Deoxyribonucleic acid (DNA) has become an ideal medium for long-term storage and retrieval due to its extremely high storage density and long-term stability. But access efficiency is an existing bottleneck in DNA storage, especially the lack of high-quality random access address sequences. Therefore, in this paper, we report a series of approaches based on k-weakly mutually uncorrelated (k-WMU) codes to design the address sequence to improve the access efficiency of DNA storage. To address the problem of DNA sequences that are poorly scalable at the base level, we propose a 0-m-ruling coding scheme combined with k-WMU codes that can make address sequences avoid generating secondary structure with stem lengths ranging from 3 to 9. Based on the decoupled structure, We further extend the k-WMU codes with error correction function while satisfying combinatorial biological constraints. In order to investigate the performance of the designed address sequences for real-world applications, we perform simulation experiments based on thermodynamic properties and error correction capability as well as compared the minimum free energy (MFE), melting temperature (TM), and average decoding success rate (ADSR) with previous work. The results show that designed address sequences have a high MFE value and ADSR and a substantial reduction in TM-variance while satisfying the combinatorial biological constraints. As the quality of address sequences improves, this will help to achieve accurate random access as well as enhance the robustness of the DNA storage system.
脱氧核糖核酸（DNA）具有极高的存储密度和长期稳定性，已成为长期存储和检索的理想介质。但存取效率是目前 DNA 存储的一个瓶颈，尤其是缺乏高质量的随机存取地址序列。因此，本文报告了一系列基于k-弱互不相关（k-WMU）码设计地址序列的方法，以提高DNA存储的访问效率。为了解决DNA序列在碱基水平上可扩展性差的问题，我们提出了一种0-m-ruling编码方案，结合k-WMU码，可以使地址序列避免产生茎长度在3到9之间的二级结构。在解耦结构的基础上，我们进一步扩展了具有纠错功能的 k-WMU 编码，同时满足了组合生物约束。为了研究设计的地址序列在实际应用中的性能，我们根据热力学特性和纠错能力进行了模拟实验，并将最小自由能（MFE）、熔化温度（TM）和平均解码成功率（ADSR）与之前的研究进行了比较。结果表明，所设计的地址序列具有较高的 MFE 值和 ADSR，并在满足组合生物约束的同时大幅降低了 TM 变异。随着地址序列质量的提高，这将有助于实现精确的随机存取，并增强 DNA 存储系统的鲁棒性。
{"title":"Family of Mutually Uncorrelated Codes for DNA Storage Address Design","authors":"Zhenlu Liu;Ben Cao;Qi Shao;Yanfen Zheng;Bin Wang;Shihua Zhou;Pan Zheng","doi":"10.1109/TNB.2025.3530470","DOIUrl":"10.1109/TNB.2025.3530470","url":null,"abstract":"Deoxyribonucleic acid (DNA) has become an ideal medium for long-term storage and retrieval due to its extremely high storage density and long-term stability. But access efficiency is an existing bottleneck in DNA storage, especially the lack of high-quality random access address sequences. Therefore, in this paper, we report a series of approaches based on k-weakly mutually uncorrelated (k-WMU) codes to design the address sequence to improve the access efficiency of DNA storage. To address the problem of DNA sequences that are poorly scalable at the base level, we propose a 0-m-ruling coding scheme combined with k-WMU codes that can make address sequences avoid generating secondary structure with stem lengths ranging from 3 to 9. Based on the decoupled structure, We further extend the k-WMU codes with error correction function while satisfying combinatorial biological constraints. In order to investigate the performance of the designed address sequences for real-world applications, we perform simulation experiments based on thermodynamic properties and error correction capability as well as compared the minimum free energy (MFE), melting temperature (TM), and average decoding success rate (ADSR) with previous work. The results show that designed address sequences have a high MFE value and ADSR and a substantial reduction in TM-variance while satisfying the combinatorial biological constraints. As the quality of address sequences improves, this will help to achieve accurate random access as well as enhance the robustness of the DNA storage system.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 3","pages":"295-304"},"PeriodicalIF":3.7,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-09DOI: 10.1109/TNB.2025.3527520
Zhen Cheng;Zhichao Zhang;Heng Liu;Dongliang Jing;Weihua Gong;Kaikai Chi
Diffusive molecular communication (DMC) is an emerging paradigm in nanotechnology, which provides biocompatibility and nanoscale communication for many promising applications, such as targeted drug delivery, environmental monitoring, etc. However, detecting and localizing abnormalities in most of these applications is challenging, such as identifying tumor cells within the body or detecting pollution in air or water. In this paper, we introduce a method for detecting and localizing abnormalities in three dimensional DMC system with multiple sensors, receivers and one fusion center by adopting Transformer-based model with attention mechanism. We make full use of the attention mechanism to capture the inter-symbol interference (ISI) to improve the accuracy of detection and localization. In addition, we simplify the model structure to significantly reduce the complexity of this model. Furthermore, two strategies that different types of molecules (DMT) and same type of molecules (SMT) are released by sensors are considered. The training dataset and testing dataset are generated under these two strategies. Simulation results show that the information about the abnormality detection and localization can be obtained at the same time based on the Transformer-based model under DMT and SMT. Especially, our model outperforms the Informer-based model, deep neural networks (DNN)-based model and log-likelihood ratio (LLR) method.
