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Fakhri MA, Salim ET, Tariq SM, Ibrahim RK, Alsultany FH, Alwahib AA, Alhasan SFH, Gopinath SCB, Salim ZT, Hashim U. A gold nanoparticles coated unclad single mode fiber-optic sensor based on localized surface plasmon resonance. Sci Rep 2023; 13:5680. [PMID: 37029253 PMCID: PMC10082208 DOI: 10.1038/s41598-023-32852-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/03/2023] [Indexed: 04/09/2023] Open
Abstract
In the last few decays, the fiber-optic was employed in the field of sensing because of its benefits in contrast to other types of sensors such as small size, easy to fabricate, high response, and flexibility. In this study, unclad single mode fiber-optic sensor is proposed to operate at 650 nm wavelength. COMSOL Multiphysics 5.1 finite element method (FEM) is used to design the sensor and tested it theoretically. The middle portion of the fiber cladding is removed and replaced by gold nanoparticles (Au NPs) of 50 nm thickness. Analytic layer of 3 μm thickness was immersed in different liquids in range of refractive index (RI) from 1.000281 to 1.39. These liquids are NaCl Deionized (DI) water solution, sucrose-Deionized (DI) water solution, and glycerol solution Deionized (DI) water. It was found that the highest obtained sensitivity and resolution are for glycerol-DI water solution with value of 3157.98 (nm/RIU) and 3.16 × 10-5 (RIU), respectively. Furthermore, it is easy to fabricate and of low cost. In experiments, pulsed laser ablation (PLA) was used to prepare Au NPs. X-ray diffraction (XRD) shown that the peak of the intensity grew as the ablated energy increased as well as the structure crystallization. Transmission electron microscopy (TEM) revealed an average diameter of 30 nm at the three ablated energies, while X-ray spectroscopy (EDX) spectrum has indicated the presence of Au NPs in the prepared solution. The photoluminescence (PL) and ultraviolet-visible UV-Vis transmission were used to study the optical properties of the prepared Au NPs. An optical spectrum analyzer was used to obtain the sensor's output results. It has shown that best intensity was obtained for sucrose which confined with theoretical results.
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Affiliation(s)
- Makram A Fakhri
- Laser and Optoelectronic Engineering Department, University of Technology-Iraq, Baghdad, Iraq.
| | - Evan T Salim
- Applied science department, University of Technology-Iraq, Baghdad, Iraq.
| | - Sara M Tariq
- Laser and Optoelectronic Engineering Department, University of Technology-Iraq, Baghdad, Iraq
| | | | - Forat H Alsultany
- Department of Medical Physics, Al-Mustaqbal University College, Hillah, Iraq
| | - Ali A Alwahib
- Laser and Optoelectronic Engineering Department, University of Technology-Iraq, Baghdad, Iraq
| | | | - Subash C B Gopinath
- Institute of Nano Electronic Engineering, University Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
- Centre of Excellence for Nanobiotechnology and Nanomedicine (CoExNano), Faculty of Applied Sciences, AIMST University, 08100, Semeling, Kedah, Malaysia
| | - Zaid T Salim
- Institute of Nano Electronic Engineering, University Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
| | - U Hashim
- Institute of Nano Electronic Engineering, University Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
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Olatomiwa A, Adam T, Edet C, Adewale A, Chik A, Mohammed M, Gopinath SC, Hashim U. Recent advances in density functional theory approach for optoelectronics properties of graphene. Heliyon 2023; 9:e14279. [PMID: 36950613 PMCID: PMC10025043 DOI: 10.1016/j.heliyon.2023.e14279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Graphene has received tremendous attention among diverse 2D materials because of its remarkable properties. Its emergence over the last two decades gave a new and distinct dynamic to the study of materials, with several research projects focusing on exploiting its intrinsic properties for optoelectronic devices. This review provides a comprehensive overview of several published articles based on density functional theory and recently introduced machine learning approaches applied to study the electronic and optical properties of graphene. A comprehensive catalogue of the bond lengths, band gaps, and formation energies of various doped graphene systems that determine thermodynamic stability was reported in the literature. In these studies, the peculiarity of the obtained results reported is consequent on the nature and type of the dopants, the choice of the XC functionals, the basis set, and the wrong input parameters. The different density functional theory models, as well as the strengths and uncertainties of the ML potentials employed in the machine learning approach to enhance the prediction models for graphene, were elucidated. Lastly, the thermal properties, modelling of graphene heterostructures, the superconducting behaviour of graphene, and optimization of the DFT models are grey areas that future studies should explore in enhancing its unique potential. Therefore, the identified future trends and knowledge gaps have a prospect in both academia and industry to design future and reliable optoelectronic devices.
