{"title":"Analysis of Tapered Fibre Optic Surface Plasmon Resonance Bio-Sensor Chip With Highly Perturbed Taper Profiles","authors":"Sanjeev Kumar Raghuwanshi","doi":"10.1109/TNB.2024.3376824","DOIUrl":"10.1109/TNB.2024.3376824","url":null,"abstract":"A numerical model based on the Transfer matrix method (TMM) is proposed for the first time to study the gold coated tapered fibre optic surface plasmon resonance (SPR) with eight different types of taper profiles namely linear, exponential-linear, Gaussian, quadratic, sinusoidal, error function type and highly perturbed taper profile so-called chirp type of profile. The performance in terms of sensitivity, full width at half maximum (FWHM), detection accuracy (D.A.), amplitude dip, and half power points are estimated with respect to tapering ratio and choices of taper profile. It is found that sensitivity increased almost linearly with the taper ratio of each taper choice for the account of the reduction of detection accuracy. It has been found that sensitivity is highest for the case of chirp taper profile and lowest for the case of quadratic taper profile at low taper ratio. In this study, the aqueous solution is considered for sensor development which is adulterated by biomolecules species like DNA, blood samples, etc.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 3","pages":"439-446"},"PeriodicalIF":3.7,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140119348","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}
{"title":"Biomedical Applications of Green Synthesized Zinc Oxide and Magnesium-Doped Zinc Oxide Nanoparticles Using Aqueous Extract of Ziziphus Oxyphylla Leaves","authors":"Suliman Syed;Arshad Islam;Muhammad Shabeer;Akhtar Nadhman;Farhan Ahmad;Nadia Irfan;Shaila Mehwish;Ajmal Khan","doi":"10.1109/TNB.2024.3373777","DOIUrl":"10.1109/TNB.2024.3373777","url":null,"abstract":"Zinc oxide (ZnO) and magnesium-doped zinc oxide (Mg-doped ZnO) nanoparticles (NPs) were synthesized using Ziziphus oxyphylla ’s aqueous leaf extract as reducing agent. UV-Vis absorption peaks at 324 nm and 335 nm were indicative of ZnO and Mg-doped ZnO, respectively. FTIR absorption bands observed at 3238, 1043, 1400, 1401, 2186 and 2320 cm\u0000<inline-formula> <tex-math>$^{-1}$ </tex-math></inline-formula>\u0000 suggested the presence of phenols, alcohols, saturated hydrocarbons, and possibly alkynes. X-ray diffraction (XRD), scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy revealed pure, spherical and agglomerated NPs with average size of 35.9 nm (ZnO) and 56.8 nm (Mg-doped ZnO). Both NPs remained active against all bacterial strains with the highest inhibition zones observed against Proteus vulgaris (21.16±1.25 mm for ZnO and 24.1±0.76 mm for Mg-doped ZnO. EtBr fluorescence (cartwheel assay) indicated efflux pump blockage, suggesting its facilitation in the bacterial growth inhibition. Antioxidant potential, determined via DPPH radical scavenging assay, revealed stronger antioxidant potential for Mg-doped ZnO (IC\u0000<inline-formula> <tex-math>$_{{50}}~21.53pm 0.76~mu text{g}$ </tex-math></inline-formula>\u0000/mL) than pure ZnO (IC\u0000<inline-formula> <tex-math>$_{{50}}~30.32pm 0.73~mu text{g}$ </tex-math></inline-formula>\u0000/mL). Furthermore, both NPs showed antileishmanial activity against Leishmania tropica promastigotes (IC\u0000<inline-formula> <tex-math>$_{{50}}~47.23pm 3.22~mu text{g}$ </tex-math></inline-formula>\u0000/mL for Mg-doped ZnO and 64.34±6.56 for ZnO), while neither NP exhibited significant hemolysis, indicating biocompatibility and further assessment for their drugability.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 3","pages":"418-427"},"PeriodicalIF":3.7,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140049315","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}
{"title":"In Situ Measurement of Urea Concentration With an In-Fiber SPR-MZI Sensor","authors":"Liangliang Cheng;Wanlu Zheng;Ya-Nan Zhang;Xuegang Li;Yong Zhao","doi":"10.1109/TNB.2024.3398807","DOIUrl":"10.1109/TNB.2024.3398807","url":null,"abstract":"A fiber-optic urea sensor based on surface plasmon resonance (SPR) and Mach-Zehnder interference (MZI) combined principle was designed and implemented. By plating gold film on the single-mode-no-core-thin-core-single-mode fiber structure, we successfully excited both SPR and MZI, and constructed two parallel detection channels for simultaneously measurement of urea concentration and temperature. Urease was immobilized on the gold film by metal-organic zeolite skeleton (ZIF-8), which can not only fix a large number of urease to improve measurement sensitivity of urea, but also protect urease activity to ensure the sensor stability. Experimental results indicate that the designed urea sensor with temperature compensation function can detect urea solution with concentration of 1-9 mM, and the sensitivity is 1.4 nm/mM. The proposed measurement method provides a new choice for monitoring urea concentration in the field of medical diagnosis and human health monitoring.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 3","pages":"403-409"},"PeriodicalIF":3.7,"publicationDate":"2024-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140898232","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}
