IEEE Transactions on Molecular, Biological, and Multi-Scale Communications最新文献

{"title":"Survey for a Decade of Coding for DNA Storage","authors":"Omer Sabary;Han Mao Kiah;Paul H. Siegel;Eitan Yaakobi","doi":"10.1109/TMBMC.2024.3403488","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3403488","url":null,"abstract":"Advancements in DNA synthesis and sequencing technologies have enabled the storage of data on synthetic DNA strands. However, realizing its potential relies on the design of tailored coding techniques and algorithms. This survey paper offers an overview of past contributions, accompanied by a special issue that showcases recent developments in this field.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"253-271"},"PeriodicalIF":2.2,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422536","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}

{"title":"Testbed for Molecular Communication System Based on Light Absorption: Study of Information Transmission From Inside to Outside Body","authors":"Lin Lin;Wei Wang;Wenlong Yu;Hao Yan","doi":"10.1109/TMBMC.2024.3379282","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3379282","url":null,"abstract":"Molecular communication (MC), as a current research hotspot, provides a new method to achieve the communication between nanodevices inside the human body. However, there are still challenges in transmitting information from nanodevices inside the human body to the outside body. In this paper, a MC scheme based on light absorption is proposed for through-body communication where the information is transmitted by converting molecular signals into optical signals. A testbed is implemented, where animal blood and meat is used to mimic living environment more practically. Indocyanine green is used as information particle which is biocompatible. We carry out sequence transmission experiments with 660nm and 800nm light sources, and investigate the effect of the number of meat layers between the sensor and the light source on the transmission performance. The experimental results show that the proposed MC system can transmit information from the inside pipe through the meat, and as the thickness of the meat above the pipe increases, the light source with stronger tissue penetration ability can ensure a more reliable transmission.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"212-222"},"PeriodicalIF":2.2,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141424678","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}

{"title":"IEEE Communications Society Information","authors":"","doi":"10.1109/TMBMC.2023.3339055","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3339055","url":null,"abstract":"","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"C3-C3"},"PeriodicalIF":2.2,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10473524","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161155","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}

{"title":"Special Feature: 14th EAI International Conference on Bio-Inspired Information and Communications Technologies","authors":"Yifan Chen;Dezhong Yao;Tadashi Nakano","doi":"10.1109/TMBMC.2024.3369448","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3369448","url":null,"abstract":"The 14TH EAI International Conference on Bio-inspired Information and Communications Technologies (BICT 2023) was held in Okinawa, Japan on April 11-12, 2023. The focus of BICT 2023 is to present the latest research that leverages the understanding of key principles, processes, and mechanisms in biological systems for development of novel information and communications technologies (Bio-inspired ICT). BICT 2023 also highlights innovative research and technologies being developed for biomedicine that are inspired by ICT (ICT-inspired Biomedicine).","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"98-100"},"PeriodicalIF":2.2,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10473525","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161156","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}

{"title":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Publication Information","authors":"","doi":"10.1109/TMBMC.2023.3339053","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3339053","url":null,"abstract":"","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"C2-C2"},"PeriodicalIF":2.2,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10473523","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161126","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}

{"title":"Guest Editorial Special Issue on Microfluidic Systems for Molecular Communications","authors":"Werner Haselmayr;Yansha Deng;Tuna Tugcu;Ali Salehi-Reyhani","doi":"10.1109/TMBMC.2024.3369486","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3369486","url":null,"abstract":"Molecular communications (MC) is an emerging field, inspired by nature (e.g., endocrine signaling), that aims to use molecules to encode information. MC is attracting increasing attention as an unconventional solution to challenges posed in environments where conventional electromagnetic-based communication is not feasible or detrimental, such as inside the human body. MC is rapidly becoming a powerful tool that has the potential to drive transformative applications in chemistry, biology and medicine, and identified a key enabling communication method for the Internet of Bio-Nano Things (IoBNT). Due to the focus on energy efficiency and bio-compatibility it paves the way for efficient and reliable communication at micro- and nanoscale.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"144-146"},"PeriodicalIF":2.2,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10473609","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161157","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}

{"title":"Novel Nano-Scale Computing Unit for the IoBNT: Concept and Practical Considerations","authors":"Stefan Angerbauer;Franz Enzenhofer;Tobias Pankratz;Medina Hamidovic;Andreas Springer;Werner Haselmayr","doi":"10.1109/TMBMC.2024.3397050","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3397050","url":null,"abstract":"The Internet of Bio-Nano Things (IoBNT) is a novel framework that has the potential to enable transformative applications in healthcare and nano-medicine. It consists of artificial or natural tiny devices, so-called Bio-Nano Things (BNTs), that can be placed in the human body to carry out specific tasks (e.g., sensing) and are connected to the Internet. However, due to their small size their computation capabilities are limited, which restricts their ability to process data and make decision directly in the human body. Thus, we address this issue and propose a novel nano-scale computing architecture that performs matrix multiplications, which is one of the most important operations in signal processing and machine learning. The computation principle is based on diffusion-based propagation between connected compartments and chemical reactions within some compartments. The weights of the matrix can be set independently through adjusting the volume of the compartments. We present a stochastic and a dynamical model of the proposed structure. The stochastic model provides an analytical solution for the input-output relation in the steady state, assuming slow reaction rates. The dynamical model provides important insights into the systems temporal dynamics. Finally, micro- and mesoscopic simulations verify the proposed approach.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 4","pages":"549-565"},"PeriodicalIF":2.4,"publicationDate":"2024-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10534193","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844224","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}