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Affiliation(s)
- A.L. Olatomiwa
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
- Faculty of Electronic Engineering and Technology, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
| | - Tijjani Adam
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
- Faculty of Electronic Engineering and Technology, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
- Micro System Technology, Centre of Excellence (CoE), Universiti Malaysia Perlis (UniMAP), Pauh Campus, 02600, Arau, Perlis, Malaysia
| | - C.O. Edet
- Faculty of Electronic Engineering and Technology, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
- Institute of Engineering Mathematics, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
- Department of Physics, Cross River University of Technology, Calabar, Nigeria
| | - A.A. Adewale
- Department of Pure and Applied Physics, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Abdullah Chik
- Centre for Frontier Materials Research, Universiti Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
- Faculty of Chemical Engineering and Technology, Universiti Malaysia Perlis (UniMAP), Taman Muhibbah, Jejawi, 02600, Arau, Perlis, Malaysia
| | - Mohammed Mohammed
- Faculty of Chemical Engineering and Technology, Universiti Malaysia Perlis (UniMAP), Taman Muhibbah, Jejawi, 02600, Arau, Perlis, Malaysia
- Center of Excellence Geopolymer & Green Technology (CEGeoGTech), Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
| | - Subash C.B. Gopinath
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
- Micro System Technology, Centre of Excellence (CoE), Universiti Malaysia Perlis (UniMAP), Pauh Campus, 02600, Arau, Perlis, Malaysia
- Faculty of Chemical Engineering and Technology, Universiti Malaysia Perlis (UniMAP), Taman Muhibbah, Jejawi, 02600, Arau, Perlis, Malaysia
| | - U. Hashim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
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Dhahi TS, Adam T, Gopinath SCB, Hashim U. Gold nanogap impedimetric biosensor for precise and selective Ganoderma boninense detection. 3 Biotech 2022; 12:299. [PMID: 36276457 PMCID: PMC9522946 DOI: 10.1007/s13205-022-03368-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/17/2022] [Indexed: 11/01/2022] Open
Abstract
Ganoderma species are common wood-rotting fungi that cause root and stem rot in most monocots, dicots, and gymnosperms. It influences plantation crops such as oil palm and rubber in Malaysia, but the effects vary greatly within the genus. Because of the complex chemistry of Ganoderma, extracting and identifying the physiologically active chemicals is often time-consuming and necessitates extensive bioassays. This study investigated the specific identification of the most infectious Ganoderma species using a sub-20-nm gold electrode. Three electrodes were created using chemically controlled etching (2, 10, and 20 nm). An AutoCAD mask containing nanogap pad electrodes was used to create a chrome glass surface, which was then translated and built. Following the successful construction of the device, the sensor was evaluated using a combination of conventional photolithography and a size reduction technique to imprint the nanogap design onto the gold surface. Ganoderma boninense target DNA was synthesised and surface-modified to enable interaction at extremely low molecular concentrations. The proposed device has a detection limit of 0.001 mol/L, which is seven times lower than the detection limits of currently available devices. The capacitance, conductivity, and permittivity of complementary, non-complementary, single mismatched, and targeted biomolecules changed during hybridization. This sensor correctly differentiated between all samples. The sensor's performance is further validated by comparing experimental data from the sensor to theoretical data from the sensor's corresponding circuit model. The two data sets are very similar.