{"title":"On the Target Detection Performance of a Molecular Communication Network With Multiple Mobile Nanomachines","authors":"Nithin V. Sabu;Abhishek K. Gupta","doi":"10.1109/TNB.2024.3399188","DOIUrl":"10.1109/TNB.2024.3399188","url":null,"abstract":"A network of nanomachines (NMs) can be used to build a target detection system for a variety of promising applications. They have the potential to detect toxic chemicals, infectious bacteria, and biomarkers of dangerous diseases such as cancer within the human body. Many diseases and health disorders can be detected early and efficiently treated in the future by utilizing these systems. To fully grasp the potential of these systems, mathematical analysis is required. This paper describes an analytical framework for modeling and analyzing the performance of target detection systems composed of multiple mobile nanomachines of varying sizes with passive/absorbing boundaries. We consider both direct contact detection, in which NMs must physically contact the target to detect it, and indirect sensing, in which NMs must detect the marker molecules emitted by the target. The detection performance of such systems is calculated for degradable and non-degradable targets, as well as mobile and stationary targets. The derived expressions provide various insights, such as the effect of NM density and target degradation on detection probability.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 3","pages":"524-536"},"PeriodicalIF":3.7,"publicationDate":"2024-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140898236","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}
Jiayu Sun;Yang Jiao;Fei Pan;Shuk Han Cheng;Dong Sun
{"title":"A High-Throughput Microdroplet-Based Single Cell Transfection Method for Gene Knockout Based on the CRISPR/Cas9 System","authors":"Jiayu Sun;Yang Jiao;Fei Pan;Shuk Han Cheng;Dong Sun","doi":"10.1109/TNB.2024.3373597","DOIUrl":"10.1109/TNB.2024.3373597","url":null,"abstract":"The efficient application of the newly developed gene-editing method CRISPR/Cas9 requires more accurate intracellular gene delivery. Traditional delivery approaches, such as lipotransfection and non-viral delivery methods, must contend with major problems to overcome the drawbacks of low efficiency, high toxicity, and cell-type dependency. The high-throughput microdroplet-based single-cell transfection method presented herein provides an alternative method for delivering genome-editing reagents into single living cells. By accurately controlling the number of exogenous plasmids in microdroplets, this method can achieve high-efficiency delivery of nucleic acids to different types of single cells. This paper presents a high-throughput quantitative DNA transfection method for single cells and explores the optimal DNA transfection conditions for specific cell lines. The transfection efficiency of cells at different concentrations of DNA in microdroplets is measured. Under the optimized transfection conditions, the method is used to construct gene-knockout cancer cell lines to determine specific gene functions through the CRISPR/Cas9 knockout system. In a case study, the migration ability of TRIM72 knockout cancer cells is inhibited, and the tumorigenicity of cells in a zebrafish tumor model is reduced. A single-cell microfluidic chip is designed to achieve CRISPR/Cas9 DNA transfection, dramatically improving the transfection efficiency of difficult-to-transfect cells. This research demonstrates that the microdroplet method developed herein has a unique advantage in CRISPR/Cas9 gene-editing applications.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"378-388"},"PeriodicalIF":3.9,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039243","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}
