Pub Date : 2023-12-04DOI: 10.1109/TMBMC.2023.3338950
Hanlin Xiao;Kamela Dokaj;Ozgur B. Akan
Molecular communication, as implied by its name, uses molecules as information carriers for communication between objects. It has an advantage over traditional electromagnetic-wave-based communication in that molecule-based systems could be biocompatible, operable in challenging environments, and energetically undemanding. Consequently, they are envisioned to have a broad range of applications, such as in the Internet of Bio-Nano Things, targeted drug delivery, and agricultural monitoring. Despite the rapid development of the field, with an increasing number of theoretical models and experimental testbeds established by researchers, a fundamental aspect of the field has often been sidelined, namely, the nature of the molecule in molecular communication. The potential information molecules could exhibit a wide range of properties, making them require drastically different treatments when being modeled and experimented upon. Therefore, in this paper, we delve into the intricacies of commonly used information molecules, examining their fundamental physical characteristics, associated communication systems, and potential applications in a more realistic manner, focusing on the influence of their own properties. Through this comprehensive survey, we aim to offer a novel yet essential perspective on molecular communication, thereby bridging the current gap between theoretical research and real-world applications.
{"title":"What Really is “Molecule” in Molecular Communications? The Quest for Physics of Particle-Based Information Carriers","authors":"Hanlin Xiao;Kamela Dokaj;Ozgur B. Akan","doi":"10.1109/TMBMC.2023.3338950","DOIUrl":"10.1109/TMBMC.2023.3338950","url":null,"abstract":"Molecular communication, as implied by its name, uses molecules as information carriers for communication between objects. It has an advantage over traditional electromagnetic-wave-based communication in that molecule-based systems could be biocompatible, operable in challenging environments, and energetically undemanding. Consequently, they are envisioned to have a broad range of applications, such as in the Internet of Bio-Nano Things, targeted drug delivery, and agricultural monitoring. Despite the rapid development of the field, with an increasing number of theoretical models and experimental testbeds established by researchers, a fundamental aspect of the field has often been sidelined, namely, the nature of the molecule in molecular communication. The potential information molecules could exhibit a wide range of properties, making them require drastically different treatments when being modeled and experimented upon. Therefore, in this paper, we delve into the intricacies of commonly used information molecules, examining their fundamental physical characteristics, associated communication systems, and potential applications in a more realistic manner, focusing on the influence of their own properties. Through this comprehensive survey, we aim to offer a novel yet essential perspective on molecular communication, thereby bridging the current gap between theoretical research and real-world applications.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"43-74"},"PeriodicalIF":2.2,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139234475","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 : 2023-11-29DOI: 10.1109/TMBMC.2023.3336259
Guodong Yue;Guoying Lin;Qiang Liu;Kun Yang
Molecular communication (MC) is a significant technology in the field of nano-biology, which uses molecules as message carriers to transmit information. Diffusion channel model is the most common channel model base on Brownian motion in molecular communication since molecules can diffuse to the destination without the need of extra energy supply. However, the random Brownian motion brings high delay and uncertainty to the communication process and thus modulation methods are required to improve the communication performance. The molecular communication system in the SISO (Single Input Single Output) scenario will be seriously affected by ISI (Inter Symbol Interference). In MIMO (Multi-Input Multi-Output) scenario, since there are multiple transmitters and receivers, in addition to ISI, there will be ILI (Inter Link Interference) as well. At present, most modulations are based on the concentration, type, time and space of molecules and only focus on SISO scenario. In this study, inspired by the MoSK (Molecule Shift Keying) modulation method, we proposed a new joint modulation method for MIMO communication in order to minimize the effect of ISI and ILI. Numerical results show that compared with the current modulation scheme, the proposed scheme allows the MIMO system achieve better BER (Bit error rate) performance and transmission rate.