{"title":"Constructions and Properties of Efficient DNA Synthesis Codes","authors":"Kees A. Schouhamer Immink;Kui Cai;Tuan Thanh Nguyen;Jos H. Weber","doi":"10.1109/TMBMC.2024.3401583","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3401583","url":null,"abstract":"We report on coding methods for efficiently synthesizing deoxyribonucleic acid (DNA) for massive data storage, where a plurality of DNA strands are synthesized in parallel. We examine the trade-offs between the information contents, redundancy, and the average or maximum number of cycles required for synthesizing a plurality of parallel DNA strands. We analyze coding methods such as guided scrambling and constrained codes for minimizing the cycle count.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"289-296"},"PeriodicalIF":2.2,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422640","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}

{"title":"Protecting the Future of Information: LOCO Coding With Error Detection for DNA Data Storage","authors":"Canberk İrimağzı;Yusuf Uslan;Ahmed Hareedy","doi":"10.1109/TMBMC.2024.3400794","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3400794","url":null,"abstract":"From the information-theoretic perspective, DNA strands serve as a storage medium for 4-ary data over the alphabet \u0000<inline-formula> <tex-math>${A,T,G,C}$ </tex-math></inline-formula>\u0000. DNA data storage promises formidable information density, long-term durability, and ease of replicability. However, information in this intriguing storage technology might be corrupted because of error-prone data sequences as well as insertion, deletion, and substitution errors. Experiments have revealed that DNA sequences with long homopolymers and/or with low GC-content are notably more subject to errors upon storage. In order to address this biochemical challenge, constrained codes are proposed for usage in DNA data storage systems, and they are studied in the literature accordingly. This paper investigates the utilization of the recently-introduced method for designing lexicographically-ordered constrained (LOCO) codes in DNA data storage to improve performance. LOCO codes offer capacity-achievability, low complexity, and ease of reconfigurability. This paper introduces novel constrained codes, namely DNA LOCO (D-LOCO) codes, over the alphabet \u0000<inline-formula> <tex-math>${A,T,G,C}$ </tex-math></inline-formula>\u0000 with limited runs of identical symbols. Due to their ordered structure, these codes come with an encoding-decoding rule we derive, which provides simple and affordable encoding-decoding algorithms. In terms of storage overhead, the proposed encoding-decoding algorithms outperform those in the existing literature. Our algorithms are based on small-size adders, and therefore they are readily reconfigurable. D-LOCO codes are intrinsically balanced, which allows us to achieve balanced AT- and GC-content over the entire DNA strand with minimal rate penalty. Moreover, we propose four schemes to bridge consecutive codewords, three of which guarantee single substitution error detection per codeword. We examine the probability of undetecting errors over a presumed symmetric DNA storage channel subject to substitution errors only. We also show that D-LOCO codes are capacity-achieving and that they offer remarkably high rates even at moderate lengths.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"317-333"},"PeriodicalIF":2.2,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422496","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}

{"title":"Game of Resource Exploitation in Molecular Communications with Unintended Nanomachine","authors":"Sunil Kumar;Prabhat Kumar Sharma;Manav R. Bhatnagar","doi":"10.1109/TMBMC.2024.3396398","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3396398","url":null,"abstract":"In many natural molecular communication systems, the transmitters exhibit the ability to collect and store the food or energy from the environment. The collected food or energy is used to produce information-carrying (IC) molecules. In scenarios, when more than one transmit node exist in the environment, they interact with each other to share the available common food molecular budget (CFMB). These strategic interactions among the nano-machines are critical to overall performance of the system. This work uses game theory to explore the effect of behavioral interactions among transmitter nanomachines (TNs) in a three-dimensional (3-D) diffusive environment where \u0000<inline-formula> <tex-math>$K$ </tex-math></inline-formula>\u0000 TNs are deployed around the region of interest (RoI). The TNs share their observations to a supervisor nano-machine (SN) in presence of an eavesdropper called unintended receiver nano-machine (URN). For AND and OR fusion techniques at SN, the system performance is analyzed in terms of secured success rate \u0000<inline-formula> <tex-math>$(overline {P}_{s})$ </tex-math></inline-formula>\u0000, receiver operating characteristics (ROC), and average error rate \u0000<inline-formula> <tex-math>$(overline {P}_{e})$ </tex-math></inline-formula>\u0000. Several insights into the effects of cooperative and greedy behaviors of TNs are obtained. The results are verified through the Monte-Carlo and particle-based simulations (PBS).","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 4","pages":"595-601"},"PeriodicalIF":2.4,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844594","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}