Pub Date : 2024-04-16DOI: 10.1109/TMBMC.2024.3388971
Ward J. P. Spee;Jos H. Weber
Recent advances in DNA data storage have attracted renewed attention towards deletion, insertion and substitution correcting codes. Compared to codes aimed at correcting either substitution errors or deletion and insertion (indel) errors, the understanding of codes that correct combinations of substitution and indel errors lags behind. In this paper, we focus on the maximal size of q-ary t-indel s-substitution correcting codes.Our main contributions include two Gilbert-Varshamov inspired lower bounds on this size. On the upper bound side, we prove a Singleton-like bound, a family of sphere-packing upper bounds and an integer linear programming bound. Several of these bounds are shown to improve upon existing results. Moreover, we use these bounds to derive a lower bound and an upper bound on the asymptotic redundancy of maximally sized t-indel s-substitution correcting codes.
DNA 数据存储领域的最新进展再次吸引了人们对删除、插入和置换纠错码的关注。与旨在纠正置换错误或删除和插入（indel）错误的代码相比，人们对纠正置换和indel错误组合的代码的理解相对滞后。在本文中，我们重点研究了 qary t-indel s-substitution 纠错码的最大大小。我们的主要贡献包括两个受 Gilbert-Varshamov 启发的关于该大小的下界。在上界方面，我们证明了一个类似 Singleton- 的上界、一系列球形堆积上界和一个整数线性规划上界。我们证明了其中几个边界对现有结果的改进。此外，我们还利用这些边界推导出了最大尺寸 t-indel s 置换校正码渐近冗余度的下界和上界。
{"title":"Bounds on the Maximum Cardinality of Indel and Substitution Correcting Codes","authors":"Ward J. P. Spee;Jos H. Weber","doi":"10.1109/TMBMC.2024.3388971","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3388971","url":null,"abstract":"Recent advances in DNA data storage have attracted renewed attention towards deletion, insertion and substitution correcting codes. Compared to codes aimed at correcting either substitution errors or deletion and insertion (indel) errors, the understanding of codes that correct combinations of substitution and indel errors lags behind. In this paper, we focus on the maximal size of q-ary t-indel s-substitution correcting codes.Our main contributions include two Gilbert-Varshamov inspired lower bounds on this size. On the upper bound side, we prove a Singleton-like bound, a family of sphere-packing upper bounds and an integer linear programming bound. Several of these bounds are shown to improve upon existing results. Moreover, we use these bounds to derive a lower bound and an upper bound on the asymptotic redundancy of maximally sized t-indel s-substitution correcting codes.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"349-358"},"PeriodicalIF":2.2,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422495","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 : 2024-04-15DOI: 10.1109/TMBMC.2024.3388977
Steven S. Andrews
Biological systems often include spatial regions with different diffusion coefficients. Explicitly simulating their physical causes is computationally intensive, so it is typically preferable to simply vary the coefficients. This raises the question of how to address the boundaries between the regions. Making them fully permeable in both directions seems intuitively reasonable, but causes molecular motion to be simulated as active diffusion, meaning that it arises from energy that is continuously added to the system; in this case, molecules accumulate on the slow-diffusing side. However, molecular motion in most biochemical systems is better described as thermal diffusion, meaning that it occurs even at equilibrium. This can be simulated by reducing the transmission probability into the slow-diffusing side, which yields the correct result that spatially varying diffusion coefficients that arise from macromolecular crowding, changes in viscosity, or other energy-neutral influences do not affect equilibrium molecular concentrations. This work presents transmission coefficients and transmission probability equations for simulating thermal diffusion, including for cases with free energy differences and/or volume exclusion by crowders. They have been implemented in the Smoldyn particle-based simulation software.