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Affiliation(s)
- Thikra S. Dhahi
- Electronics Technical Department, Southern Technical University, Basra, Iraq
- Faculty of Electronic Engineering & Technology, Universiti Malaysia Perlis, 02600 Arau, Perlis Malaysia
| | - Tijjani Adam
- Faculty of Electronic Engineering & Technology, Universiti Malaysia Perlis, 02600 Arau, Perlis Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis Malaysia
| | - Subash C. B. Gopinath
- Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis, 02600 Arau, Perlis Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis Malaysia
- Centre of Excellence for Nanobiotechnology and Nanomedicine (CoExNano), Faculty of Applied Sciences, AIMST University, Semeling, 08100 Kedah, Malaysia
| | - U. Hashim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis Malaysia
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Tariq SM, Fakhri MA, Salim ET, Hashim U, Alsultany FH. Design of an unclad single-mode fiber-optic biosensor based on localized surface plasmon resonance by using COMSOL Multiphysics 5.1 finite element method. Appl Opt 2022; 61:6257-6267. [PMID: 36256240 DOI: 10.1364/ao.458175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/20/2022] [Indexed: 06/16/2023]
Abstract
This study proposed an unclad optical fiber biosensor based on the localized surface plasmon resonance phenomenon and operating at 650 nm using COMSOL Multiphysics 5.1 finite element method (FEM). Gold nanoparticles (50 nm thickness) were coated on the middle portion of the unclad fiber. Air, water, blood plasma, liver tissue, colon tissue, and pentanol (C5H11OH) were used as analytical layers with 3 µm. The sensor serves as a theoretical foundation for experimental research. The blood plasma had the highest sensitivity with a sensitivity of 10,638.297 nm/RIU and a resolution of 9.410-6RIU. The proposed sensor is a promising candidate for a low-cost, simple-geometry biochemical sensing solution.
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Adam T, Dhahi TS, Gopinath SCB, Hashim U, Uda MNA. Recent advances in techniques for fabrication and characterization of nanogap biosensors: A review. Biotechnol Appl Biochem 2021; 69:1395-1417. [PMID: 34143905 DOI: 10.1002/bab.2212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
Nanogap biosensors have fascinated researchers due to their excellent electrical properties. Nanogap biosensors comprise three arrays of electrodes that form nanometer-size gaps. The sensing gaps have become the major building blocks of several sensing applications, including bio- and chemosensors. One of the advantages of nanogap biosensors is that they can be fabricated in nanoscale size for various downstream applications. Several studies have been conducted on nanogap biosensors, and nanogap biosensors exhibit potential material properties. The possibilities of combining these unique properties with a nanoscale-gapped device and electrical detection systems allow excellent and potential prospects in biomolecular detection. However, their fabrication is challenging as the gap is becoming smaller. It includes high-cost, low-yield, and surface phenomena to move a step closer to the routine fabrications. This review summarizes different feasible techniques in the fabrication of nanogap electrodes, such as preparation by self-assembly with both conventional and nonconventional approaches. This review also presents a comprehensive analysis of the fabrication, potential applications, history, and the current status of nanogap biosensors with a special focus on nanogap-mediated bio- and chemical sonsors.
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Affiliation(s)
- Tijjani Adam
- Faculty of Electronic Engineering Technology, Universiti Malaysia Perlis, Kampus Uniciti Alam Sg. Chuchuh, Padang Besar (U), Perlis, Malaysia.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - Th S Dhahi
- Physics Department, University of Basrah, Basra, Iraq.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - Subash C B Gopinath
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, Perlis, 02600, Malaysia.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - U Hashim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - M N A Uda
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, Perlis, 02600, Malaysia.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
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6
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Nadzirah S, Hashim U, Gopinath SCB, Parmin NA, Hamzah AA, Yu HW, Dee CF. Titanium dioxide-mediated resistive nanobiosensor for E. coli O157:H7. Mikrochim Acta 2020; 187:235. [PMID: 32185529 DOI: 10.1007/s00604-020-4214-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/03/2020] [Indexed: 12/19/2022]
Abstract
A titanium dioxide nanoparticle (TiO2 NP)-mediated resistive biosensor is described for the determination of DNA fragments of Escherichia coli O157:H7 (E. coli O157:H7). The sol-gel method was used to synthesize the TiO2 NP, and microlithography was applied to fabricate the interdigitated sensor electrodes. Conventional E. coli DNA detections are facing difficulties in long-preparation-and-detection-time (more than 3 days). Hence, electronic biosensor was introduced by measuring the current-voltage (I-V) DNA probe without amplification of DNA fragments. The detection scheme is based on the interaction between the electron flow on the sensor and the introduction of negative charges from DNA probe and target DNA. The biosensor has a sensitivity of 1.67 × 1013 Ω/M and a wide analytical range. The limit detection is down to 1 × 10-11 M of DNA. The sensor possesses outstanding repeatability and reproducibility and is cabable to detect DNA within 15 min in a minute-volume sample (1 μL). Graphical abstract Fig. (a) Graphical illustration of electronic biosensor set up and (b) relationship between limit of detection (LOD) and the unaffected poultry samples on E. coli O157:H7.