分子通讯（MC）是纳米生物学领域的一项重要技术，它利用分子作为信息载体来传输信息。扩散信道模型是分子通讯中最常见的基于布朗运动的信道模型，因为分子可以扩散到目的地而不需要额外的能量供应。然而，随机布朗运动会给通信过程带来高延迟和不确定性，因此需要采用调制方法来提高通信性能。在 SISO（单输入单输出）情况下，分子通信系统会受到 ISI（符号间干扰）的严重影响。在 MIMO（多输入多输出）情况下，由于有多个发射器和接收器，除了 ISI 外，还会出现 ILI（链路间干扰）。目前，大多数调制都是基于分子的浓度、类型、时间和空间，并且只关注 SISO 场景。本研究受 MoSK（分子移频键控）调制方法的启发，提出了一种用于 MIMO 通信的新型联合调制方法，以最大限度地降低 ISI 和 ILI 的影响。数值结果表明，与当前的调制方案相比，所提出的方案能使多输入多输出系统获得更好的误码率（BER）性能和传输速率。
{"title":"Diffusion-Based Anti-Interference Joint Modulation in MIMO Molecular Communication","authors":"Guodong Yue;Guoying Lin;Qiang Liu;Kun Yang","doi":"10.1109/TMBMC.2023.3336259","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3336259","url":null,"abstract":"Molecular communication (MC) is a significant technology in the field of nano-biology, which uses molecules as message carriers to transmit information. Diffusion channel model is the most common channel model base on Brownian motion in molecular communication since molecules can diffuse to the destination without the need of extra energy supply. However, the random Brownian motion brings high delay and uncertainty to the communication process and thus modulation methods are required to improve the communication performance. The molecular communication system in the SISO (Single Input Single Output) scenario will be seriously affected by ISI (Inter Symbol Interference). In MIMO (Multi-Input Multi-Output) scenario, since there are multiple transmitters and receivers, in addition to ISI, there will be ILI (Inter Link Interference) as well. At present, most modulations are based on the concentration, type, time and space of molecules and only focus on SISO scenario. In this study, inspired by the MoSK (Molecule Shift Keying) modulation method, we proposed a new joint modulation method for MIMO communication in order to minimize the effect of ISI and ILI. Numerical results show that compared with the current modulation scheme, the proposed scheme allows the MIMO system achieve better BER (Bit error rate) performance and transmission rate.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"112-121"},"PeriodicalIF":2.2,"publicationDate":"2023-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161241","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}
Cells communicate with each other exploiting a variety of chemical signals. Among them, Extracellular Vesicles (EVs) have attracted large interest by the scientific community. In fact, thanks to the advances in bio-nano-technology and the possibility of engineering EVs, they are envisioned as a perfect means for distributing biological information among receiving cells. However, deciphering the molecular mechanisms that regulate the delivery of EV cargo is, today, a necessary, yet challenging, step toward the exploitation of EV signaling to support innovative and efficient therapeutic protocols, alternative to current drug delivery technologies. In particular, very little information is currently available on the processes of EV fusion, which is the EV internalization process occurring when the EV membrane dissolves into the plasma membrane of the target cell, and the EV content is released into the cytosol. In order to understand the dynamics of this process, this paper introduces an analytical model of the evolution of the fusion process. Moreover, since the measurement of the biological parameters driving the fusion process is far to be achieved, in this paper we use the model as a tool to infer likely values of such parameters from parameters that are measurable with current technology.
