The formation of spatial patterns plays a crucial role in the study of system spatiotemporal dynamics. Previous research has demonstrated that spatial patterns can effectively characterize the macroscopic spatial structure of the reaction-diffusion system. While specific pattern structures, such as the hexagonal, mixed, and stripe pattern, have been identified, the interconnection between these patterns appears to be isolated and invariant. To facilitate the selection and switching between individual spatial patterns, the hybrid control strategy is applied to the bimolecular model for the first time. For the classical bimolecular model of the chemical reaction-diffusion system, the incorporation of two-dimensional diffusion extends its reaction space to the two-dimensional plane. The Turing instability conditions are obtained for the controlled bimolecular system. Through the weakly nonlinear analysis, the amplitude equations are derived near the Turing bifurcation threshold. Furthermore, we investigate the impact of each control parameter on the Turing bifurcation threshold and determine the distribution of spatial patterns and their stability through the amplitude equations. Simulation results indicate that by selecting appropriate control parameters, we can suppress the occurrence of Turing instability and facilitate transitions between the spatial patterns. The findings of the analysis offer valuable insights into the dynamics and control of pattern formation in reaction-diffusion systems.
{"title":"Spatial Pattern Switching Strategy: A Successful Application in the Bimolecular Model","authors":"Yifeng Luan;Min Xiao;Jinling Liang;Wenwu Yu;Wei Xing Zheng","doi":"10.1109/TNB.2025.3546665","DOIUrl":"10.1109/TNB.2025.3546665","url":null,"abstract":"The formation of spatial patterns plays a crucial role in the study of system spatiotemporal dynamics. Previous research has demonstrated that spatial patterns can effectively characterize the macroscopic spatial structure of the reaction-diffusion system. While specific pattern structures, such as the hexagonal, mixed, and stripe pattern, have been identified, the interconnection between these patterns appears to be isolated and invariant. To facilitate the selection and switching between individual spatial patterns, the hybrid control strategy is applied to the bimolecular model for the first time. For the classical bimolecular model of the chemical reaction-diffusion system, the incorporation of two-dimensional diffusion extends its reaction space to the two-dimensional plane. The Turing instability conditions are obtained for the controlled bimolecular system. Through the weakly nonlinear analysis, the amplitude equations are derived near the Turing bifurcation threshold. Furthermore, we investigate the impact of each control parameter on the Turing bifurcation threshold and determine the distribution of spatial patterns and their stability through the amplitude equations. Simulation results indicate that by selecting appropriate control parameters, we can suppress the occurrence of Turing instability and facilitate transitions between the spatial patterns. The findings of the analysis offer valuable insights into the dynamics and control of pattern formation in reaction-diffusion systems.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 3","pages":"280-294"},"PeriodicalIF":3.7,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541780","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 : 2025-02-21DOI: 10.1109/TNB.2025.3544401
Yuyang Lu;Zhihao Zhang;Jing Yang;Cheng Zhang
DNA-based storage has emerged as a promising storage paradigm due to its immense storage potential. However, the error-prone nature of DNA sequencing and synthesis processes limits this potential. Image data is typically compressed before storage, and even a single mismatch can lead to catastrophic error propagation during decompression, rendering the image unrecoverable. To reduce the error rate of DNA storage-based image compression, we have designed a high fault-tolerant DNA image storage system and applied it to image compression for DNA storage. This system achieves significant improvements in both image data compression ratio and resilience through three key innovations: 1) Using a Variational Autoencoder (VAE) to compress the image into uniformly sized latent variable blocks, followed by further compression via Singular Value Decomposition (SVD); 2) Quantizing the floating-point numbers in the latent variable blocks and applying rotational coding to the resulting ternary sequences, effectively ensuring positive constraints on homopolymer run lengths and GC content; 3) Optimizing the error-correction scheme to best recover each type of error by quantizing it back to its original value. Through image scaling, we adjust the compression ratio, and the comparative results of image compression simulations demonstrate the performance of the proposed model, highlighting its superiority in fault tolerance and storage density.