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Affiliation(s)
- Sh Nadzirah
- Institute of Microengineering and Nanoelectronics, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| | - U Hashim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000, Kangar, Perlis, Malaysia.,School of Bioprocess Engineering, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
| | - N A Parmin
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000, Kangar, Perlis, Malaysia.,School of Bioprocess Engineering, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
| | - Azrul Azlan Hamzah
- Institute of Microengineering and Nanoelectronics, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Hung Wei Yu
- Department of Materials Science and Engineering, National Chiao Tung University, Hsinchu, 30010, Taiwan
| | - Chang Fu Dee
- Institute of Microengineering and Nanoelectronics, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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8
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Mohammed AM, Al-Khateeb IK, Haider AJ, Rahim RA, Hashim U. Preparation of DNA biosensor application from fuel oil waste by functionalization and characterization of MWCNT. Sensing and Bio-Sensing Research 2017. [DOI: 10.1016/j.sbsr.2017.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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9
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Humayun Q, Hashim U, Ruzaidi CM, Noriman NZ. A strategy for design and fabrication of low cost microchannel for future reproductivity of bio/chemical lab-on-chip application. ACTA ACUST UNITED AC 2017. [DOI: 10.1063/1.4975255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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11
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Lee HC, Liu WW, Chai SP, Mohamed AR, Aziz A, Khe CS, Hidayah NS, Hashim U. Review of the synthesis, transfer, characterization and growth mechanisms of single and multilayer graphene. RSC Adv 2017. [DOI: 10.1039/c7ra00392g] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Graphene has emerged as the most popular topic in the active research field since graphene's discovery in 2004 by Andrei Geim and Kostya Novoselov.
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Affiliation(s)
- H. Cheun Lee
- Institute of Nano Electronic Engineering
- Universiti Malaysia Perlis
- 01000 Kangar
- Malaysia
| | - Wei-Wen Liu
- Institute of Nano Electronic Engineering
- Universiti Malaysia Perlis
- 01000 Kangar
- Malaysia
| | | | - Abdul Rahman Mohamed
- School of Chemical Engineering
- Engineering Campus
- Universiti Sains Malaysia
- 14300 Nibong Tebal
- Malaysia
| | - Azizan Aziz
- School of Material and Mineral Resources Engineering
- Engineering Campus
- Universiti Sains Malaysia
- 14300 Nibong Tebal
- Malaysia
| | - Cheng-Seong Khe
- Department of Fundamental and Applied Sciences
- Universiti Teknologi PETRONAS
- Bandar Seri Iskandar
- Malaysia
| | - N. M. S. Hidayah
- Institute of Nano Electronic Engineering
- Universiti Malaysia Perlis
- 01000 Kangar
- Malaysia
| | - U. Hashim
- Institute of Nano Electronic Engineering
- Universiti Malaysia Perlis
- 01000 Kangar
- Malaysia
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12
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Lee HC, Liu WW, Chai SP, Mohamed AR, Aziz A, Khe CS, Hidayah NMS, Hashim U. Correction: Review of the synthesis, transfer, characterization and growth mechanisms of single and multilayer graphene. RSC Adv 2017. [DOI: 10.1039/c7ra90066j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Correction for ‘Review of the synthesis, transfer, characterization and growth mechanisms of single and multilayer graphene’ by H. Cheun Lee et al., RSC Adv., 2017, 7, 15644–15693.