细胞之间利用各种化学信号进行交流。其中，细胞外囊泡（EVs）引起了科学界的极大兴趣。事实上，得益于生物纳米技术的进步以及对 EVs 进行工程化的可能性，EVs 被认为是在接收细胞间传播生物信息的完美手段。然而，破译调控 EV 货物递送的分子机制是当今利用 EV 信号支持创新和高效治疗方案、替代当前药物递送技术的一个必要但极具挑战性的步骤。特别是，目前有关 EV 融合过程的信息非常少，而 EV 融合是指 EV 膜溶解到靶细胞的质膜上，EV 内容释放到细胞质中的 EV 内化过程。为了了解这一过程的动态，本文介绍了融合过程演变的分析模型。此外，由于对驱动融合过程的生物参数的测量远未实现，我们在本文中将该模型作为一种工具，从现有技术可测量的参数中推断出这些参数的可能值。
{"title":"Intercellular Chemical Communication Through EV Exchange: Evaluation of the EV Fusion Process Parameters at the Receiving Cell","authors":"Alfio Lombardo;Giacomo Morabito;Carla Panarello;Fabrizio Pappalardo","doi":"10.1109/TMBMC.2023.3336322","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3336322","url":null,"abstract":"Cells communicate with each other exploiting a variety of chemical signals. Among them, Extracellular Vesicles (EVs) have attracted large interest by the scientific community. In fact, thanks to the advances in bio-nano-technology and the possibility of engineering EVs, they are envisioned as a perfect means for distributing biological information among receiving cells. However, deciphering the molecular mechanisms that regulate the delivery of EV cargo is, today, a necessary, yet challenging, step toward the exploitation of EV signaling to support innovative and efficient therapeutic protocols, alternative to current drug delivery technologies. In particular, very little information is currently available on the processes of EV fusion, which is the EV internalization process occurring when the EV membrane dissolves into the plasma membrane of the target cell, and the EV content is released into the cytosol. In order to understand the dynamics of this process, this paper introduces an analytical model of the evolution of the fusion process. Moreover, since the measurement of the biological parameters driving the fusion process is far to be achieved, in this paper we use the model as a tool to infer likely values of such parameters from parameters that are measurable with current technology.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"21-31"},"PeriodicalIF":2.2,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10330635","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161171","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 : 2023-11-28DOI: 10.1109/TMBMC.2023.3336254
Grant Greenberg;Ilan Shomorony
The goal of metagenomics is to study the composition of microbial communities, typically using high-throughput shotgun sequencing. In the metagenomic binning problem, we observe random substrings (called contigs) from a mixture of genomes and aim to cluster them according to their genome of origin. Based on the empirical observation that genomes of different bacterial species can be distinguished based on their tetranucleotide frequencies, we model this task as the problem of clustering ${N}$ sequences generated by ${M}$ distinct Markov processes, where $M ll N$ . Utilizing the large-deviation principle for Markov processes, we establish the information-theoretic limit for perfect binning. Specifically, we show that the length of the contigs must scale with the inverse of the Chernoff divergence rate between the two most similar species. Furthermore, our result implies that contigs should be binned using the KL divergence rate as a measure of distance, as opposed to the Euclidean distance often used in practice.
{"title":"The Metagenomic Binning Problem: Clustering Markov Sequences","authors":"Grant Greenberg;Ilan Shomorony","doi":"10.1109/TMBMC.2023.3336254","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3336254","url":null,"abstract":"The goal of metagenomics is to study the composition of microbial communities, typically using high-throughput shotgun sequencing. In the metagenomic binning problem, we observe random substrings (called contigs) from a mixture of genomes and aim to cluster them according to their genome of origin. Based on the empirical observation that genomes of different bacterial species can be distinguished based on their tetranucleotide frequencies, we model this task as the problem of clustering \u0000<inline-formula> <tex-math>${N}$ </tex-math></inline-formula>\u0000 sequences generated by \u0000<inline-formula> <tex-math>${M}$ </tex-math></inline-formula>\u0000 distinct Markov processes, where \u0000<inline-formula> <tex-math>$M ll N$ </tex-math></inline-formula>\u0000. Utilizing the large-deviation principle for Markov processes, we establish the information-theoretic limit for perfect binning. Specifically, we show that the length of the contigs must scale with the inverse of the Chernoff divergence rate between the two most similar species. Furthermore, our result implies that contigs should be binned using the KL divergence rate as a measure of distance, as opposed to the Euclidean distance often used in practice.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"32-42"},"PeriodicalIF":2.2,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161172","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 : 2023-11-09DOI: 10.1109/TMBMC.2023.3331579
Wenfeng Wu;Luping Xiang;Qiang Liu;Kun Yang
In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme for DNA image storage, designated as DJSCC-DNA. This paradigm distinguishes itself from conventional DNA storage techniques through three key modifications: 1) it employs advanced deep learning methodologies, employing convolutional neural networks for DNA encoding and decoding processes; 2) it seamlessly integrates DNA polymerase chain reaction (PCR) amplification into the network architecture, thereby augmenting data recovery precision; and 3) it restructures the loss function by targeting biological constraints for optimization. The performance of the proposed model is demonstrated via numerical results from specific channel testing, suggesting that it surpasses conventional deep learning methodologies in terms of peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM). Additionally, the model effectively ensures positive constraints on both homopolymer run-length and GC content.