{"title":"Exploring the Potential of DNA Computing for Complex Big Data Problems: A Case Study on the Traveling Car Renter Problem","authors":"Zhao-Cai Wang;Xian Wu;Kun Liang;Tun-Hua Wu","doi":"10.1109/TNB.2024.3396142","DOIUrl":"10.1109/TNB.2024.3396142","url":null,"abstract":"The traveling car renter problem (TCRP) is a variant of the Traveling Salesman Problem (TSP) wherein the salesman utilizes rented cars for travel. The primary objective of this problem is to identify a solution that minimizes the cumulative operating costs. Given its classification as a non-deterministic polynomial (NP) problem, traditional computers are not proficient in effectively resolving it. Conversely, DNA computing exhibits unparalleled advantages when confronted with NP-hard problems. This paper presents a DNA algorithm, based on the Adleman-Lipton model, as a proposed approach to address TCRP. The solution for TCRP can be acquired by following a series of fundamental steps, including coding, interaction, and extraction. The time computing complexity of the proposed DNA algorithm is \u0000<inline-formula> <tex-math>$boldsymbol {O}(boldsymbol {n}^{boldsymbol {2}}boldsymbol {m})$ </tex-math></inline-formula>\u0000 for TCRP with n cities and m types of cars. By conducting simulation experiments, the solutions for certain instances of TCRP are computed and compared to those obtained by alternative algorithms. The proposed algorithm further illustrates the potential of DNA computing, as a form of parallel computing, to address more intricate large-scale problems.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 3","pages":"391-402"},"PeriodicalIF":3.7,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140854996","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}
{"title":"Characterizations of Centrifugal Electrospun Polyvinyl Alcohol/Sodium Alginate/Tamanu Oil/Silver Nanoparticles Wound Dressing","authors":"Thi Phuong Anh Tran;Anh Hue Luong;Wei-Chih Lin","doi":"10.1109/TNB.2024.3371224","DOIUrl":"10.1109/TNB.2024.3371224","url":null,"abstract":"Known for its water solubility, flexibility, strong adhesion, and eco-friendly nature, polyvinyl alcohol (PVA) is widely used in various industries. In the medical field, it is used for applications such as creating bandages and orthopaedic devices. Incorporating sodium alginate (SA) into PVA membranes enhances their structural integrity, breathability, and permeability, thereby minimising the risk of cellular damage in the wound zone. Moreover, the addition of tamanu oil (C alophyllum inophyllum L.) and silver nanoparticles, both of which are known for their antibacterial properties and benefits in traditional wound healing, further enhances the membranes’ wound-healing effectiveness. Following production, the membranes undergo a series of tests designed to evaluate their physical properties as well as their antioxidant and antibacterial capabilities. Subsequently, in vitro testing is conducted using human skin cells; experiments on Wistar rats are then performed. Numerous experiments have consistently demonstrated that the performance of polyvinyl alcohol/sodium alginate/tamanu oil (PVA/SA/Oil) membrane is superior to that of polyvinyl alcohol/sodium alginate/tamanu oil/silver nanoparticles (PVA/SA/Oil/Ag NP) membrane. Specifically, the polyvinyl alcohol/sodium alginate (PVA/SA) combination exhibits an impressive wound-healing rate of 98.82% after 15 days, with cells maintaining a high viability of 92% in a nourishing environment. Moreover, these membranes exhibit exceptional resistance to the oxidation of free radicals, surpassing the 70% threshold, and they possess antibacterial activity against Staphylococcus aureus subsp. aureus in vitro. Based on the obtained results, the nanofiber membranes composed of polyvinyl alcohol/ alginate/ tamanu oil, with or without silver nanoparticles, have shown potential as wound dressings in the wound care discipline.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"368-377"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10457035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140012540","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}
Ghazaleh Kianfar;Mehdi Azadi;Jamshid Abouei;Arash Mohammadi;Konstantinos N. Plataniotis
{"title":"Wireless Body Area Nanonetworks via Vascular Molecular Communication","authors":"Ghazaleh Kianfar;Mehdi Azadi;Jamshid Abouei;Arash Mohammadi;Konstantinos N. Plataniotis","doi":"10.1109/TNB.2024.3365737","DOIUrl":"10.1109/TNB.2024.3365737","url":null,"abstract":"Advancements in biotechnology and molecular communication have enabled the utilization of nanomachines in Wireless Body Area Networks (WBAN2) for applications such as drug delivery, cancer detection, and emergency rescue services. To study these networks effectively, it is essential to develop an ideal propagation model that includes the channel response between each pair of in-range nanomachines and accounts for the interference received at each receiver node. In this paper, we employ an advection-diffusion equation to obtain a deterministic channel matrix through a vascular WBAN2. Additionally, the closed forms of inter-symbol interference (ISI) and co-channel interference (CCI) are derived for both full duplex (FDX) and half duplex transmission (HDX) modes. By applying these deterministic formulations, we then present the stochastic equivalents of the ideal channel model and interference to provide an innovative communication model by simultaneously incorporating CCI, ISI, and background noise. Finally, we evaluate the results with numerous experiments and use signal-to-interference-plus-noise ratio (SINR) and capacity as metrics.