IEEE Transactions on NanoBioscience最新文献_第6页

Influence of Red Blood Cells on Channel Characterization in Cylindrical Vasculature 红细胞对圆柱形血管中通道特性的影响

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-08-07 DOI: 10.1109/TNB.2024.3436022

Kathan S. Joshi;Dhaval K. Patel;Shivam Thakker;Miguel López-Benítez;Janne J. Lehtomäki

引用次数: 0

High-Risk Sequence Prediction Model in DNA Storage: The LQSF Method DNA 储存中的高风险序列预测模型：LQSF 方法

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-07-08 DOI: 10.1109/TNB.2024.3424576

Yitong Ma;Shuai Chen;Qi Xu;Zuhong Lu;Kun Bi

{"title":"High-Risk Sequence Prediction Model in DNA Storage: The LQSF Method","authors":"Yitong Ma;Shuai Chen;Qi Xu;Zuhong Lu;Kun Bi","doi":"10.1109/TNB.2024.3424576","DOIUrl":"10.1109/TNB.2024.3424576","url":null,"abstract":"Traditional DNA storage technologies rely on passive filtering methods for error correction during synthesis and sequencing, which result in redundancy and inadequate error correction. Addressing this, the Low Quality Sequence Filter (LQSF) was introduced, an innovative method employing deep learning models to predict high-risk sequences. The LQSF approach leverages a classification model trained on error-prone sequences, enabling efficient pre-sequencing filtration of low-quality sequences and reducing time and resources in subsequent stages. Analysis has demonstrated a clear distinction between high and low-quality sequences, confirming the efficacy of the LQSF method. Extensive training and testing were conducted across various neural networks and test sets. The results showed all models achieving an AUC value above 0.91 on ROC curves and over 0.95 on PR curves across different datasets. Notably, models such as Alexnet, VGG16, and VGG19 achieved a perfect AUC of 1.0 on the Original dataset, highlighting their precision in classification. Further validation using Illumina sequencing data substantiated a strong correlation between model scores and sequence error-proneness, emphasizing the model’s applicability. The LQSF method marks a significant advancement in DNA storage technology, introducing active sequence filtering at the encoding stage. This pioneering approach holds substantial promise for future DNA storage research and applications.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 1","pages":"89-101"},"PeriodicalIF":3.7,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141558613","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}

引用次数: 0

A Thermal Study of Terahertz Induced Protein Interactions 太赫兹诱导蛋白质相互作用的热学研究

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-07-02 DOI: 10.1109/TNB.2024.3422280

Hadeel Elayan;Samar Elmaadawy;Andrew W. Eckford;Raviraj Adve;Josep Jornet

{"title":"A Thermal Study of Terahertz Induced Protein Interactions","authors":"Hadeel Elayan;Samar Elmaadawy;Andrew W. Eckford;Raviraj Adve;Josep Jornet","doi":"10.1109/TNB.2024.3422280","DOIUrl":"10.1109/TNB.2024.3422280","url":null,"abstract":"Proteins can be regarded as thermal nanosensors in an intra-body network. Upon being stimulated by Terahertz (THz) frequencies that match their vibrational modes, protein molecules experience resonant absorption and dissipate their energy as heat, undergoing a thermal process. This paper aims to analyze the effect of THz signaling on the protein heat dissipation mechanism. We therefore deploy a mathematical framework based on the heat diffusion model to characterize how proteins absorb THz-electromagnetic (EM) energy from the stimulating EM fields and subsequently release this energy as heat to their immediate surroundings. We also conduct a parametric study to explain the impact of the signal power, pulse duration, and inter-particle distance on the protein thermal analysis. In addition, we demonstrate the relationship between the change in temperature and the opening probability of thermally-gated ion channels. Our results indicate that a controlled temperature change can be achieved in an intra-body environment by exciting protein particles at their resonant frequencies. We further verify our results numerically using COMSOL Multiphysics® and introduce an experimental framework that assesses the effects of THz radiation on protein particles. We conclude that under controlled heating, protein molecules can serve as hotspots that impact thermally-gated ion channels. Through the presented work, we infer that the heating process can be engineered on different time and length scales by controlling the THz-EM signal input.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 1","pages":"78-88"},"PeriodicalIF":3.7,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141491740","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}