{"title":"Modeling Diffusion Between Regions With Different Diffusion Coefficients","authors":"Steven S. Andrews","doi":"10.1109/TMBMC.2024.3388977","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3388977","url":null,"abstract":"Biological systems often include spatial regions with different diffusion coefficients. Explicitly simulating their physical causes is computationally intensive, so it is typically preferable to simply vary the coefficients. This raises the question of how to address the boundaries between the regions. Making them fully permeable in both directions seems intuitively reasonable, but causes molecular motion to be simulated as active diffusion, meaning that it arises from energy that is continuously added to the system; in this case, molecules accumulate on the slow-diffusing side. However, molecular motion in most biochemical systems is better described as thermal diffusion, meaning that it occurs even at equilibrium. This can be simulated by reducing the transmission probability into the slow-diffusing side, which yields the correct result that spatially varying diffusion coefficients that arise from macromolecular crowding, changes in viscosity, or other energy-neutral influences do not affect equilibrium molecular concentrations. This work presents transmission coefficients and transmission probability equations for simulating thermal diffusion, including for cases with free energy differences and/or volume exclusion by crowders. They have been implemented in the Smoldyn particle-based simulation software.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 3","pages":"425-432"},"PeriodicalIF":2.4,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142320474","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 : 2024-03-31DOI: 10.1109/TMBMC.2024.3408053
Inbal Preuss;Ben Galili;Zohar Yakhini;Leon Anavy
This study introduces a novel model for analyzing and determining the required sequencing coverage in DNA-based data storage, focusing on combinatorial DNA encoding. We seek to characterize the distribution of the number of sequencing reads required for message reconstruction. We use a variant of the coupon collector distribution for this purpose. For any given number of observed reads, $Rin mathbb {N}$ , we use a Markov Chain representation of the process to compute the probability of error-free reconstruction. We develop theoretical bounds on the decoding probability and use empirical simulations to validate these bounds and assess tightness. This work contributes to understanding sequencing coverage in DNA-based data storage, offering insights into decoding complexity, error correction, and sequence reconstruction. We provide a Python package, with its input being the code design and other message parameters, all of which are denoted as $boldsymbol {Theta }$ , and a desired confidence level $1-delta $ . This package computes the required read coverage, guaranteeing the message reconstruction $R=R(delta,boldsymbol {Theta })$ .
本研究介绍了一个新模型，用于分析和确定基于 DNA 的数据存储所需的测序覆盖率，重点是组合 DNA 编码。我们试图描述信息重建所需的测序读数数量的分布特征。为此，我们使用了一种变异的收集券分布。对于任何给定的观测读数数（$Rin mathbb {N}$），我们使用马尔可夫链表示过程，计算无差错重建的概率。我们提出了解码概率的理论界限，并使用经验模拟来验证这些界限并评估其严密性。这项工作有助于理解基于 DNA 的数据存储中的测序覆盖率，为解码复杂性、纠错和序列重建提供见解。我们提供了一个 Python 软件包，其输入为代码设计和其他信息参数（均表示为 $boldsymbol {Theta }$），以及所需的置信度 1-delta $。 该软件包计算所需的读取覆盖率，保证信息重建 $R=R(delta,boldsymbol {Theta })$ 。
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Pub Date : 2024-03-31DOI: 10.1109/TMBMC.2024.3408063
Aditya Powari;Ozgur B. Akan
Molecular communication is a new, active area of research that has created a paradigm shift in the way a communication system is perceived. An artificial molecular communication network is created using biological molecules for encoding, transmitting and decoding the symbols to convey information. In addition to typical biological molecules, we are also exploring other classes of molecules that possess unique distinctive features which can be potentially exploited for establishing reliable communications. Odor molecules are one such class of molecules which possess several distinctive features such as Intensity, Headonic tone which provides a basis to convey the information in an olfactory communication system. In our work, we investigate the ICT (information and communication theory) perspective of the olfactory communications by evaluating the channel capacity of an odor molecular communication (OMC) system with the help of a novel modulation scheme viz. odor intensity shift keying (OISK), where information is being conveyed from the intensity level of an odor. Furthermore, we also analyse the effects of critical parameters like temperature and noise on the achievable channel capacity to provide an insight about the resilience of the proposed OMC system towards any such anomaly faced by it.