{"title":"High Fault-Tolerant DNA Image Storage System Based on VAE","authors":"Yuyang Lu;Zhihao Zhang;Jing Yang;Cheng Zhang","doi":"10.1109/TNB.2025.3544401","DOIUrl":"10.1109/TNB.2025.3544401","url":null,"abstract":"DNA-based storage has emerged as a promising storage paradigm due to its immense storage potential. However, the error-prone nature of DNA sequencing and synthesis processes limits this potential. Image data is typically compressed before storage, and even a single mismatch can lead to catastrophic error propagation during decompression, rendering the image unrecoverable. To reduce the error rate of DNA storage-based image compression, we have designed a high fault-tolerant DNA image storage system and applied it to image compression for DNA storage. This system achieves significant improvements in both image data compression ratio and resilience through three key innovations: 1) Using a Variational Autoencoder (VAE) to compress the image into uniformly sized latent variable blocks, followed by further compression via Singular Value Decomposition (SVD); 2) Quantizing the floating-point numbers in the latent variable blocks and applying rotational coding to the resulting ternary sequences, effectively ensuring positive constraints on homopolymer run lengths and GC content; 3) Optimizing the error-correction scheme to best recover each type of error by quantizing it back to its original value. Through image scaling, we adjust the compression ratio, and the comparative results of image compression simulations demonstrate the performance of the proposed model, highlighting its superiority in fault tolerance and storage density.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 3","pages":"339-347"},"PeriodicalIF":3.7,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541767","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 : 2025-02-10DOI: 10.1109/TNB.2025.3540102
Jitesh Pradhan;Hathiram Nenavath
DNA is emerging as a promising medium for storing huge volumes of data in a confined space that remains intact for thousands of years. Although this technique is very efficient, especially for multimedia data like images, there is a lack of efficient searching and retrieval technique. This paper addresses this issue and proposes a novel Content Based Image Retrieval (CBIR) technique to retrieve similar images from the generated DNA-based image feature vectors. The features are obtained by a novel encoding scheme that uses the three Most-Significant Bits from the images and converts them into a string of nucleotides that follow run length and GC constraints to form DNA planes stored in a DNA medium. The nucleotides in these planes are interpreted through three consecutive sequences forming codons. The codon-based features are then utilized to perform instance-based image retrieval. The DNA planes are further adapted and implemented on diverse deep learning architectures, including ResNet-50, VGG-16, VGG-19, and Inception V3, to facilitate classification-based image retrieval tasks. The system’s performance has been assessed using a range of datasets, encompassing coral, medical, and multi-label images. Experimental results demonstrate that the proposed approach achieves notable improvements when compared to existing state-of-the-art methods.
{"title":"DNA-CBIR: DNA Translation Inspired Codon Pattern-Based Deep Image Feature Extraction for Content-Based Image Retrieval","authors":"Jitesh Pradhan;Hathiram Nenavath","doi":"10.1109/TNB.2025.3540102","DOIUrl":"10.1109/TNB.2025.3540102","url":null,"abstract":"DNA is emerging as a promising medium for storing huge volumes of data in a confined space that remains intact for thousands of years. Although this technique is very efficient, especially for multimedia data like images, there is a lack of efficient searching and retrieval technique. This paper addresses this issue and proposes a novel Content Based Image Retrieval (CBIR) technique to retrieve similar images from the generated DNA-based image feature vectors. The features are obtained by a novel encoding scheme that uses the three Most-Significant Bits from the images and converts them into a string of nucleotides that follow run length and GC constraints to form DNA planes stored in a DNA medium. The nucleotides in these planes are interpreted through three consecutive sequences forming codons. The codon-based features are then utilized to perform instance-based image retrieval. The DNA planes are further adapted and implemented on diverse deep learning architectures, including ResNet-50, VGG-16, VGG-19, and Inception V3, to facilitate classification-based image retrieval tasks. The system’s performance has been assessed using a range of datasets, encompassing coral, medical, and multi-label images. Experimental results demonstrate that the proposed approach achieves notable improvements when compared to existing state-of-the-art methods.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 3","pages":"318-330"},"PeriodicalIF":3.7,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541757","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 proposed a miniaturized multi-sensor device prepared using a flexible printed circuit board (FPCB) and applied to detect glucose (Glu) and pH value, where both the readout circuit board and the sensors possess flexible characteristics. Additionally, this work implemented the potentiometric readout circuit. It integrated the die onto the readout circuit board using wire bonding techniques, while the area of the readout circuit board is 5.5 cm $times 4.0$ cm. The readout circuit board is equipped with a power supply, a readout circuit chip, and a multi-sensor. It is worth mentioning that this study designs the multi-sensor in a double-sided manner. The advantage of this design lies in the fact that both sides of the sensor can be utilized as a working electrode or reference electrode, providing convenience to users during measurement analysis. In addition, the magnesium oxide (MgO) multi-sensor is interconnected with the readout circuit board using slot type. This means the MgO multi-sensor can also be used as a disposable sensor. In this study, the multi-sensor system can measure hydrogen ions and Glu at the same time. The sensitivity of the two is 25.27 mV/pH and 16.78 mV/mM, respectively, and the linearity can reach 99.9 %.