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Affiliation(s)
- H. Cheun Lee
- Institute of Nano Electronic Engineering
- Universiti Malaysia Perlis
- Malaysia
| | - Wei-Wen Liu
- Institute of Nano Electronic Engineering
- Universiti Malaysia Perlis
- Malaysia
| | | | - Abdul Rahman Mohamed
- School of Chemical Engineering
- Engineering Campus
- Universiti Sains Malaysia
- Malaysia
| | - Azizan Aziz
- School of Material and Mineral Resources Engineering
- Engineering Campus
- Universiti Sains Malaysia
- Malaysia
| | - Cheng-Seong Khe
- Department of Fundamental and Applied Sciences
- Universiti Teknologi PETRONAS
- Malaysia
| | - N. M. S. Hidayah
- Institute of Nano Electronic Engineering
- Universiti Malaysia Perlis
- Malaysia
| | - U. Hashim
- Institute of Nano Electronic Engineering
- Universiti Malaysia Perlis
- Malaysia
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Rahman S, Yusof N, Hashim U, Hushiarian R, M.N. MN, Hamidon M, Zawawi R, Fathil M. Enhanced sensing of dengue virus DNA detection using O2 plasma treated-silicon nanowire based electrical biosensor. Anal Chim Acta 2016; 942:74-85. [DOI: 10.1016/j.aca.2016.09.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/05/2016] [Accepted: 09/06/2016] [Indexed: 11/27/2022]
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Fathil M, Md Arshad M, Ruslinda A, Nuzaihan M.N. M, Gopinath SC, Adzhri R, Hashim U. Progression in sensing cardiac troponin biomarker charge transductions on semiconducting nanomaterials. Anal Chim Acta 2016; 935:30-43. [DOI: 10.1016/j.aca.2016.06.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 05/19/2016] [Accepted: 06/07/2016] [Indexed: 01/27/2023]
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Nuzaihan M.N. M, Hashim U, Md Arshad M, Kasjoo S, Rahman S, Ruslinda A, Fathil M, Adzhri R, Shahimin M. Electrical detection of dengue virus (DENV) DNA oligomer using silicon nanowire biosensor with novel molecular gate control. Biosens Bioelectron 2016; 83:106-14. [DOI: 10.1016/j.bios.2016.04.033] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/11/2016] [Accepted: 04/12/2016] [Indexed: 12/23/2022]
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M. N MN, Hashim U, Md Arshad MK, Ruslinda AR, Rahman SFA, Fathil MFM, Ismail MH. Top-Down Nanofabrication and Characterization of 20 nm Silicon Nanowires for Biosensing Applications. PLoS One 2016; 11:e0152318. [PMID: 27022732 PMCID: PMC4811568 DOI: 10.1371/journal.pone.0152318] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/11/2016] [Indexed: 11/18/2022] Open
Abstract
A top-down nanofabrication approach is used to develop silicon nanowires from silicon-on-insulator (SOI) wafers and involves direct-write electron beam lithography (EBL), inductively coupled plasma-reactive ion etching (ICP-RIE) and a size reduction process. To achieve nanometer scale size, the crucial factors contributing to the EBL and size reduction processes are highlighted. The resulting silicon nanowires, which are 20 nm in width and 30 nm in height (with a triangular shape) and have a straight structure over the length of 400 μm, are fabricated precisely at the designed location on the device. The device is applied in biomolecule detection based on the changes in drain current (Ids), electrical resistance and conductance of the silicon nanowires upon hybridization to complementary target deoxyribonucleic acid (DNA). In this context, the scaled-down device exhibited superior performances in terms of good specificity and high sensitivity, with a limit of detection (LOD) of 10 fM, enables for efficient label-free, direct and higher-accuracy DNA molecules detection. Thus, this silicon nanowire can be used as an improved transducer and serves as novel biosensor for future biomedical diagnostic applications.
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Affiliation(s)
- M. Nuzaihan M. N
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis, Malaysia
- * E-mail:
| | - U. Hashim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis, Malaysia
- School of Microelectronic Engineering, Universiti Malaysia Perlis (UniMAP), 02600 Pauh, Perlis, Malaysia
| | - M. K. Md Arshad
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis, Malaysia
- School of Microelectronic Engineering, Universiti Malaysia Perlis (UniMAP), 02600 Pauh, Perlis, Malaysia
| | - A. Rahim Ruslinda
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis, Malaysia
| | - S. F. A. Rahman
- Chemistry Department, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - M. F. M. Fathil
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis, Malaysia
| | - Mohd. H. Ismail
- School of Microelectronic Engineering, Universiti Malaysia Perlis (UniMAP), 02600 Pauh, Perlis, Malaysia
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Lee HC, Liu WW, Chai SP, Mohamed AR, Lai CW, Khe CS, Voon C, Hashim U, Hidayah N. Synthesis of Single-layer Graphene: A Review of Recent Development. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.proche.2016.03.135] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Fatin MF, Ruslinda AR, Md Arshad MK, Tee KK, Ayub RM, Hashim U, Kamarulzaman A, Gopinath SCB. HIV-1 Tat biosensor: Current development and trends for early detection strategies. Biosens Bioelectron 2015; 78:358-366. [PMID: 26655174 DOI: 10.1016/j.bios.2015.11.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/20/2015] [Accepted: 11/24/2015] [Indexed: 02/07/2023]
Abstract
Human immunodeficiency virus (HIV) has infected almost 35 million people worldwide. Various tests have been developed to detect the presence of HIV during the early stages of the disease in order to reduce the risk of transmission to other humans. The HIV-1 Tat protein is one of the proteins present in HIV that are released abundantly approximately 2-4 weeks after infection. In this review, we have outlined various strategies for detecting the Tat protein, which helps transcribe the virus and enhances replication. Detection strategies presented include immunoassays, biosensors and gene expression, which utilize antibodies or aptamers as common probes to sense the presence of Tat. Alternatively, measuring the levels of gene transcription is a direct method of analysing the HIV gene to confirm the presence of Tat. By detection of the Tat protein, virus transmission can be detected in high-risk individuals in the early stages of the disease to reduce the risk of an HIV pandemic.
