IEEE Transactions on Molecular, Biological, and Multi-Scale Communications最新文献_第9页

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":"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}

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":"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}

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":"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}

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":"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}

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":"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}

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":"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}

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":"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}

引用次数: 0

Area Rate Efficiency in Multi-Link Molecular Communications 多链路分子通信中的区域速率效率

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-10-02 DOI: 10.1109/TMBMC.2023.3321193

Lukas Brand;Sebastian Lotter;Vahid Jamali;Robert Schober;Maximilian Schäfer

{"title":"Area Rate Efficiency in Multi-Link Molecular Communications","authors":"Lukas Brand;Sebastian Lotter;Vahid Jamali;Robert Schober;Maximilian Schäfer","doi":"10.1109/TMBMC.2023.3321193","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3321193","url":null,"abstract":"We consider a multi-link diffusion-based molecular communication (MC) system where multiple spatially distributed transmitter (TX)-receiver (RX) pairs establish point-to-point communication links employing the same type of signaling molecules. To exploit the full potential of such a system, an in-depth understanding of the interplay between the spatial link density and inter-link interference (ILI) and its impact on system performance is needed. In this paper, we consider a three-dimensional unbounded domain with multiple spatially distributed point-to-point non-cooperative transmission links, where both the TXs and RXs are positioned on a regular fixed grid. For this setup, we first derive an analytical expression for the channel impulse responses (CIRs) between the TXs and RXs in the system. Then, we derive the maximum likelihood (ML) detector for the RXs and show that it reduces to a threshold-based detector. Moreover, we derive an analytical expression for the corresponding detection threshold which depends on the statistics of the desired signal from the dedicated TX, the statistics of the MC channel, and the statistics of the ILI. We also provide a low-complexity suboptimal decision threshold. Furthermore, we derive an analytical expression for the bit error rate (BER) and the achievable rate of a single transmission link. Finally, we propose two new performance metrics, namely area rate efficiency (ARE) and area and time rate efficiency (ARTE), suitable for holistically evaluating spatially distributed multi-link MC systems. In particular, ARE and ARTE capture the tradeoff between transmission link density and achievable rate per link and the tradeoff between transmission link density, achievable rate per link, and inter-symbol interference (ISI), respectively. Hence, ARE and ARTE can be exploited to determine the optimal transmission link density for maximizing the throughput of the entire system.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"391-407"},"PeriodicalIF":2.2,"publicationDate":"2023-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138739495","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

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Publication Information IEEE分子、生物学和多尺度通信出版信息汇刊

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-09-19 DOI: 10.1109/TMBMC.2023.3292628

引用次数: 0