{"title":"Neural Network With Attention Mechanism for Abnormality Detection and Localization in Diffusive Molecular Communication","authors":"Zhen Cheng;Zhichao Zhang;Heng Liu;Dongliang Jing;Weihua Gong;Kaikai Chi","doi":"10.1109/TNB.2025.3527520","DOIUrl":"10.1109/TNB.2025.3527520","url":null,"abstract":"Diffusive molecular communication (DMC) is an emerging paradigm in nanotechnology, which provides biocompatibility and nanoscale communication for many promising applications, such as targeted drug delivery, environmental monitoring, etc. However, detecting and localizing abnormalities in most of these applications is challenging, such as identifying tumor cells within the body or detecting pollution in air or water. In this paper, we introduce a method for detecting and localizing abnormalities in three dimensional DMC system with multiple sensors, receivers and one fusion center by adopting Transformer-based model with attention mechanism. We make full use of the attention mechanism to capture the inter-symbol interference (ISI) to improve the accuracy of detection and localization. In addition, we simplify the model structure to significantly reduce the complexity of this model. Furthermore, two strategies that different types of molecules (DMT) and same type of molecules (SMT) are released by sensors are considered. The training dataset and testing dataset are generated under these two strategies. Simulation results show that the information about the abnormality detection and localization can be obtained at the same time based on the Transformer-based model under DMT and SMT. Especially, our model outperforms the Informer-based model, deep neural networks (DNN)-based model and log-likelihood ratio (LLR) method.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 2","pages":"257-267"},"PeriodicalIF":3.7,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-08DOI: 10.1109/TNB.2025.3526975
Oindrila Banik;Bansod Sneha Bharat;Anju R. Babu;Prasoon Kumar;Santosh Kumar;Earu Banoth
Eggshell (ES) wastes have been ranked as the $15^{text {th}}$ food industry pollution due to the ever-increasing regular consumption of primary dietary products, eggs. Management and treatment of tons of discarded eggshells produced daily on a global scale are realized to be a predicament, and an immediate solution must be advocated to address the pollution. This sets a tone for the recyclability of this biowaste in a myriad of fields, like nanotechnology, biomedical, and environmental pollution control. Calcium carbonate in the shells makes it a safe precursor for producing calcium oxide as a nanomaterial by the top-down approach – calcination. This paper highlights a facile way to procure waste eggshell-derived metal oxide nanoparticles with reproducibility and recyclability. Calcium Oxide Nanoparticles (CaO NPs) obtained at two different calcination temperatures for optimization and this was characterized by SEM, FTIR, XRD, DLS, and Zeta Potential analyzer. CaONPs are less-studied metal oxide nanoparticles but hold promising applications in different fields. Hence, there is a scope for further investigation on the non-toxic, non-hazardous CaO NPs obtained facilely – an effort to minimize and regulate food wastes.