引用次数: 0

Machine Learning-Enhanced Predictive Modeling for Arbitrary Deterministic Lateral Displacement Design and Test 用于任意确定性侧向位移设计和测试的机器学习增强型预测建模。

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-06-17 DOI: 10.1109/TNB.2024.3415365

Yidan Zhang;Junchao Wang;Jinkai Chen;Guodong Su;Wen-Sheng Zhao;Jun Liu

{"title":"Machine Learning-Enhanced Predictive Modeling for Arbitrary Deterministic Lateral Displacement Design and Test","authors":"Yidan Zhang;Junchao Wang;Jinkai Chen;Guodong Su;Wen-Sheng Zhao;Jun Liu","doi":"10.1109/TNB.2024.3415365","DOIUrl":"10.1109/TNB.2024.3415365","url":null,"abstract":"The separation of biological particles like cells and macromolecules from liquid samples is vital in clinical medicine, supporting liquid biopsies and diagnostics. Deterministic Lateral Displacement (DLD) is prominent for sorting particles in microfluidics by size. However, the design, fabrication, and testing of DLDs are complex and time-consuming. Researchers typically rely on finite element analysis to predict particle trajectories, which are crucial in evaluating the performance of DLD. Traditional particle trajectory predictions through finite element analysis often inaccurately reflect experimental results due to manufacturing and experimental variabilities. To address this issue, we introduced a machine learning-enhanced approach, combining past experimental data and advanced modeling techniques. Our method, using a dataset of 132 experiments from 40 DLD chips and integrating finite element simulation with a microfluidic-optimized particle simulation algorithm (MOPSA) and a Random Forest model, improves trajectory prediction and critical size determination without physical tests. This enhanced accuracy in simulation across various DLD chips speeds up development. Our model, validated against three DLD chip designs, showed a high correlation between predicted and experimental particle trajectories, streamlining chip development for clinical applications.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 1","pages":"46-62"},"PeriodicalIF":3.7,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141418735","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}

引用次数: 0

Bioinspired Quantum Oracle Circuits for Biomolecular Solutions of the Maximum Cut Problem 最大切割问题生物分子解决方案的生物启发量子甲骨文电路

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-04-30 DOI: 10.1109/TNB.2024.3395420

Weng-Long Chang;Renata Wong;Yu-Hao Chen;Wen-Yu Chung;Ju-Chin Chen;Athanasios V. Vasilakos

{"title":"Bioinspired Quantum Oracle Circuits for Biomolecular Solutions of the Maximum Cut Problem","authors":"Weng-Long Chang;Renata Wong;Yu-Hao Chen;Wen-Yu Chung;Ju-Chin Chen;Athanasios V. Vasilakos","doi":"10.1109/TNB.2024.3395420","DOIUrl":"10.1109/TNB.2024.3395420","url":null,"abstract":"Given an undirected, unweighted graph with n vertices and m edges, the maximum cut problem is to find a partition of the n vertices into disjoint subsets \u0000<inline-formula> <tex-math>${V}_{{1}}$ </tex-math></inline-formula>\u0000 and \u0000<inline-formula> <tex-math>${V}_{{2}}$ </tex-math></inline-formula>\u0000 such that the number of edges between them is as large as possible. Classically, it is an NP-complete problem, which has potential applications ranging from circuit layout design, statistical physics, computer vision, machine learning and network science to clustering. In this paper, we propose a biomolecular and a quantum algorithm to solve the maximum cut problem for any graph G. The quantum algorithm is inspired by the biomolecular algorithm and has a quadratic speedup over its classical counterparts, where the temporal and spatial complexities are reduced to, respectively, \u0000<inline-formula> <tex-math>${O}text {(}sqrt {{2}^{n}/{r}}text {)}$ </tex-math></inline-formula>\u0000 and \u0000<inline-formula> <tex-math>${O}text {(}{m}^{{2}}text {)}$ </tex-math></inline-formula>\u0000. With respect to oracle-related quantum algorithms for NP-complete problems, we identify our algorithm as optimal. Furthermore, to justify the feasibility of the proposed algorithm, we successfully solve a typical maximum cut problem for a graph with three vertices and two edges by carrying out experiments on IBM’s quantum simulator.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 3","pages":"499-506"},"PeriodicalIF":3.7,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140835568","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}