当今时代，基于脱氧核糖核酸（DNA）的数据存储成为一种引人入胜的方法，引起了学术界的极大兴趣和研究。本文介绍了一种用于 DNA 图像存储的新型深度联合源信道编码（DJSCC）方案，命名为 DJSCC-DNA。该范例通过三个关键修改将自己与传统的 DNA 存储技术区分开来：1）它采用了先进的深度学习方法，在 DNA 编码和解码过程中使用卷积神经网络；2）它将 DNA 聚合酶链式反应（PCR）扩增无缝集成到网络架构中，从而提高了数据恢复精度；3）它通过针对生物约束进行优化来重组损失函数。通过特定信道测试的数值结果证明了所提模型的性能，表明它在峰值信噪比（PSNR）和结构相似性指数（SSIM）方面超越了传统的深度学习方法。此外，该模型还有效地确保了对均聚物运行长度和 GC 含量的正向约束。
{"title":"Deep Joint Source-Channel Coding for DNA Image Storage: A Novel Approach With Enhanced Error Resilience and Biological Constraint Optimization","authors":"Wenfeng Wu;Luping Xiang;Qiang Liu;Kun Yang","doi":"10.1109/TMBMC.2023.3331579","DOIUrl":"10.1109/TMBMC.2023.3331579","url":null,"abstract":"In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme for DNA image storage, designated as DJSCC-DNA. This paradigm distinguishes itself from conventional DNA storage techniques through three key modifications: 1) it employs advanced deep learning methodologies, employing convolutional neural networks for DNA encoding and decoding processes; 2) it seamlessly integrates DNA polymerase chain reaction (PCR) amplification into the network architecture, thereby augmenting data recovery precision; and 3) it restructures the loss function by targeting biological constraints for optimization. The performance of the proposed model is demonstrated via numerical results from specific channel testing, suggesting that it surpasses conventional deep learning methodologies in terms of peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM). Additionally, the model effectively ensures positive constraints on both homopolymer run-length and GC content.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"461-471"},"PeriodicalIF":2.2,"publicationDate":"2023-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135562109","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 : 2023-11-08DOI: 10.1109/TMBMC.2023.3329801
Mustafa Can Gursoy;Urbashi Mitra
Diffusion-based molecular communications (DBMC) systems rely on diffusive propagation of molecules to convey information. In a DBMC system, as each emitted molecule experiences a stochastic delay, pulse shaping is crucial for a DBMC system’s reliability and overall performance. To this end, acknowledging the inherent resource-limited nature of a DBMC system, a novel framework to model and optimize a DBMC transmitter is introduced in this paper. Leveraging tools from wireless packet scheduling theory, the DBMC pulse shaping problem is formulated as an energy-constrained resource allocation problem. Through the developed framework, it is shown that the provably optimal pulse shape that minimizes the error probability is the delayed-spike pulse, where the incurred delay is a decreasing function of the available energy budget. The framework is then extended to both absorbing and passive/observing receiver structures, as well as systems where molecules can degrade in the transmitter body prior to release. Numerical results corroborate the developed analysis, and show that the delayed-spike outperforms conventional, non-zero-width pulse shapes in terms of error performance.