本研究提出了一种采用柔性印刷电路板（FPCB）制备的用于葡萄糖（Glu）和pH值检测的小型化多传感器器件，该器件的读出电路板和传感器均具有柔性特性。此外，本工作还实现了电位读出电路。它使用线键合技术将芯片集成到读出电路板上，而读出电路板的面积为5.5 cm × 4.0 cm。读出电路板配有电源、读出电路芯片和多传感器。值得一提的是，本研究采用双面方式设计了多传感器。这种设计的优点在于传感器的两侧都可以作为工作电极或参比电极，方便用户进行测量分析。此外，氧化镁（MgO）多传感器通过槽型与读出电路板互连。这意味着MgO多传感器也可以用作一次性传感器。在本研究中，多传感器系统可以同时测量氢离子和谷氨酸。两者的灵敏度分别为25.27 mV/pH和16.78 mV/mM，线性度可达99.9%。
{"title":"A Miniaturized MgO Multi-Sensor Device Based on a Flexible Printed Circuit Board for Glucose and pH Detection","authors":"Po-Hui Yang;Jyun-Ming Huang;Jung-Chuan Chou;Chih-Hsien Lai;Po-Yu Kuo;Yu-Hsun Nien;Wei-Shun Chen;Ming-Tai Hsu;Chi-Han Liao","doi":"10.1109/TNB.2025.3536456","DOIUrl":"10.1109/TNB.2025.3536456","url":null,"abstract":"This study proposed a miniaturized multi-sensor device prepared using a flexible printed circuit board (FPCB) and applied to detect glucose (Glu) and pH value, where both the readout circuit board and the sensors possess flexible characteristics. Additionally, this work implemented the potentiometric readout circuit. It integrated the die onto the readout circuit board using wire bonding techniques, while the area of the readout circuit board is 5.5 cm <inline-formula> <tex-math>$times 4.0$ </tex-math></inline-formula> cm. The readout circuit board is equipped with a power supply, a readout circuit chip, and a multi-sensor. It is worth mentioning that this study designs the multi-sensor in a double-sided manner. The advantage of this design lies in the fact that both sides of the sensor can be utilized as a working electrode or reference electrode, providing convenience to users during measurement analysis. In addition, the magnesium oxide (MgO) multi-sensor is interconnected with the readout circuit board using slot type. This means the MgO multi-sensor can also be used as a disposable sensor. In this study, the multi-sensor system can measure hydrogen ions and Glu at the same time. The sensitivity of the two is 25.27 mV/pH and 16.78 mV/mM, respectively, and the linearity can reach 99.9 %.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 3","pages":"331-338"},"PeriodicalIF":3.7,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541727","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}
Phyto-mediated synthesis can be used for the sustainable fabrication of metallic nanoparticles (NPs). Ethanolic leaf extract of Acacia jacquemontii was used to phyto-fabricate iron oxide nanoparticles (FeO NPs). Synthesized FeO NPs were examined by various analytical techniques for their detailed chemical elemental and morphological features. High-performance thin-layer chromatography (HPTLC) was used for the analysis of the ethanolic extracts of the leaves, which ensured the presence of phenols and terpenoids in the extract. FeO NPs show a peak between 350-400nm when analyzed by UV-Vis spectroscopy, and the typical bands were found in the range of 745 cm−1 for Fe-O and 1595 cm−1, 3177 cm−1 for some other organic molecules by Fourier transform-infrared (FTIR). The spherical shape of FeO NPs was investigated with the help of a Field emission scanning electron microscope (FESEM) analysis which exhibited the size varied from 13.35 to 31.29 nm. Electron diffraction spectroscopy (EDS) confirmed the Fe, O, and C peaks, along with N, Cl, S, and K traces. The adsorption capacity of the FeO NPs for brilliant green (BG) dye was evaluated at different pH, dosages of adsorbent, and contact time. The highest adsorption parentage of 57.2% for 10 ppm BG dye was observed at 9 pH and 10 mg doses of FeO NPs. The highest absorption capacity of FeO NPs is 60 mg/g. The recyclability potential of the FeO NPs continuously decreased with the repletion of the cycle from first to fourth whose value reached 19.33% after the fourth cycle. Such phytofabricated FeO NPs and their application in the removal of organic could prove to be eco-friendly and economical.