引用次数: 0

High Sensitivity of Dielectrically Modulated Tunnel Field Effect Transistor for Biosensor Applications 用于生物传感器应用的高灵敏度电介质调制隧道场效应晶体管。

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-04-24 DOI: 10.1109/TNB.2024.3386586

P. Harika;Girija Sravani Kondavitee;Srinivasa Rao Karumuri;Aime Lay-Ekuakille

{"title":"High Sensitivity of Dielectrically Modulated Tunnel Field Effect Transistor for Biosensor Applications","authors":"P. Harika;Girija Sravani Kondavitee;Srinivasa Rao Karumuri;Aime Lay-Ekuakille","doi":"10.1109/TNB.2024.3386586","DOIUrl":"10.1109/TNB.2024.3386586","url":null,"abstract":"The Dielectrically Modulated Full Gate Tunnel Field Effect Transistor (FET) with dual nanocavities, as described in the paper, is a novel device designed as a label-free biosensor for detecting cancer cell biomolecules. This biosensor utilizes the principles of field-effect transistors and incorporates nanocavities to enhance the detection sensitivity. The simulations are conducted using the Silvaco Atlas model, which allowed for the analysis of the device’s electrical characteristics in the presence of various cancer cell biomolecules. The performance of the proposed device is evaluated using several sensing metrics, including current, threshold voltage, and subthreshold slope. These metrics are examined to assess their sensitivity to the presence of different cancer cell biomolecules. By analyzing these electrical characteristics, we can able to determine the device’s ability to detect and differentiate between specific biomolecules associated with cancer cells. One important aspect discussed in the paper is the incorporation of nanocavities in the device design. These nanocavities have a significant impact on enhancing the sensing capabilities of the biosensor. The paper also introduces the concept of the filling factor parameter, which describes the fraction of the nanocavity volume occupied by the cancer cell biomolecules. This parameter plays a crucial role in achieving optimal sensing performance. Overall, the paper presents a comprehensive analysis of the proposed Dielectrically Modulated Full gate Tunnel FET embedded with dual nanocavities as a label-free biosensor for cancer cell biomolecules. The simulations conducted using the Silvaco Atlas model provide valuable insights into the device’s electrical characteristics and its sensitivity to different biomolecules. The study emphasizes the significance of nanocavities and their filling factor parameter in achieving enhanced sensing performance for cancer cell detection.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 1","pages":"25-36"},"PeriodicalIF":3.7,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140663155","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}

引用次数: 0

Preliminary Exploration of the Biophysical Mechanisms of Pulsed Magnetic Field- Induced Cell Permeabilization 脉冲磁场诱导细胞渗透的生物物理机制初探

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-04-16 DOI: 10.1109/TNB.2024.3385413

Chi Ma;Mengnan Zhang;Fei Teng;Wei Zheng;Yan Mi

{"title":"Preliminary Exploration of the Biophysical Mechanisms of Pulsed Magnetic Field- Induced Cell Permeabilization","authors":"Chi Ma;Mengnan Zhang;Fei Teng;Wei Zheng;Yan Mi","doi":"10.1109/TNB.2024.3385413","DOIUrl":"10.1109/TNB.2024.3385413","url":null,"abstract":"Pulsed magnetic field treatment can enhance cell membrane permeability, allowing large molecular substances that normally cannot pass through the cell membrane to enter the cell. This research holds significant prospects for biomedical applications. However, the mechanism underlying pulsed magnetic field-induced cell permeabilization remains unclear, impeding further progress in research related to pulsed magnetic field. Currently, hypotheses about the mechanism are struggling to explain experimental results. Therefore, this study developed a parameter-adjustable pulsed magnetic field generator and designed experiments. Starting from the widely accepted hypothesis of “induced electric fields by pulsed magnetic field,” we conducted a preliminary exploration of the biophysical mechanisms underlying pulsed magnetic field-induced cell permeabilization. Finally, we have arrived at an intriguing conclusion: under the current technical parameters, the impact of the pulsed magnetic field itself is the primary factor influencing changes in cell membrane permeability, rather than the induced electric field. This conclusion holds significant implications for understanding the biophysical mechanisms behind pulsed magnetic field therapy and its potential biomedical applications.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 3","pages":"482-490"},"PeriodicalIF":3.7,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140612766","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}