{"title":"Odor Intensity Shift Keying (OISK) and Channel Capacity of Odor-Based Molecular Communications in Internet of Everything","authors":"Aditya Powari;Ozgur B. Akan","doi":"10.1109/TMBMC.2024.3408063","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3408063","url":null,"abstract":"Molecular communication is a new, active area of research that has created a paradigm shift in the way a communication system is perceived. An artificial molecular communication network is created using biological molecules for encoding, transmitting and decoding the symbols to convey information. In addition to typical biological molecules, we are also exploring other classes of molecules that possess unique distinctive features which can be potentially exploited for establishing reliable communications. Odor molecules are one such class of molecules which possess several distinctive features such as Intensity, Headonic tone which provides a basis to convey the information in an olfactory communication system. In our work, we investigate the ICT (information and communication theory) perspective of the olfactory communications by evaluating the channel capacity of an odor molecular communication (OMC) system with the help of a novel modulation scheme viz. odor intensity shift keying (OISK), where information is being conveyed from the intensity level of an odor. Furthermore, we also analyse the effects of critical parameters like temperature and noise on the achievable channel capacity to provide an insight about the resilience of the proposed OMC system towards any such anomaly faced by it.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 3","pages":"396-408"},"PeriodicalIF":2.4,"publicationDate":"2024-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142320484","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 : 2024-03-27DOI: 10.1109/TMBMC.2024.3382499
Yonatan Yehezkeally;Nikita Polyanskii
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems, interest in this channel has renewed in recent years. In contrast to existing literature, we consider a noisy channel model where information is subject to noise before its substrings are sampled, motivated by in-vivo storage. We study two separate noise models, substitutions or deletions. In both cases, we examine families of codes which may be utilized for error-correction and present combinatorial bounds on their sizes. Through a generalization of the concept of repeat-free strings, we show that the added required redundancy due to this imperfect observation assumption is sublinear, either when the fraction of errors in the observed substring length is sufficiently small, or when that length is sufficiently long. This suggests that no asymptotic cost in rate is incurred by this channel model in these cases. Moreover, we develop an efficient encoder for such constrained strings in some cases. Finally, we show how a similar encoder can be used to avoid formation of secondary-structures in coded DNA strands, even when accounting for imperfect structures.
我们考虑的是子串信道的编码问题，在这种信道中，只能通过（多组）子串来观察信息串。由于现有的 DNA 测序技术和在基于 DNA 的存储系统中的应用，近年来人们对这种信道的兴趣再次高涨。与现有文献不同的是，我们从体内存储的角度出发，考虑了一种噪声信道模型，即在对信息子串进行采样之前，信息会受到噪声的影响。我们研究了两种不同的噪声模型：替换或删除。在这两种情况下，我们都研究了可用于纠错的编码系列，并提出了编码大小的组合界限。通过对无重复字符串概念的概括，我们证明，当观察到的子串长度中的错误率足够小，或子串长度足够长时，由于这种不完全观察假设而增加的所需冗余度是亚线性的。这表明，在这些情况下，这种信道模型不会产生速率上的渐进成本。此外，在某些情况下，我们还为这种受限字符串开发了一种高效的编码器。最后，我们展示了如何使用类似的编码器来避免在编码 DNA 链中形成次级结构，即使在考虑到不完美结构的情况下也是如此。
{"title":"On Codes for the Noisy Substring Channel","authors":"Yonatan Yehezkeally;Nikita Polyanskii","doi":"10.1109/TMBMC.2024.3382499","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3382499","url":null,"abstract":"We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems, interest in this channel has renewed in recent years. In contrast to existing literature, we consider a noisy channel model where information is subject to noise before its substrings are sampled, motivated by in-vivo storage. We study two separate noise models, substitutions or deletions. In both cases, we examine families of codes which may be utilized for error-correction and present combinatorial bounds on their sizes. Through a generalization of the concept of repeat-free strings, we show that the added required redundancy due to this imperfect observation assumption is sublinear, either when the fraction of errors in the observed substring length is sufficiently small, or when that length is sufficiently long. This suggests that no asymptotic cost in rate is incurred by this channel model in these cases. Moreover, we develop an efficient encoder for such constrained strings in some cases. Finally, we show how a similar encoder can be used to avoid formation of secondary-structures in coded DNA strands, even when accounting for imperfect structures.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"368-381"},"PeriodicalIF":2.2,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10480728","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422599","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 : 2024-03-21DOI: 10.1109/TMBMC.2024.3403759
Aditya Narayan Ravi;Alireza Vahid;Ilan Shomorony
Recent advancements in DNA-based storage prototypes focus on encoding information across multiple DNA molecules. This approach utilizes high-throughput sequencing technologies, leading to outputs that are out-of-order. We study the shuffling channel, where input codewords are split into fixed-size fragments. We show that achieving channel capacity uses index-based coding, which assigns unique indices to each fragment. We also introduce two more complex channels, which aim to model popular sequencing strategies in DNA sequencing. In the torn-paper channel, the input codeword is torn up into fragments of random sizes, while in the shotgun sequencing channel, fixed-length random substrings of the input codeword are observed at the output. In both of these channels, the lack of ordering cannot be circumvented by simply adding unique indices to the fragments. We show how the capacity of both of these channels can be achieved using random codes. We introduce and analyze code constructions based on index sequences. While these codes are computationally efficient, they are not capacity-achieving, and we leave the questions of finding efficient capacity-achieving codes for these settings as open problems.