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"355-367"},"PeriodicalIF":3.9,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139729535","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}
Shobhit K. Patel;Jaymit Surve;Abdullah Baz;Yagnesh Parmar
{"title":"Optimization of Novel 2D Material Based SPR Biosensor Using Machine Learning","authors":"Shobhit K. Patel;Jaymit Surve;Abdullah Baz;Yagnesh Parmar","doi":"10.1109/TNB.2024.3354810","DOIUrl":"10.1109/TNB.2024.3354810","url":null,"abstract":"Biosensors are needed for today’s health monitoring system for detecting different biomolecules. Graphene is a monolayer material that can be utilized to sense biomolecules and design biosensors. We have proposed a Graphene-Gold-Silver hybrid structure design based on Zinc Oxide which gives sensitive performance to detect hemoglobin biomolecules. The advanced biosensor designed based on this hybrid structure shows the highest sensitivity of 1000 nm/RIU which is far better concerning similar structure previously analyzed. The graphene-gold-silver hybrid structure is presented for its possible reflectance results and electric field results. The E-field results match well with the reflectance results given by the sensitive hybrid structure. The sensing biomolecules are presented above the structure where a combination of graphene-gold-silver hybrid structure improves the sensitivity to a great extent. The optimized parameters are obtained by applying variations in the physical parameters of the design. The machine learning algorithm employed for reflectance prediction shows a high prediction accuracy and can be utilized for simulation resource reduction. The proposed biosensor can be used in real-time hemoglobin monitoring.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"328-335"},"PeriodicalIF":3.9,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139563924","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}
{"title":"An Encoding Table Corresponding to ASCII Codes for DNA Data Storage and a New Error Correction Method HMSA","authors":"Xuncai Zhang;Fuzhen Zhou","doi":"10.1109/TNB.2024.3356522","DOIUrl":"10.1109/TNB.2024.3356522","url":null,"abstract":"DNA storage stands out from other storage media due to its high capacity, eco-friendliness, long lifespan, high stability, low energy consumption, and low data maintenance costs. To standardize the DNA encoding system, maintain consistency in character representation and transmission, and link binary, base, and character together, this paper combines the encoding method with ASCII code to construct an ASCII-DNA encoding table. The encoding method can encode not only pure text information but also audio and video information and satisfies the GC content constraint and the homopolymer constraint, with the encoding density reaching 1.4 bits/nt. In particular, when encoding textual information, it directly skips the binary conversion process, which reduces the complexity of encoding, and increasing the encoding density to 1.6 bits/nt. In order to solve the problem of errors in sequences, under the influence of heuristic algorithms, this paper proposes a new error correction method (HMSA) by combining minimum Hamming distance, multiple sequence alignment, and encoding scheme. It can correct not only substitution, insertion, and deletion errors in Reads but also consecutive errors in Reads. It greatly improves the utilization of the Reads and avoids the waste of resources. Simulation results show that the recovery rate of Reads increases with the increasing number of sequencing times. When the number of erroneous bases in a 150nt sequence reaches 5nt, the error correction rate can exceed 96% by sequencing the base sequence only 10 times regardless of whether the errors are consecutive or not. Additionally, the HMSA error correction method is applicable to all coding schemes for lookup code table types.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"344-354"},"PeriodicalIF":3.9,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139520221","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}