引用次数: 0

Benchmarking Power Generation From Multiple Wastewater Electrolytes in Microbial Fuel Cells With 3D Printed Disk-Electrodes 微生物燃料电池中多种废水电解质的发电基准与 3D 打印磁盘电极

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-04-08 DOI: 10.1109/TNB.2024.3385739

Yuvraj Maphrio Mao;Khairunnisa Amreen;Sanket Goel

{"title":"Benchmarking Power Generation From Multiple Wastewater Electrolytes in Microbial Fuel Cells With 3D Printed Disk-Electrodes","authors":"Yuvraj Maphrio Mao;Khairunnisa Amreen;Sanket Goel","doi":"10.1109/TNB.2024.3385739","DOIUrl":"10.1109/TNB.2024.3385739","url":null,"abstract":"Microbial Fuel Cells (MFCs) have recently gained attention, as they are inexpensive, green in nature, and sustainable. As per the report, by Allied Market Research the global market size of MFCs will increase from \u0000<inline-formula> <tex-math>${$}$ </tex-math></inline-formula>\u0000 264.8 million in 2021 to \u0000<inline-formula> <tex-math>${$}$ </tex-math></inline-formula>\u0000 452.2 million in 2030, growing at a CAGR of 4.5%. The present work is a comparative study of various types of electrolytes that can be used in MFCs. The working electrodes were printed using conducting graphene-based Polylactic Acid (PLA) filaments with the help of a 3D printer under the principle of the fused deposition method. Simulated electrolytes and natural environmental microbial electrolytes were used here. Also, electrolytes of pure E. coli culture were studied. Lake water reported the highest power density of 8.259 mW/cm2 while Stale E. Coli reported the lowest around 0.184 mW/cm2. The study comprehensively lists potential wastewaters that can fuel the MFCs. With the pioneering of various comparative studies of electrolytes, one can insight into the recruitment of electrolytes with high-performance benchmarks for miniaturized energy storage and other microelectronics applications.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 3","pages":"491-498"},"PeriodicalIF":3.7,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140570103","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}

引用次数: 0

A Molecular Communication Perspective on Synchronization of Coupled Microfluidic-Spectroscopy 微流控光谱耦合同步的分子通讯视角

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-04-02 DOI: 10.1109/TNB.2024.3384082

Xuewen Qian;Stefan Angerbauer;Malcolm Egan;Marco Di Renzo;Werner Haselmayr

{"title":"A Molecular Communication Perspective on Synchronization of Coupled Microfluidic-Spectroscopy","authors":"Xuewen Qian;Stefan Angerbauer;Malcolm Egan;Marco Di Renzo;Werner Haselmayr","doi":"10.1109/TNB.2024.3384082","DOIUrl":"10.1109/TNB.2024.3384082","url":null,"abstract":"A challenge for real-time monitoring of biochemical processes, such as cells, is detection of biologically relevant molecules. This is due to the fact that spectroscopy methods for detection may perturb the cellular environment. One approach to overcome this problem is coupled microfluidic-spectroscopy, where a microfluidic output channel is introduced in order to observe biologically relevant molecules. This approach allows for non-passive spectroscopy methods, such as mass spectrometry, to identify the structure of molecules released by the cell. Due to the non-negligible length of the microfluidic channel, when a sequence of stimuli are applied to a cell it is not straightforward to determine which spectroscopy samples correspond to a given stimulus. In this paper, we propose a solution to this problem by taking a molecular communication (MC) perspective on the coupled microfluidic-spectroscopy system. In particular, assignment of samples to a stimulus is viewed as a synchronization problem. We develop two new algorithms for synchronization in this context and carry out a detailed theoretical and numerical study of their performance. Our results show improvements over maximum-likelihood synchronization algorithms in terms of detection performance when there are uncertainties in the composition of the microfluidic channel.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 3","pages":"458-471"},"PeriodicalIF":3.7,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140570107","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}

引用次数: 0

IEEE Transactions on NanoBioscience Publication Information 电气和电子工程师学会《纳米生物科学论文集》出版信息

IF 3.9 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-03-28 DOI: 10.1109/TNB.2024.3378371

引用次数: 0