{"title":"Adsorption of Brilliant Green Dye by Iron Oxide Nanoparticles Synthesized From the Leaf Extracts of Acacia jacquemontii","authors":"Nisha Choudhary;Bhakti Patel;Reema Desai;Vinars Dawane;Kuldeep Luhana;Suhas Vyas;Titus Chinedu Egbosiuba;Dipak Kumar Sahoo;Virendra Kumar Yadav;Ashish Patel","doi":"10.1109/TNB.2025.3528131","DOIUrl":"10.1109/TNB.2025.3528131","url":null,"abstract":"Phyto-mediated synthesis can be used for the sustainable fabrication of metallic nanoparticles (NPs). Ethanolic leaf extract of Acacia jacquemontii was used to phyto-fabricate iron oxide nanoparticles (FeO NPs). Synthesized FeO NPs were examined by various analytical techniques for their detailed chemical elemental and morphological features. High-performance thin-layer chromatography (HPTLC) was used for the analysis of the ethanolic extracts of the leaves, which ensured the presence of phenols and terpenoids in the extract. FeO NPs show a peak between 350-400nm when analyzed by UV-Vis spectroscopy, and the typical bands were found in the range of 745 cm−1 for Fe-O and 1595 cm−1, 3177 cm−1 for some other organic molecules by Fourier transform-infrared (FTIR). The spherical shape of FeO NPs was investigated with the help of a Field emission scanning electron microscope (FESEM) analysis which exhibited the size varied from 13.35 to 31.29 nm. Electron diffraction spectroscopy (EDS) confirmed the Fe, O, and C peaks, along with N, Cl, S, and K traces. The adsorption capacity of the FeO NPs for brilliant green (BG) dye was evaluated at different pH, dosages of adsorbent, and contact time. The highest adsorption parentage of 57.2% for 10 ppm BG dye was observed at 9 pH and 10 mg doses of FeO NPs. The highest absorption capacity of FeO NPs is 60 mg/g. The recyclability potential of the FeO NPs continuously decreased with the repletion of the cycle from first to fourth whose value reached 19.33% after the fourth cycle. Such phytofabricated FeO NPs and their application in the removal of organic could prove to be eco-friendly and economical.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 2","pages":"234-248"},"PeriodicalIF":3.7,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541749","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 : 2025-01-20DOI: 10.1109/TNB.2025.3532441
Robin Requadt;Manuel Fink;Patrick Kubica;Claudia Steinem;Axel Munk;Housen Li
Recent experimental studies have shed light on the intriguing possibility that ion channels exhibit cooperative behaviour. However, a comprehensive understanding of such cooperativity remains elusive, primarily due to limitations in measuring separately the response of each channel. Rather, only the superimposed channel response can be observed, challenging existing data analysis methods. To address this gap, we propose IDC (Idealisation, Discretisation, and Cooperativity inference), a robust statistical data analysis methodology that requires only voltage-clamp current recordings of an ensemble of ion channels. The framework of IDC enables us to integrate recent advancements in idealisation techniques and coupled Markov models. Further, in the cooperativity inference phase of IDC, we introduce a minimum distance estimator and establish its statistical guarantee in the form of asymptotic consistency. We demonstrate the effectiveness and robustness of IDC through extensive simulation studies. As an application, we investigate gramicidin D channels. Our findings reveal that these channels act independently, even at varying applied voltages during voltage-clamp experiments. An implementation of IDC is available from GitLab.
{"title":"Robust Inference of Cooperative Behavior of Multiple Ion Channels in Voltage-Clamp Recordings","authors":"Robin Requadt;Manuel Fink;Patrick Kubica;Claudia Steinem;Axel Munk;Housen Li","doi":"10.1109/TNB.2025.3532441","DOIUrl":"10.1109/TNB.2025.3532441","url":null,"abstract":"Recent experimental studies have shed light on the intriguing possibility that ion channels exhibit cooperative behaviour. However, a comprehensive understanding of such cooperativity remains elusive, primarily due to limitations in measuring separately the response of each channel. Rather, only the superimposed channel response can be observed, challenging existing data analysis methods. To address this gap, we propose IDC (Idealisation, Discretisation, and Cooperativity inference), a robust statistical data analysis methodology that requires only voltage-clamp current recordings of an ensemble of ion channels. The framework of IDC enables us to integrate recent advancements in idealisation techniques and coupled Markov models. Further, in the cooperativity inference phase of IDC, we introduce a minimum distance estimator and establish its statistical guarantee in the form of asymptotic consistency. We demonstrate the effectiveness and robustness of IDC through extensive simulation studies. As an application, we investigate gramicidin D channels. Our findings reveal that these channels act independently, even at varying applied voltages during voltage-clamp experiments. An implementation of IDC is available from GitLab.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 3","pages":"305-317"},"PeriodicalIF":3.7,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541779","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}
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。
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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}
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