IEEE Transactions on Molecular, Biological, and Multi-Scale Communications最新文献_第6页

What Really is “Molecule” in Molecular Communications? The Quest for Physics of Particle-Based Information Carriers 分子通讯中的 "分子 "究竟是什么？探索基于粒子的信息载体的物理学原理

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-12-04 DOI: 10.1109/TMBMC.2023.3338950

Hanlin Xiao;Kamela Dokaj;Ozgur B. Akan

{"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":null,"pages":null},"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}

引用次数: 0

Diffusion-Based Anti-Interference Joint Modulation in MIMO Molecular Communication 多输入多输出分子通信中基于扩散的抗干扰联合调制

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-11-29 DOI: 10.1109/TMBMC.2023.3336259

Guodong Yue;Guoying Lin;Qiang Liu;Kun Yang

{"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":null,"pages":null},"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}

引用次数: 0

Intercellular Chemical Communication Through EV Exchange: Evaluation of the EV Fusion Process Parameters at the Receiving Cell 通过 EV 交换进行细胞间化学交流：评估接收细胞的电动汽车融合过程参数

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-11-28 DOI: 10.1109/TMBMC.2023.3336322

Alfio Lombardo;Giacomo Morabito;Carla Panarello;Fabrizio Pappalardo

{"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":null,"pages":null},"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}

引用次数: 0

The Metagenomic Binning Problem: Clustering Markov Sequences 元基因组分选问题：马尔可夫序列聚类

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-11-28 DOI: 10.1109/TMBMC.2023.3336254

Grant Greenberg;Ilan Shomorony

{"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":null,"pages":null},"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}

引用次数: 0

Deep Joint Source-Channel Coding for DNA Image Storage: A Novel Approach With Enhanced Error Resilience and Biological Constraint Optimization 用于 DNA 图像存储的深度源-信道联合编码：增强抗错能力和生物约束优化的新方法

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-11-09 DOI: 10.1109/TMBMC.2023.3331579

Wenfeng Wu;Luping Xiang;Qiang Liu;Kun Yang

{"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":null,"pages":null},"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}

引用次数: 0

Scheduling-Based Transmit Signal Shaping in Energy-Constrained Molecular Communications 能量受限分子通信中基于调度的传输信号整形

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-11-08 DOI: 10.1109/TMBMC.2023.3329801

Mustafa Can Gursoy;Urbashi Mitra

{"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":null,"pages":null},"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}

引用次数: 0

Channel Characterization of Molecular Communications for Cytokine Storm in COVID-19 Patients COVID-19 患者细胞因子风暴分子通讯的通道特征

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-10-26 DOI: 10.1109/TMBMC.2023.3327869

Saswati Pal;Sudip Misra;Nabiul Islam;Sasitharan Balasubramaniam

{"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":null,"pages":null},"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}

引用次数: 0

Terahertz Induced Protein Interactions in a Random Medium 随机介质中的太赫兹诱导蛋白质相互作用

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-10-24 DOI: 10.1109/TMBMC.2023.3327302

Hadeel Elayan;Andrew W. Eckford;Raviraj S. Adve

{"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":null,"pages":null},"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}

引用次数: 0

Channel Parameter Studies of a Molecular Communication Testbed With Biocompatible Information Carriers: Methods and Data 使用生物兼容信息载体的分子通信试验台的信道参数研究：方法与数据

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-10-19 DOI: 10.1109/TMBMC.2023.3325405

Max Bartunik;Janina Teller;Georg Fischer;Jens Kirchner

引用次数: 0

Deterministic Identification for Molecular Communications Over the Poisson Channel 泊松信道上分子通信的确定性识别

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-10-13 DOI: 10.1109/TMBMC.2023.3324487

Mohammad Javad Salariseddigh;Vahid Jamali;Uzi Pereg;Holger Boche;Christian Deppe;Robert Schober

{"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":null,"pages":null},"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}

引用次数: 0