad;Andrew W. Eckford
Biological systems transduce signals from their surroundings in numerous ways. This paper introduces a communication system using the light-gated ion channel Channelrhodopsin-2 (ChR2), which causes an ion current to flow in response to light. Our design includes a ChR2-based receiver along with encoding, modulation techniques and detection. Analyzing the resulting communication system, we discuss the effect of different parameters on the performance of the system. Finally, we discuss its potential design in the context of bio-engineering and light-based communication and show that the data rate scales up with the number of receptors, indicating that high-speed communication may be possible.
{"title":"Designing a Light-Based Communication System With a Biomolecular Receiver","authors":"Taha Sajjad;Andrew W. Eckford","doi":"10.1109/TMBMC.2024.3427660","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3427660","url":null,"abstract":"Biological systems transduce signals from their surroundings in numerous ways. This paper introduces a communication system using the light-gated ion channel Channelrhodopsin-2 (ChR2), which causes an ion current to flow in response to light. Our design includes a ChR2-based receiver along with encoding, modulation techniques and detection. Analyzing the resulting communication system, we discuss the effect of different parameters on the performance of the system. Finally, we discuss its potential design in the context of bio-engineering and light-based communication and show that the data rate scales up with the number of receptors, indicating that high-speed communication may be possible.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 4","pages":"566-575"},"PeriodicalIF":2.4,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844242","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}
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