{"title":"Scheduling-Based Transmit Signal Shaping in Energy-Constrained Molecular Communications","authors":"Mustafa Can Gursoy;Urbashi Mitra","doi":"10.1109/TMBMC.2023.3329801","DOIUrl":"10.1109/TMBMC.2023.3329801","url":null,"abstract":"Diffusion-based molecular communications (DBMC) systems rely on diffusive propagation of molecules to convey information. In a DBMC system, as each emitted molecule experiences a stochastic delay, pulse shaping is crucial for a DBMC system’s reliability and overall performance. To this end, acknowledging the inherent resource-limited nature of a DBMC system, a novel framework to model and optimize a DBMC transmitter is introduced in this paper. Leveraging tools from wireless packet scheduling theory, the DBMC pulse shaping problem is formulated as an energy-constrained resource allocation problem. Through the developed framework, it is shown that the provably optimal pulse shape that minimizes the error probability is the delayed-spike pulse, where the incurred delay is a decreasing function of the available energy budget. The framework is then extended to both absorbing and passive/observing receiver structures, as well as systems where molecules can degrade in the transmitter body prior to release. Numerical results corroborate the developed analysis, and show that the delayed-spike outperforms conventional, non-zero-width pulse shapes in terms of error performance.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"447-460"},"PeriodicalIF":2.2,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135508660","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}
In the most severe COVID-19 cases, often the cytokine molecules produced by the immune system to fight off coronavirus infection become hyperactive. This leads to “cytokine storm”, which is a serious adverse medical condition causing multiple organ failures. In this work, we propose a system model that captures the transmission of cytokines from the alveoli, the propagation via the vascular channel, and the reception in the blood vessel wall. We analyze the impact of different diseases on induced cytokine storm. The proposed analytical model helps observe the behavior of cytokine storm in different medical conditions. We perform particle-based simulations to analyze the proposed end-to-end channel model describing the cytokine storm in terms of gain and delay, which is inspired from the existing molecular communication channel models from literature. We observe that the channel gain mostly remains unaffected for upto three times increase in the channel length, while, with four times increase, the gain increases upto 16% at 1000 rad/s frequency. We analyze the channel response to the different stimuli of interactions between the cytokines and their varying release rates. We evaluate the cytokine signal at the receiver and observe that lesser diffusion leads to higher cytokine concentration at the receiver.
{"title":"Channel Characterization of Molecular Communications for Cytokine Storm in COVID-19 Patients","authors":"Saswati Pal;Sudip Misra;Nabiul Islam;Sasitharan Balasubramaniam","doi":"10.1109/TMBMC.2023.3327869","DOIUrl":"10.1109/TMBMC.2023.3327869","url":null,"abstract":"In the most severe COVID-19 cases, often the cytokine molecules produced by the immune system to fight off coronavirus infection become hyperactive. This leads to “cytokine storm”, which is a serious adverse medical condition causing multiple organ failures. In this work, we propose a system model that captures the transmission of cytokines from the alveoli, the propagation via the vascular channel, and the reception in the blood vessel wall. We analyze the impact of different diseases on induced cytokine storm. The proposed analytical model helps observe the behavior of cytokine storm in different medical conditions. We perform particle-based simulations to analyze the proposed end-to-end channel model describing the cytokine storm in terms of gain and delay, which is inspired from the existing molecular communication channel models from literature. We observe that the channel gain mostly remains unaffected for upto three times increase in the channel length, while, with four times increase, the gain increases upto 16% at 1000 rad/s frequency. We analyze the channel response to the different stimuli of interactions between the cytokines and their varying release rates. We evaluate the cytokine signal at the receiver and observe that lesser diffusion leads to higher cytokine concentration at the receiver.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"425-434"},"PeriodicalIF":2.2,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135212692","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 : 2023-10-24DOI: 10.1109/TMBMC.2023.3327302
Hadeel Elayan;Andrew W. Eckford;Raviraj S. Adve
Folding of proteins into their correct native structure is key to their function. Simultaneously, the intricate interplay between cell movement and protein conformation highlights the complex nature of cellular processes. In this work, we demonstrate the impact of Terahertz (THz) signaling on controlling protein conformational changes in a random medium. Our system of interest consists of a communication link that involves a nanoantenna transmitter, a protein receiver, and a channel composed of moving red blood cells. Due to the system dynamics, we investigate the influence of both the fast and slow channel variations on protein folding. Specifically, we analyze the system’s selectivity to asses the effectiveness of the induced THz interaction in targeting a specific group of proteins under fading conditions. By optimizing the selectivity metric with respect to the nanoantenna power and frequency, it is possible to enhance the controllability of protein interactions. Our probabilistic analysis provides a new perspective regarding electromagnetically triggered protein molecules, their micro-environment and their interaction with surrounding particles. It helps elucidate how external conditions impact the protein folding kinetics and pathways. This results in not only understanding the mechanisms underlying THz-induced protein interactions but also engineering these still-emerging tools.
