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

{"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}

{"title":"Localization of a Passive Source With a Sensor Network-Based Experimental Molecular Communication Platform","authors":"Fatih Gulec;Damla Yagmur Koda;Baris Atakan;Andrew W. Eckford","doi":"10.1109/TMBMC.2024.3375236","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3375236","url":null,"abstract":"In a practical molecular communication scenario such as monitoring air pollutants released from an unknown source, it is essential to estimate the location of the molecular transmitter (TX). This paper presents a novel Sensor Network-based Localization Algorithm (SNCLA) for passive transmission by using a novel experimental platform which mainly comprises a clustered sensor network (SN) with 24 sensor nodes and evaporating ethanol molecules as the passive TX. In SNCLA, a Gaussian plume model is employed to derive the location estimator. The parameters such as transmitted mass, wind velocity, detection time, and actual concentration are calculated or estimated from the measured signals via the SN to be employed as the input for the location estimator. The numerical results show that the performance of SNCLA is better for stronger winds in the medium. Our findings show that evaporated molecules do not propagate homogeneously through the SN due to the presence of the wind. In addition, our statistical analysis based on the measured experimental data shows that the sensed signals by the SN have a log-normal distribution, while the additive noise follows a Student’s t-distribution in contrast to the Gaussian assumption in the literature.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"223-235"},"PeriodicalIF":2.2,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422494","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":"An Energy-Efficient Ternary Modulation With Water for Molecular Communication Systems: From Solvent to Information Carrier","authors":"Yu Huang;Wancheng Gan;Xuan Chen;Dong Tang;Jingyang Li;Miaowen Wen","doi":"10.1109/TMBMC.2024.3373380","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3373380","url":null,"abstract":"In this paper, a ternary-order modulation is proposed for molecular communication (MC) systems, achieving the balance between both energy efficiency and transmission efficiency. When the hydrogen ions are of interest, acidic and basic are conventional binary states in response to acidic and basic solutions, respectively, where water typically acts as the solvent. Yet, the neutrality of water in terms of the pH scale indicates a third state rather than being either acidic or basic, serving as an energy-efficient information carrier due to its abundance in nature. In light of this, bipolar signaling is enabled in MC, leading to a unique ternary modulation. Except for the energy efficiency resulting from an extra neutral state, its transmission efficiency can be further enhanced compared with the binary counterparts given the fixed symbol interval. Finally, field experiments were exemplified to validate the feasibility of the proposed modulation scheme.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"236-242"},"PeriodicalIF":2.2,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422493","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":"The Capacity of Secondary Structure Avoidance Codes for DNA Sequences","authors":"Chen Wang;Hui Chu;Gennian Ge;Yiwei Zhang","doi":"10.1109/TMBMC.2024.3396404","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3396404","url":null,"abstract":"In DNA sequences, we have the celebrated Watson-Crick complement \u0000<inline-formula> <tex-math>$overline {T}=A, overline {A}=T, overline {C}=G$ </tex-math></inline-formula>\u0000, and \u0000<inline-formula> <tex-math>$overline {G}=C$ </tex-math></inline-formula>\u0000. The phenomenon of secondary structure refers to the tendency of a single stranded DNA sequence to fold back upon itself, which is usually caused by the existence of two non-overlapping reverse complement substrings. The property of secondary structure avoidance (SSA) forbids a sequence to contain such reverse complement substrings, and it is a key criterion in the design of single-stranded DNA sequences for both DNA storage and DNA computing. In this paper, we prove that the problem of constructing SSA sequences for any given secondary structure stem length \u0000<italic>m</i>\u0000 can be characterized by a constrained system, and thus the capacity of SSA sequences can be calculated by the classic spectral radius approach in constrained coding theory. We analyze how to choose the generating set, which is a subset of vertices in a de Bruijn graph, for the constrained system, which leads to some explicit constructions of SSA codes. In particular, our constructions have optimal rates 1.1679bits/nt and 1.5515bits/nt when \u0000<inline-formula> <tex-math>${m} = 2$ </tex-math></inline-formula>\u0000 and \u0000<inline-formula> <tex-math>${m} = 3$ </tex-math></inline-formula>\u0000, respectively. In addition, we combine the SSA constraint together with the homopolymer run-length-limit constraint and analyze the capacity of sequences satisfying both constraints.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"359-367"},"PeriodicalIF":2.2,"publicationDate":"2024-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422491","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}