蛋壳（ES）废物已被列为食品工业的第 15 大污染，原因是人们经常食用的主要膳食产品--鸡蛋的消费量不断增加。全球范围内每天产生的数吨废弃蛋壳的管理和处理已成为一个难题，必须立即提倡解决这一污染问题。这为这种生物垃圾在纳米技术、生物医学和环境污染控制等众多领域的可回收性奠定了基调。贝壳中的碳酸钙使其成为一种安全的前体，可通过自上而下的方法--煅烧--生产纳米材料氧化钙。本文重点介绍了一种从废弃蛋壳中提取金属氧化物纳米粒子的简便方法，该方法具有可重复性和可回收性。在两种不同的煅烧温度下获得的氧化钙纳米颗粒（CaO NPs）进行了优化，并通过扫描电镜、傅立叶变换红外光谱、X射线衍射、DLS和Zeta电位分析仪对其进行了表征。CaONPs 是一种研究较少的金属氧化物纳米粒子，但在不同领域的应用前景广阔。因此，我们有必要进一步研究轻松获得的无毒、无害的 CaO NPs，从而最大限度地减少和规范食品废物。
{"title":"Recycling Eggshell Waste Into Calcium Oxide Nanoparticles: A Sustainable Approach for Nanomaterial Synthesis and Potential Applications","authors":"Oindrila Banik;Bansod Sneha Bharat;Anju R. Babu;Prasoon Kumar;Santosh Kumar;Earu Banoth","doi":"10.1109/TNB.2025.3526975","DOIUrl":"10.1109/TNB.2025.3526975","url":null,"abstract":"Eggshell (ES) wastes have been ranked as the <inline-formula> <tex-math>$15^{text {th}}$ </tex-math></inline-formula> food industry pollution due to the ever-increasing regular consumption of primary dietary products, eggs. Management and treatment of tons of discarded eggshells produced daily on a global scale are realized to be a predicament, and an immediate solution must be advocated to address the pollution. This sets a tone for the recyclability of this biowaste in a myriad of fields, like nanotechnology, biomedical, and environmental pollution control. Calcium carbonate in the shells makes it a safe precursor for producing calcium oxide as a nanomaterial by the top-down approach – calcination. This paper highlights a facile way to procure waste eggshell-derived metal oxide nanoparticles with reproducibility and recyclability. Calcium Oxide Nanoparticles (CaO NPs) obtained at two different calcination temperatures for optimization and this was characterized by SEM, FTIR, XRD, DLS, and Zeta Potential analyzer. CaONPs are less-studied metal oxide nanoparticles but hold promising applications in different fields. Hence, there is a scope for further investigation on the non-toxic, non-hazardous CaO NPs obtained facilely – an effort to minimize and regulate food wastes.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 2","pages":"249-256"},"PeriodicalIF":3.7,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-02DOI: 10.1109/TNB.2024.3514239
{"title":"IEEE Transactions on NanoBioscience Information for Authors","authors":"","doi":"10.1109/TNB.2024.3514239","DOIUrl":"https://doi.org/10.1109/TNB.2024.3514239","url":null,"abstract":"","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 1","pages":"C3-C3"},"PeriodicalIF":3.7,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10820093","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142912453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-23DOI: 10.1109/TNB.2024.3520137
Zhongyi Guo;Nana Ai;Wei Ge;Qingsong Xu
Zebrafish have emerged as a powerful model organism in cardiovascular disease research. Accurately identifying zebrafish blood vessels and evaluating blood flow velocity without injury has a wide range of biological applications. This paper presents the design and development of a non-invasive microvision system for vascular recognition and blood flow monitoring of zebrafish larvae. For the first time, a visual algorithm based on color thresholding and discrete Fourier transform filtering is proposed to determine the position of zebrafish dorsal cardinal vein vessels. Next, the blood flow velocity is determined based on the change rate of pixel values near the centroid point of the blood vessel recognition results. Then, an independent software system is developed based on the producer-consumer underlying framework. A user-friendly interface is specifically designed for biomedical workers, and a complete prototype system is built in combination with hardware devices. In addition, relevant experiments were conducted, and the results indicated that the system can effectively recognize the position of vessels and monitor blood flow velocity in zebrafish larvae under different anesthesia concentrations and developmental days. The heart rate information obtained based on blood flow velocity is consistent with the heart beating frequency. Moreover, the system has also been successfully applied to blood flow velocity monitoring under fluorescence conditions. In future work, this system will be applied in drug screening research for cardiovascular-related diseases of zebrafish larvae.
