IEEE Transactions on Molecular, Biological, and Multi-Scale Communications最新文献_第4页

Bounds on the Maximum Cardinality of Indel and Substitution Correcting Codes 吲哚码和替换校正码的最大心数界限

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2024-04-16 DOI: 10.1109/TMBMC.2024.3388971

Ward J. P. Spee;Jos H. Weber

引用次数: 0

Modeling Diffusion Between Regions With Different Diffusion Coefficients 不同扩散系数区域间的扩散建模

IF 2.4

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2024-04-15 DOI: 10.1109/TMBMC.2024.3388977

Steven S. Andrews

{"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}

引用次数: 0

Sequencing Coverage Analysis for Combinatorial DNA-Based Storage Systems 基于 DNA 的组合存储系统的测序覆盖率分析

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2024-03-31 DOI: 10.1109/TMBMC.2024.3408053

Inbal Preuss;Ben Galili;Zohar Yakhini;Leon Anavy

{"title":"Sequencing Coverage Analysis for Combinatorial DNA-Based Storage Systems","authors":"Inbal Preuss;Ben Galili;Zohar Yakhini;Leon Anavy","doi":"10.1109/TMBMC.2024.3408053","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3408053","url":null,"abstract":"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, \u0000<inline-formula> <tex-math>$Rin mathbb {N}$ </tex-math></inline-formula>\u0000, 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 \u0000<inline-formula> <tex-math>$boldsymbol {Theta }$ </tex-math></inline-formula>\u0000, and a desired confidence level \u0000<inline-formula> <tex-math>$1-delta $ </tex-math></inline-formula>\u0000. This package computes the required read coverage, guaranteeing the message reconstruction \u0000<inline-formula> <tex-math>$R=R(delta,boldsymbol {Theta })$ </tex-math></inline-formula>\u0000.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"297-316"},"PeriodicalIF":2.2,"publicationDate":"2024-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10543138","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422488","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}

引用次数: 0

Odor Intensity Shift Keying (OISK) and Channel Capacity of Odor-Based Molecular Communications in Internet of Everything 万物互联中基于气味的分子通信的气味强度偏移键控（OISK）和信道容量

IF 2.4

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2024-03-31 DOI: 10.1109/TMBMC.2024.3408063

Aditya Powari;Ozgur B. Akan

{"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}

引用次数: 0

On Codes for the Noisy Substring Channel 关于噪声子串信道的编码

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2024-03-27 DOI: 10.1109/TMBMC.2024.3382499

Yonatan Yehezkeally;Nikita Polyanskii

{"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}

引用次数: 0

An Information Theory for Out-of-Order Media With Applications in DNA Data Storage 无序介质的信息论及其在 DNA 数据存储中的应用

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2024-03-21 DOI: 10.1109/TMBMC.2024.3403759

Aditya Narayan Ravi;Alireza Vahid;Ilan Shomorony

{"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}

引用次数: 0

Codes Correcting Long Duplication Errors 纠正长重复错误的代码

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2024-03-21 DOI: 10.1109/TMBMC.2024.3403755

Daniil Goshkoder;Nikita Polyanskii;Ilya Vorobyev

{"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}

引用次数: 0

Survey for a Decade of Coding for DNA Storage DNA 储存编码十年调查

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2024-03-20 DOI: 10.1109/TMBMC.2024.3403488

Omer Sabary;Han Mao Kiah;Paul H. Siegel;Eitan Yaakobi

引用次数: 0

Testbed for Molecular Communication System Based on Light Absorption: Study of Information Transmission From Inside to Outside Body 基于光吸收的分子通信系统试验台：从体内到体外的信息传输研究

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2024-03-19 DOI: 10.1109/TMBMC.2024.3379282

Lin Lin;Wei Wang;Wenlong Yu;Hao Yan

{"title":"Testbed for Molecular Communication System Based on Light Absorption: Study of Information Transmission From Inside to Outside Body","authors":"Lin Lin;Wei Wang;Wenlong Yu;Hao Yan","doi":"10.1109/TMBMC.2024.3379282","DOIUrl":"https://doi.org/10.1109/TMBMC.2024.3379282","url":null,"abstract":"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.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 2","pages":"212-222"},"PeriodicalIF":2.2,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141424678","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}

引用次数: 0

IEEE Communications Society Information IEEE 通信学会信息

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2024-03-18 DOI: 10.1109/TMBMC.2023.3339055

引用次数: 0