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

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

{"title":"Modeling of Droplet Speed Shift Keying in Microfluidic Communications","authors":"Laura Galluccio;Alfio Lombardo;Giacomo Morabito;Fabrizio Pappalardo;Salvatore Quattropani","doi":"10.1109/TMBMC.2024.3369391","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3369391","url":null,"abstract":"Droplet microfluidics is a research area rapidly evolving due to its vast range of potential applications in several fields ranging from medicine to biodefense, and drug administration. In this context, it is crucial to identify efficient and effective methods for communicating by means of droplets. Various techniques have been proposed in the past to encode data by exploiting droplets, such as utilizing droplet size, droplet composition, or the presence/absence of droplets. Nevertheless, these methods are plagued by propagation delays within the channel, resulting in the impossibility to rapidly deliver information at the receiver. To address this issue, this paper introduces a novel methodology for encoding information. The proposed approach involves the instantaneous manipulation of a train of dye drops within a continuous oil phase to induce variations in flow properties. By capitalizing on the stable and laminar flow of the drops, our objective is to encode data instantaneously by altering the dye-oil pressure pairs. To better predict and explain the microfluidic dynamics in the channel, we develop a model of the proposed scheme.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161245","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":"Microfluidic Systems for Molecular Communications: A Review From Theory to Practice","authors":"Medina Hamidović;Stefan Angerbauer;Dadi Bi;Yansha Deng;Tuna Tugcu;Werner Haselmayr","doi":"10.1109/TMBMC.2024.3368768","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3368768","url":null,"abstract":"The paper presents the significance of microfluidic technology in advancing Molecular Communications (MC). It highlights the transition from theoretical MC models to practical applications, emphasizing the role of microfluidics in validating and advancing MC concepts. The paper covers various aspects including theoretical principles, simulation tools, practical realizations, and envisioned applications. We also present various microfluidic testbeds, detailing their design, capabilities, and applications in advancing MC. To bridge the gap between theoretical models and practical outcomes in MC, this work demonstrates the potential of microfluidics in the practical realization of MC systems.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10443866","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161158","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":"Experimental Implementation of Molecule Shift Keying for Enhanced Molecular Communication","authors":"Federico Calì;Salvatore Barreca;Giovanni Li-Destri;Alberto Torrisi;Antonino Licciardello;Nunzio Tuccitto","doi":"10.1109/TMBMC.2024.3368759","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3368759","url":null,"abstract":"Molecular communication is a communication paradigm inspired by biological systems, where chemical signals are used to encode and transmit information. MoSK (Molecule Shift Keying) is proposed as a modulation technique that utilizes different types of signaling molecules to encode digital information. A prototype platform for MoSK implementation is presented, including a transmitter with infusion and selection valves, and a fluorescence-based receiver. The receiver detects and decodes fluorescence signals emitted by Graphene Quantum Dots (GQDs), which are water-soluble and fluorescent molecular messengers. The fluorescence signals of Blue-GQDs and Cyan-GQDs are acquired by the receiver, and the performance of the system is evaluated in terms of synchronization, detection threshold, and symbol recognition using Principal Component Analysis (PCA). The results demonstrate the successful detection and recognition of different symbols, even at lower concentrations. PCA proves to be an efficient method for qualitative recognition of molecular messengers in MoSK-based molecular communication systems.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161244","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":"Spheroidal Molecular Communication via Diffusion: Signaling Between Homogeneous Cell Aggregates","authors":"Mitra Rezaei;Hamidreza Arjmandi;Mohammad Zoofaghari;Kajsa Kanebratt;Liisa Vilén;David Janzén;Peter Gennemark;Adam Noel","doi":"10.1109/TMBMC.2024.3366420","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3366420","url":null,"abstract":"Recent molecular communication (MC) research has integrated more detailed computational models to capture the dynamics of practical biophysical systems. This paper focuses on developing realistic models for MC transceivers inspired by spheroids – three-dimensional cell aggregates commonly used in organ-on-chip experimental systems. Potential applications that can be used or modeled with spheroids include nutrient transport in organ-on-chip systems, the release of biomarkers or reception of drug molecules by cancerous tumor sites, or transceiver nanomachines participating in information exchange. In this paper, a simple diffusive MC system is considered where a spheroidal transmitter and spheroidal receiver are in an unbounded fluid environment. These spheroidal antennas are modeled as porous media for diffusive signaling molecules, then their boundary conditions and effective diffusion coefficients are characterized. Furthermore, for either a point source or spheroidal transmitter, the Green’s function for concentration (GFC) outside and inside the receiving spheroid is analytically derived and formulated in terms of an infinite series and confirmed with a particle-based simulator (PBS). The provided GFCs enable computation of the transmitted and received signals in the proposed spheroidal communication system. This study shows that the porous structure of the receiving spheroid amplifies diffusion signals but also disperses them, thus there is a trade-off between porosity and information transmission rate. Furthermore, the results reveal that the porous arrangement of the transmitting spheroid not only disperses the received signal but also attenuates it in comparison to a point source transmitter. System performance is also evaluated in terms of the bit error rate (BER). Decreasing the porosity of the receiving spheroid is shown to enhance the system performance. Conversely, reducing the porosity of the transmitting spheroid can adversely affect system performance.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161173","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":"Absorption Shift Keying for Molecular Communication via Diffusion","authors":"Miaowen Wen;Feng Liang;Wen Ye;Xuan Chen","doi":"10.1109/TMBMC.2024.3364019","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3364019","url":null,"abstract":"In molecular communication (MC), molecules can play dual roles, one as information carriers and the other as energy providers based on chemical reactions, the importance of which is self-evident. In this paper, we propose a novel modulation scheme, termed absorption shift keying (AbSK), to harvest unused molecules while boosting system performance. It relies on a third switch-controllable molecule harvesting node in addition to both transmitter and receiver in a conventional point-to-point MC scenario. In this setting, the proposed AbSK encodes information onto the ON/OFF state of the third node, so that it can act as a secondary source while capturing redundant molecules released by the primary source (or transmitter). Two detectors are designed for AbSK, namely ideal maximum likelihood and two-step detectors. Asymptotically tight bounds on the bit error rates of both detectors are derived in closed-form. Simulation results validate our theoretical analysis and show that the proposed AbSK outperforms benchmarks and additionally captures molecules to power future transmissions.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422598","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}