基于 DNA 的存储原型的最新进展主要集中在对多个 DNA 分子进行信息编码。这种方法利用了高通量测序技术，导致输出不按顺序排列。我们研究了洗码信道，在这种信道中，输入码字被分割成固定大小的片段。我们的研究表明，要实现信道容量，需要使用基于索引的编码，为每个片段分配唯一的索引。我们还引入了两个更复杂的信道，旨在模拟 DNA 测序中常用的测序策略。在 "撕纸 "信道中，输入码字被撕成随机大小的片段；而在 "散弹枪测序 "信道中，输出端观察到的是输入码字的固定长度随机子串。在这两种信道中，都不能通过简单地为片段添加唯一索引来规避缺乏排序的问题。我们展示了如何利用随机码实现这两种信道的容量。我们介绍并分析了基于索引序列的编码结构。虽然这些编码的计算效率很高，但它们的容量并不高，因此我们将为这些环境寻找高效容量编码的问题作为开放问题。
{"title":"An Information Theory for Out-of-Order Media With Applications in DNA Data Storage","authors":"Aditya Narayan Ravi;Alireza Vahid;Ilan Shomorony","doi":"10.1109/TMBMC.2024.3403759","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3403759","url":null,"abstract":"Recent advancements in DNA-based storage prototypes focus on encoding information across multiple DNA molecules. This approach utilizes high-throughput sequencing technologies, leading to outputs that are out-of-order. We study the shuffling channel, where input codewords are split into fixed-size fragments. We show that achieving channel capacity uses index-based coding, which assigns unique indices to each fragment. We also introduce two more complex channels, which aim to model popular sequencing strategies in DNA sequencing. In the torn-paper channel, the input codeword is torn up into fragments of random sizes, while in the shotgun sequencing channel, fixed-length random substrings of the input codeword are observed at the output. In both of these channels, the lack of ordering cannot be circumvented by simply adding unique indices to the fragments. We show how the capacity of both of these channels can be achieved using random codes. We introduce and analyze code constructions based on index sequences. While these codes are computationally efficient, they are not capacity-achieving, and we leave the questions of finding efficient capacity-achieving codes for these settings as open problems.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"334-348"},"PeriodicalIF":2.2,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10536001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141424677","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 : 2024-03-21DOI: 10.1109/TMBMC.2024.3403755
Daniil Goshkoder;Nikita Polyanskii;Ilya Vorobyev
We consider the problem of constructing codes capable of correcting long tandem duplication errors of variable length. We present a subquadratic-complexity algorithm that uses only one symbol of redundancy to encode q-ary length-n words into codewords, which can correct a single duplication of length at least $K=4cdot lceil log _{q} nrceil +1$ . We enhance the error-correcting capability by introducing codes without efficient encoding, leading to an improved value of $K= lceil log _{q} nrceil +phi (n)$ , where $phi (n)$ is an arbitrary function such that $phi (n)to infty $ as $nto infty $ . In the class of codes correcting a single long duplication with redundancy 1, the value K in our constructions is order-optimal. Finally, k-repeat-free codes, in which every codeword contains any k-tuple at most once, are shown to correct any number of independent long duplications, each of length at least ${K} = 2{k}$ , occurring simultaneously without any mutual interference.