{"title":"Terahertz Induced Protein Interactions in a Random Medium","authors":"Hadeel Elayan;Andrew W. Eckford;Raviraj S. Adve","doi":"10.1109/TMBMC.2023.3327302","DOIUrl":"10.1109/TMBMC.2023.3327302","url":null,"abstract":"Folding of proteins into their correct native structure is key to their function. Simultaneously, the intricate interplay between cell movement and protein conformation highlights the complex nature of cellular processes. In this work, we demonstrate the impact of Terahertz (THz) signaling on controlling protein conformational changes in a random medium. Our system of interest consists of a communication link that involves a nanoantenna transmitter, a protein receiver, and a channel composed of moving red blood cells. Due to the system dynamics, we investigate the influence of both the fast and slow channel variations on protein folding. Specifically, we analyze the system’s selectivity to asses the effectiveness of the induced THz interaction in targeting a specific group of proteins under fading conditions. By optimizing the selectivity metric with respect to the nanoantenna power and frequency, it is possible to enhance the controllability of protein interactions. Our probabilistic analysis provides a new perspective regarding electromagnetically triggered protein molecules, their micro-environment and their interaction with surrounding particles. It helps elucidate how external conditions impact the protein folding kinetics and pathways. This results in not only understanding the mechanisms underlying THz-induced protein interactions but also engineering these still-emerging tools.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"435-446"},"PeriodicalIF":2.2,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135158256","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 : 2023-10-19DOI: 10.1109/TMBMC.2023.3325405
Max Bartunik;Janina Teller;Georg Fischer;Jens Kirchner
Testbeds play an essential role in the development of real-life molecular communication applications and experimental validation of communication channel models. Although some testbed concepts have been published in recent years, very few setups are inherently suitable for biomedical applications. Furthermore, systematic experimental data of a wide parameter field for molecular communication is scarce and often difficult to generate. In this work, a biocompatible testbed for molecular communication with magnetic nanoparticles is used to investigate a series of transmission channel parameters. The observed results are discussed in the context of a laminar flow channel. All experimental data regarding the parameter studies as well as an additional data set for a large binary transmission sequence is provided as a supplement to this publication. The data is available on a public server to allow for further use by other researchers.
