Pub Date : 2024-03-15DOI: 10.1109/TMBMC.2024.3401583
Kees A. Schouhamer Immink;Kui Cai;Tuan Thanh Nguyen;Jos H. Weber
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.
我们报告了高效合成用于海量数据存储的脱氧核糖核酸（DNA）的编码方法，其中多条 DNA 链是并行合成的。我们研究了信息内容、冗余度以及合成多条并行 DNA 链所需的平均或最大周期数之间的权衡。我们分析了编码方法，如将周期数最小化的引导扰码和约束码。
{"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}
Pub Date : 2024-03-14DOI: 10.1109/TMBMC.2024.3400794
Canberk İrimağzı;Yusuf Uslan;Ahmed Hareedy
From the information-theoretic perspective, DNA strands serve as a storage medium for 4-ary data over the alphabet ${A,T,G,C}$ . 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 ${A,T,G,C}$ 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.
从信息论的角度来看，DNA 链是字母 ${A,T,G,C}$ 上 4ary 数据的存储介质。DNA 数据存储具有强大的信息密度、长期耐久性和易于复制的特点。然而，由于容易出错的数据序列以及插入、删除和替换错误，这种有趣的存储技术中的信息可能会被破坏。实验表明，同聚物较长和/或 GC 含量较低的 DNA 序列在存储时明显更容易出错。为了应对这一生化挑战，有人提出在 DNA 数据存储系统中使用约束码，并在文献中对其进行了相应的研究。本文研究了在 DNA 数据存储中如何利用最近推出的词典排序受限（LOCO）代码设计方法来提高性能。LOCO 代码具有容量可实现性、低复杂性和易重构性。本文介绍了在字母表 ${A,T,G,C}$ 上有限运行相同符号的新型约束码，即 DNA LOCO（D-LOCO）码。由于它们的有序结构，这些编码带有我们推导出的编码-解码规则，它提供了简单、经济的编码-解码算法。就存储开销而言，所提出的编码-解码算法优于现有文献中的算法。我们的算法基于小尺寸加法器，因此很容易重新配置。D-LOCO 编码本质上是平衡的，这使我们能够在整个 DNA 链上实现 AT 和 GC 含量的平衡，同时将速率损失降到最低。此外，我们还提出了四种桥接连续码字的方案，其中三种方案可保证每个码字只检测到一次替换错误。我们研究了在假定的对称 DNA 存储信道上，仅受替换错误影响的未检测到错误的概率。我们还证明，D-LOCO 编码具有很高的容量，即使长度适中，也能提供很高的速率。
{"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}
Pub Date : 2024-03-12DOI: 10.1109/TMBMC.2024.3375236
Fatih Gulec;Damla Yagmur Koda;Baris Atakan;Andrew W. Eckford
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.
在实际分子通信场景中，例如监测未知来源释放的空气污染物时，估算分子发射器（TX）的位置至关重要。本文利用一个新颖的实验平台，提出了一种用于无源传输的基于传感器网络的新型定位算法（SNCLA），该平台主要包括一个由 24 个传感器节点组成的集群传感器网络（SN）和作为无源发射机的蒸发乙醇分子。SNCLA 采用高斯羽流模型来推导位置估计器。传输质量、风速、检测时间和实际浓度等参数都是通过传感器网络从测量信号中计算或估计出来的，作为位置估计器的输入。数值结果表明，SNCLA 在介质风力较强的情况下性能更好。我们的研究结果表明，由于风的存在，蒸发的分子并不能均匀地通过 SN 传播。此外，我们根据测量到的实验数据进行的统计分析显示，SN 感测到的信号呈对数正态分布，而加性噪声则呈 Student's t 分布，这与文献中的高斯假设不同。
{"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}
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.
本文为分子通信（MC）系统提出了一种三阶调制方式，实现了能量效率和传输效率之间的平衡。当氢离子受到关注时，酸性和碱性是传统的二元状态，分别与酸性和碱性溶液相对应，其中水通常充当溶剂。然而，从 pH 值的角度来看，水的中性表明了第三种状态，而不是酸性或碱性，由于水在自然界中含量丰富，因此水是一种高能效的信息载体。有鉴于此，双极信号在 MC 中得以实现，形成了独特的三元调制。除了额外的中性态带来的能量效率外，由于符号间隔固定，其传输效率与二进制调制相比还能进一步提高。最后，现场实验验证了所提调制方案的可行性。
{"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}
Pub Date : 2024-03-03DOI: 10.1109/TMBMC.2024.3396404
Chen Wang;Hui Chu;Gennian Ge;Yiwei Zhang
In DNA sequences, we have the celebrated Watson-Crick complement $overline {T}=A, overline {A}=T, overline {C}=G$ , and $overline {G}=C$ . 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 m 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 ${m} = 2$ and ${m} = 3$ , 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.