{"title":"Codes Correcting Long Duplication Errors","authors":"Daniil Goshkoder;Nikita Polyanskii;Ilya Vorobyev","doi":"10.1109/TMBMC.2024.3403755","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3403755","url":null,"abstract":"We consider the problem of constructing codes capable of correcting long tandem duplication errors of variable length. We present a subquadratic-complexity algorithm that uses only one symbol of redundancy to encode q-ary length-n words into codewords, which can correct a single duplication of length at least \u0000<inline-formula> <tex-math>$K=4cdot lceil log _{q} nrceil +1$ </tex-math></inline-formula>\u0000. We enhance the error-correcting capability by introducing codes without efficient encoding, leading to an improved value of \u0000<inline-formula> <tex-math>$K= lceil log _{q} nrceil +phi (n)$ </tex-math></inline-formula>\u0000, where \u0000<inline-formula> <tex-math>$phi (n)$ </tex-math></inline-formula>\u0000 is an arbitrary function such that \u0000<inline-formula> <tex-math>$phi (n)to infty $ </tex-math></inline-formula>\u0000 as \u0000<inline-formula> <tex-math>$nto infty $ </tex-math></inline-formula>\u0000. In the class of codes correcting a single long duplication with redundancy 1, the value K in our constructions is order-optimal. Finally, k-repeat-free codes, in which every codeword contains any k-tuple at most once, are shown to correct any number of independent long duplications, each of length at least \u0000<inline-formula> <tex-math>${K} = 2{k}$ </tex-math></inline-formula>\u0000, occurring simultaneously without any mutual interference.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"272-288"},"PeriodicalIF":2.2,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422492","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 : 2024-03-20DOI: 10.1109/TMBMC.2024.3403488
Omer Sabary;Han Mao Kiah;Paul H. Siegel;Eitan Yaakobi
Advancements in DNA synthesis and sequencing technologies have enabled the storage of data on synthetic DNA strands. However, realizing its potential relies on the design of tailored coding techniques and algorithms. This survey paper offers an overview of past contributions, accompanied by a special issue that showcases recent developments in this field.
DNA 合成和测序技术的进步使数据存储在合成 DNA 链上成为可能。然而，实现其潜力有赖于设计量身定制的编码技术和算法。本调查报告概述了过去的贡献，并附有特刊，展示了该领域的最新发展。
{"title":"Survey for a Decade of Coding for DNA Storage","authors":"Omer Sabary;Han Mao Kiah;Paul H. Siegel;Eitan Yaakobi","doi":"10.1109/TMBMC.2024.3403488","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3403488","url":null,"abstract":"Advancements in DNA synthesis and sequencing technologies have enabled the storage of data on synthetic DNA strands. However, realizing its potential relies on the design of tailored coding techniques and algorithms. This survey paper offers an overview of past contributions, accompanied by a special issue that showcases recent developments in this field.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"253-271"},"PeriodicalIF":2.2,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-19DOI: 10.1109/TMBMC.2024.3379282
Lin Lin;Wei Wang;Wenlong Yu;Hao Yan
Molecular communication (MC), as a current research hotspot, provides a new method to achieve the communication between nanodevices inside the human body. However, there are still challenges in transmitting information from nanodevices inside the human body to the outside body. In this paper, a MC scheme based on light absorption is proposed for through-body communication where the information is transmitted by converting molecular signals into optical signals. A testbed is implemented, where animal blood and meat is used to mimic living environment more practically. Indocyanine green is used as information particle which is biocompatible. We carry out sequence transmission experiments with 660nm and 800nm light sources, and investigate the effect of the number of meat layers between the sensor and the light source on the transmission performance. The experimental results show that the proposed MC system can transmit information from the inside pipe through the meat, and as the thickness of the meat above the pipe increases, the light source with stronger tissue penetration ability can ensure a more reliable transmission.
分子通讯（MC）作为当前的研究热点，为实现人体内纳米器件之间的通讯提供了一种新方法。然而，从人体内部的纳米器件向体外传输信息仍面临挑战。本文提出了一种基于光吸收的穿越人体通信 MC 方案，通过将分子信号转换为光信号来传输信息。本文使用动物血液和肉类作为试验平台，以更实际地模拟生活环境。吲哚菁绿被用作信息粒子，它具有生物相容性。我们用 660nm 和 800nm 光源进行了序列传输实验，并研究了传感器和光源之间的肉层数量对传输性能的影响。实验结果表明，所提出的 MC 系统可以从管道内部通过肉层传输信息，而且随着管道上方肉层厚度的增加，组织穿透能力更强的光源可以确保更可靠的传输。
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Pub Date : 2024-03-18DOI: 10.1109/TMBMC.2023.3339055
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