Pub Date : 2024-03-18DOI: 10.1109/TMBMC.2024.3369448
Yifan Chen;Dezhong Yao;Tadashi Nakano
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).
{"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}
Pub Date : 2024-03-18DOI: 10.1109/TMBMC.2023.3339053
{"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}
Pub Date : 2024-03-18DOI: 10.1109/TMBMC.2024.3369486
Werner Haselmayr;Yansha Deng;Tuna Tugcu;Ali Salehi-Reyhani
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.
{"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}
Pub Date : 2024-03-17DOI: 10.1109/TMBMC.2024.3397050
Stefan Angerbauer;Franz Enzenhofer;Tobias Pankratz;Medina Hamidovic;Andreas Springer;Werner Haselmayr
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.
{"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}
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 : 2024-03-13DOI: 10.1109/TMBMC.2024.3396398
Sunil Kumar;Prabhat Kumar Sharma;Manav R. Bhatnagar
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 $K$ 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 $(overline {P}_{s})$ , receiver operating characteristics (ROC), and average error rate $(overline {P}_{e})$ . 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).
{"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}
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。
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