在 DNA 序列中，我们有著名的沃森-克里克补码 $/overline {T}=A, overline {A}=T, overline {C}=G$ 和 $/overline {G}=C$ 。二级结构现象指的是单链 DNA 序列折回自身的趋势，这通常是由于存在两个非重叠的反向互补子串造成的。避免二级结构（SSA）的特性禁止序列包含这种反向互补子串，它是设计用于 DNA 存储和 DNA 计算的单链 DNA 序列的关键标准。本文证明，对于任意给定的二级结构茎长度 m，构建 SSA 序列的问题可以用一个约束系统来表征，因此 SSA 序列的容量可以用约束编码理论中经典的谱半径方法来计算。我们分析了如何为约束系统选择生成集（即 de Bruijn 图中的顶点子集），从而得出一些 SSA 编码的明确构造。特别是，当 ${m} = 2$ 和 ${m} = 3$ 时，我们的构造分别具有 1.1679bits/nt 和 1.5515bits/nt 的最佳速率。此外，我们还结合了 SSA 约束和同源多聚物运行长度限制约束，并分析了满足这两个约束的序列的容量。
{"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}
Pub Date : 2024-02-23DOI: 10.1109/TMBMC.2024.3369391
Laura Galluccio;Alfio Lombardo;Giacomo Morabito;Fabrizio Pappalardo;Salvatore Quattropani
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.
{"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":"10 1","pages":"164-174"},"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}
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.
本文介绍了微流控技术在推进分子通讯（MC）方面的重要意义。它强调了从理论 MC 模型到实际应用的过渡，强调了微流控技术在验证和推进 MC 概念方面的作用。论文涵盖了理论原理、模拟工具、实际实现和设想应用等各个方面。我们还介绍了各种微流控实验平台，详细说明了它们的设计、功能以及在推进 MC 方面的应用。为了缩小 MC 理论模型与实际成果之间的差距，这项工作展示了微流控技术在实际实现 MC 系统方面的潜力。
{"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":"10 1","pages":"147-163"},"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}
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.
{"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":"10 1","pages":"175-184"},"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}
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.
最近的分子通讯（MC）研究已经整合了更详细的计算模型，以捕捉实际生物物理系统的动态。本文的重点是受球体--器官芯片实验系统中常用的三维细胞聚集体--的启发，为 MC 收发器开发逼真的模型。可以使用球体或利用球体建模的潜在应用包括片上器官系统中的营养输送、生物标记物的释放或癌症肿瘤部位对药物分子的接收，或参与信息交换的收发纳米机械。本文考虑了一个简单的扩散 MC 系统，在该系统中，球形发射器和球形接收器处于无界流体环境中。这些球形天线被模拟为扩散信号分子的多孔介质，然后对其边界条件和有效扩散系数进行表征。此外，对于点源或球形发射器，接收球体内外的浓度格林函数（GFC）都是通过无穷级数分析得出和制定的，并通过粒子模拟器（PBS）进行了确认。利用所提供的 GFC，可以计算拟议球形通信系统中的发射和接收信号。这项研究表明，接收球体的多孔结构会放大扩散信号，但同时也会分散这些信号，因此在多孔性和信息传输速率之间存在权衡。此外，研究结果表明，与点源发射器相比，发射球面的多孔结构不仅能分散接收信号，还能衰减接收信号。系统性能还根据误码率（BER）进行了评估。结果表明，降低接收球面的孔隙率可提高系统性能。相反，降低发射球面的孔隙率则会对系统性能产生不利影响。
{"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":"10 1","pages":"197-210"},"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}
Pub Date : 2024-02-08DOI: 10.1109/TMBMC.2024.3364019
Miaowen Wen;Feng Liang;Wen Ye;Xuan Chen
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.
在分子通信（MC）中，分子可以扮演双重角色，一个是信息载体，另一个是基于化学反应的能量提供者，其重要性不言而喻。在本文中，我们提出了一种新颖的调制方案，称为吸收偏移键控（AbSK），用于收集未使用的分子，同时提高系统性能。在传统的点对点 MC 方案中，除了发射器和接收器之外，它还依赖于第三个开关可控的分子收集节点。在这种情况下，拟议的 AbSK 将信息编码到第三个节点的开/关状态，这样它就可以充当辅助源，同时捕获主源（或发射器）释放的多余分子。为 AbSK 设计了两种检测器，即理想最大似然检测器和两步检测器。以闭合形式推导出这两种检测器误码率的渐近紧约束。仿真结果验证了我们的理论分析，并表明所提出的 AbSK 性能优于基准，而且还能捕获分子，为未来的传输提供动力。
{"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":"10 2","pages":"243-248"},"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}
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