{"title":"Channel Parameter Studies of a Molecular Communication Testbed With Biocompatible Information Carriers: Methods and Data","authors":"Max Bartunik;Janina Teller;Georg Fischer;Jens Kirchner","doi":"10.1109/TMBMC.2023.3325405","DOIUrl":"10.1109/TMBMC.2023.3325405","url":null,"abstract":"Testbeds play an essential role in the development of real-life molecular communication applications and experimental validation of communication channel models. Although some testbed concepts have been published in recent years, very few setups are inherently suitable for biomedical applications. Furthermore, systematic experimental data of a wide parameter field for molecular communication is scarce and often difficult to generate. In this work, a biocompatible testbed for molecular communication with magnetic nanoparticles is used to investigate a series of transmission channel parameters. The observed results are discussed in the context of a laminar flow channel. All experimental data regarding the parameter studies as well as an additional data set for a large binary transmission sequence is provided as a supplement to this publication. The data is available on a public server to allow for further use by other researchers.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"489-498"},"PeriodicalIF":2.2,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135056618","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 : 2023-10-13DOI: 10.1109/TMBMC.2023.3324487
Mohammad Javad Salariseddigh;Vahid Jamali;Uzi Pereg;Holger Boche;Christian Deppe;Robert Schober
Various applications of molecular communications (MC) are event-triggered, and, as a consequence, the prevalent Shannon capacity may not be the right measure for performance assessment. Thus, in this paper, we motivate and establish the identification capacity as an alternative metric. In particular, we study deterministic identification (DI) for the discrete-time Poisson channel (DTPC), subject to an average and a peak molecule release rate constraint, which serves as a model for MC systems employing molecule counting receivers. It is established that the number of different messages that can be reliably identified for this channel scales as $2^{(nlog n)R}$ , where ${n}$ and ${R}$ are the codeword length and coding rate, respectively. Lower and upper bounds on the DI capacity of the DTPC are developed. The obtained large capacity of the DI channel sheds light on the performance of natural DI systems such as natural olfaction, which are known for their extremely large chemical discriminatory power in biology. Furthermore, numerical results for the empirical miss-identification and false identification error rates are provided for finite length codes. This allows us to characterize the behaviour of the error rate for increasing codeword lengths, which complements our theoretically-derived scale for asymptotically large codeword lengths.
分子通信（MC）的各种应用都是由事件触发的，因此，流行的香农容量可能不是性能评估的正确指标。因此，在本文中，我们提出并确立了识别能力作为替代指标。特别是，我们研究了离散时间泊松信道（DTPC）的确定性识别（DI），该信道受平均分子释放率和峰值分子释放率的限制，可作为采用分子计数接收器的 MC 系统的模型。研究证明，在该信道中可以可靠识别的不同信息的数量为 $2^{(nlog n)R}$ ，其中 ${n}$ 和 ${R}$ 分别为码字长度和编码率。本文提出了 DTPC 的 DI 容量的下限和上限。DI 信道所获得的大容量揭示了自然 DI 系统（如自然嗅觉）的性能，众所周知，自然嗅觉在生物学中具有极强的化学判别能力。此外，我们还提供了有限长度编码的经验误识别率和误识别错误率的数值结果。这使我们能够描述误码率在码字长度增加时的表现，从而补充了我们从理论上推导出的渐近大码字长度的规模。
{"title":"Deterministic Identification for Molecular Communications Over the Poisson Channel","authors":"Mohammad Javad Salariseddigh;Vahid Jamali;Uzi Pereg;Holger Boche;Christian Deppe;Robert Schober","doi":"10.1109/TMBMC.2023.3324487","DOIUrl":"10.1109/TMBMC.2023.3324487","url":null,"abstract":"Various applications of molecular communications (MC) are event-triggered, and, as a consequence, the prevalent Shannon capacity may not be the right measure for performance assessment. Thus, in this paper, we motivate and establish the identification capacity as an alternative metric. In particular, we study deterministic identification (DI) for the discrete-time Poisson channel (DTPC), subject to an average and a peak molecule release rate constraint, which serves as a model for MC systems employing molecule counting receivers. It is established that the number of different messages that can be reliably identified for this channel scales as \u0000<inline-formula> <tex-math>$2^{(nlog n)R}$ </tex-math></inline-formula>\u0000, where \u0000<inline-formula> <tex-math>${n}$ </tex-math></inline-formula>\u0000 and \u0000<inline-formula> <tex-math>${R}$ </tex-math></inline-formula>\u0000 are the codeword length and coding rate, respectively. Lower and upper bounds on the DI capacity of the DTPC are developed. The obtained large capacity of the DI channel sheds light on the performance of natural DI systems such as natural olfaction, which are known for their extremely large chemical discriminatory power in biology. Furthermore, numerical results for the empirical miss-identification and false identification error rates are provided for finite length codes. This allows us to characterize the behaviour of the error rate for increasing codeword lengths, which complements our theoretically-derived scale for asymptotically large codeword lengths.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"408-424"},"PeriodicalIF":2.2,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136303272","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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