{"title":"ZebraVas: A Non-Invasive Microvision System for Vascular Recognition and Blood Flow Monitoring of Zebrafish Larvae","authors":"Zhongyi Guo;Nana Ai;Wei Ge;Qingsong Xu","doi":"10.1109/TNB.2024.3520137","DOIUrl":"10.1109/TNB.2024.3520137","url":null,"abstract":"Zebrafish have emerged as a powerful model organism in cardiovascular disease research. Accurately identifying zebrafish blood vessels and evaluating blood flow velocity without injury has a wide range of biological applications. This paper presents the design and development of a non-invasive microvision system for vascular recognition and blood flow monitoring of zebrafish larvae. For the first time, a visual algorithm based on color thresholding and discrete Fourier transform filtering is proposed to determine the position of zebrafish dorsal cardinal vein vessels. Next, the blood flow velocity is determined based on the change rate of pixel values near the centroid point of the blood vessel recognition results. Then, an independent software system is developed based on the producer-consumer underlying framework. A user-friendly interface is specifically designed for biomedical workers, and a complete prototype system is built in combination with hardware devices. In addition, relevant experiments were conducted, and the results indicated that the system can effectively recognize the position of vessels and monitor blood flow velocity in zebrafish larvae under different anesthesia concentrations and developmental days. The heart rate information obtained based on blood flow velocity is consistent with the heart beating frequency. Moreover, the system has also been successfully applied to blood flow velocity monitoring under fluorescence conditions. In future work, this system will be applied in drug screening research for cardiovascular-related diseases of zebrafish larvae.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 2","pages":"225-233"},"PeriodicalIF":3.7,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mechanical stress on cells is transmitted through many biological processes, for example, cell shape control, tissue patterning, and axonal homeostasis. Microtubules, a cytoskeletal component, presumably play a significant role in the mechanoregulation of cellular processes. We investigate motor protein-driven transport of quantum dots along mechanically deformed microtubules. We found that microtubule deformation significantly slowed kinesin-driven transport, whereas we previously reported dynein-driven transport was rather robust. Such dualistic modulation of transportation dynamics of the motor proteins by microtubule deformation can be attributed to the altered affinity of the motor proteins for buckled microtubules. Our results may form the basis for understanding microtubules’ role in regulating cellular processes in a mechanically adverse environment through its detection ability and response to mechanical stress.
{"title":"Microtubule Deformation Modulates Intracellular Transport by Kinesin Differently Than Dynein","authors":"Syeda Rubaiya Nasrin;Tanjina Afrin;Arif Md. Rashedul Kabir;Daisuke Inoue;Takefumi Yamashita;Makoto Oura;Johtaro Yamamoto;Masataka Kinjo;Kazuki Sada;Akira Kakugo","doi":"10.1109/TNB.2024.3507021","DOIUrl":"10.1109/TNB.2024.3507021","url":null,"abstract":"Mechanical stress on cells is transmitted through many biological processes, for example, cell shape control, tissue patterning, and axonal homeostasis. Microtubules, a cytoskeletal component, presumably play a significant role in the mechanoregulation of cellular processes. We investigate motor protein-driven transport of quantum dots along mechanically deformed microtubules. We found that microtubule deformation significantly slowed kinesin-driven transport, whereas we previously reported dynein-driven transport was rather robust. Such dualistic modulation of transportation dynamics of the motor proteins by microtubule deformation can be attributed to the altered affinity of the motor proteins for buckled microtubules. Our results may form the basis for understanding microtubules’ role in regulating cellular processes in a mechanically adverse environment through its detection ability and response to mechanical stress.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 2","pages":"218-224"},"PeriodicalIF":3.7,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-22DOI: 10.1109/TNB.2024.3504540
Fatemeh Sadat Saeidi;Naghmeh Sadat Moayedian
In molecular communication networks, understanding the security level allows us to assess the quality of information transmitted accurately. The presence of unintended nodes in these networks is one of the factors compromising the security of information. This paper considers the simultaneous presence of a jammer and an eavesdropper as unintended nodes. This existence of unintended nodes prompts us to explore methods for assessing the security of a proposed system. Physical layer approaches can be regarded as one of the most efficient methods for assessing security in molecular communication networks. In this paper, we have utilized these approaches instead of the conventional cryptographic methods. At this layer, we have used several metrics to evaluate the security of our system; secrecy capacity (SC), the average probability of error (APOE), and comprehensive secure distance (CSD). By using SC, we also employed other approaches to improve security, such as changing the time interval, jamming molecules, and varying the distance between the transmitter and the receiver. As the last step, Monte Carlo simulation is used to verify the results obtained through analytical analysis.
{"title":"Investigating Physical Layer Security in Molecular Communication Networks","authors":"Fatemeh Sadat Saeidi;Naghmeh Sadat Moayedian","doi":"10.1109/TNB.2024.3504540","DOIUrl":"10.1109/TNB.2024.3504540","url":null,"abstract":"In molecular communication networks, understanding the security level allows us to assess the quality of information transmitted accurately. The presence of unintended nodes in these networks is one of the factors compromising the security of information. This paper considers the simultaneous presence of a jammer and an eavesdropper as unintended nodes. This existence of unintended nodes prompts us to explore methods for assessing the security of a proposed system. Physical layer approaches can be regarded as one of the most efficient methods for assessing security in molecular communication networks. In this paper, we have utilized these approaches instead of the conventional cryptographic methods. At this layer, we have used several metrics to evaluate the security of our system; secrecy capacity (SC), the average probability of error (APOE), and comprehensive secure distance (CSD). By using SC, we also employed other approaches to improve security, such as changing the time interval, jamming molecules, and varying the distance between the transmitter and the receiver. As the last step, Monte Carlo simulation is used to verify the results obtained through analytical analysis.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 2","pages":"208-217"},"PeriodicalIF":3.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This study presents a biosensor utilizing electrospun SnO2 nanofiber films for real-time monitoring of C2C12 cells. The biosensor demonstrates sensitivity towards cellular behaviors, including adhesion, proliferation, and detachment. Alterations in semi-circle and dielectric properties are validated through Nyquist plot and an EEC model, highlighting the biosensor’s potential for analyzing cellular dynamics.
{"title":"Electrospun Stannic Oxide Nanofiber Thin-Film Based Sensing Device for Monitoring Functional Behaviors of Adherent Mammalian Cells","authors":"Uvanesh Kasiviswanathan;Chandan Kumar;Ajay Kumar Sahi;Amit Kumar;Satyabrata Jit;Neeraj Sharma;Sanjeev Kumar Mahto","doi":"10.1109/TNB.2024.3489353","DOIUrl":"10.1109/TNB.2024.3489353","url":null,"abstract":"This study presents a biosensor utilizing electrospun SnO2 nanofiber films for real-time monitoring of C2C12 cells. The biosensor demonstrates sensitivity towards cellular behaviors, including adhesion, proliferation, and detachment. Alterations in semi-circle and dielectric properties are validated through Nyquist plot and an EEC model, highlighting the biosensor’s potential for analyzing cellular dynamics.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 1","pages":"120-126"},"PeriodicalIF":3.7,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142576049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-28DOI: 10.1109/TNB.2024.3481504
Xuncai Zhang;Yunfei Lu
DNA is considered one of the most attractive storage media because of its excellent reliability and durability. Early encoding schemes lacked flexibility and scalability. To address these limitations, we propose a combination of static mapping and dynamic encoding, named “Galaxy” encoding. This scheme uses both the “dual-rule interleaving” algorithm and the “twelve-element Huffman rotational encoding” algorithm. We tested it with “Shakespeare Sonnets” and other files, achieving an encoding information density of approximately 2.563 bits/nt. Additionally, the inclusion of Reed–Solomon error-correcting codes can correct nearly 5% of the errors. Our simulations show that it supports various file types (.gz, .tar, .exe, etc.). We also analyzed the cost and fault tolerance of “Galaxy” encoding, demonstrating its high coding efficiency and ability to fully recover original information while effectively reducing the costs of DNA synthesis and sequencing.
DNA 因其出色的可靠性和耐用性而被认为是最具吸引力的存储介质之一。早期的编码方案缺乏灵活性和可扩展性。为了解决这些局限性，我们提出了一种静态映射和动态编码相结合的方案，命名为 "银河 "编码。该方案同时使用了 "双规则交错 "算法和 "十二元素哈夫曼旋转编码 "算法。我们用 "莎士比亚十四行诗 "和其他文件对其进行了测试，编码信息密度约为 2.563 bits/nt。此外，加入里德-所罗门纠错码可纠正近 5%的错误。我们的模拟显示，它支持各种文件类型（.gz、.tar、.exe 等）。我们还分析了 "银河 "编码的成本和容错性，证明其编码效率高，能够完全恢复原始信息，同时有效降低 DNA 合成和测序的成本。
{"title":"“Galaxy” Encoding: Toward High Storage Density and Low Cost","authors":"Xuncai Zhang;Yunfei Lu","doi":"10.1109/TNB.2024.3481504","DOIUrl":"10.1109/TNB.2024.3481504","url":null,"abstract":"DNA is considered one of the most attractive storage media because of its excellent reliability and durability. Early encoding schemes lacked flexibility and scalability. To address these limitations, we propose a combination of static mapping and dynamic encoding, named “Galaxy” encoding. This scheme uses both the “dual-rule interleaving” algorithm and the “twelve-element Huffman rotational encoding” algorithm. We tested it with “Shakespeare Sonnets” and other files, achieving an encoding information density of approximately 2.563 bits/nt. Additionally, the inclusion of Reed–Solomon error-correcting codes can correct nearly 5% of the errors. Our simulations show that it supports various file types (.gz, .tar, .exe, etc.). We also analyzed the cost and fault tolerance of “Galaxy” encoding, demonstrating its high coding efficiency and ability to fully recover original information while effectively reducing the costs of DNA synthesis and sequencing.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 2","pages":"200-207"},"PeriodicalIF":3.7,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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