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Affiliation(s)
- M F Fatin
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
| | - A R Ruslinda
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia.
| | - M K Md Arshad
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
| | - K K Tee
- Center of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - R M Ayub
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
| | - U Hashim
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
| | - A Kamarulzaman
- Center of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
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Balakrishnan SR, Hashim U, Gopinath SCB, Poopalan P, Ramayya HR, Veeradasan P, Haarindraprasad R, Ruslinda AR. Polysilicon nanogap lab-on-chip facilitates multiplex analyses with single analyte. Biosens Bioelectron 2015; 84:44-52. [PMID: 26560969 DOI: 10.1016/j.bios.2015.10.075] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/15/2015] [Accepted: 10/26/2015] [Indexed: 12/27/2022]
Abstract
Rationally designed biosensing system supports multiplex analyses is warranted for medical diagnosis to determine the level of analyte interaction. The chemically functionalized novel multi-electrode polysilicon nanogap (PSNG) lab-on-chip is designed in this study, facilitates multiplex analyses for a single analyte. On the fabricated 69nm PSNG, biocompatibility and structural characteristics were verified for the efficient binding of Human Chorionic Gonadotropin (hCG). With the assistance of microfluidics, hCG sample was delivered via single-injection to 3-Aminopropyl(triethoxy)silane (APTES) and Glycidoxypropyl(trimethoxy)silane (GPMS) modified PSNG electrodes and the transduced signal was used to investigate the dielectric mechanisms for multiplex analyses. The results from amperometric response and impedance measurement delivered the scale of interaction between anti-hCG antibody and hCG that exhibited 6.5 times higher sensitivity for the chemical linker, APTES than GPMS. Under optimized experimental conditions, APTES and GPMS modified immunosensor has a limit of detection as 0.56mIU/ml and 2.93mIU/ml (at S/N=3), with dissociation constants (Kd) of 5.65±2.5mIU/ml and 7.28±2.6mIU/ml, respectively. These results suggest that multiplex analysis of single target could enhance the accuracy of detection and reliable for real-time comparative analyses. The designed PSNG is simple, feasible, requires low sample consumption and could be applied for any given multiplex analyses.
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Affiliation(s)
- Sharma Rao Balakrishnan
- Biomedical Nano Diagnostics Research Group, Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, Malaysia
| | - U Hashim
- Biomedical Nano Diagnostics Research Group, Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, Malaysia; School of Microelectronic Engineering, University Malaysia Perlis (UniMAP), Kuala Perlis, Perlis, Malaysia.
| | - Subash C B Gopinath
- Biomedical Nano Diagnostics Research Group, Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, Malaysia
| | - P Poopalan
- School of Microelectronic Engineering, University Malaysia Perlis (UniMAP), Kuala Perlis, Perlis, Malaysia
| | - H R Ramayya
- Department of Obstetrics and Gynaecology, Hospital Tuanku Fauziah, Kangar, Perlis, Malaysia
| | - P Veeradasan
- Biomedical Nano Diagnostics Research Group, Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, Malaysia
| | - R Haarindraprasad
- Biomedical Nano Diagnostics Research Group, Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, Malaysia
| | - A R Ruslinda
- Biomedical Nano Diagnostics Research Group, Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, Malaysia
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Haarindraprasad R, Hashim U, Gopinath SCB, Kashif M, Veeradasan P, Balakrishnan SR, Foo KL, Poopalan P. Low Temperature Annealed Zinc Oxide Nanostructured Thin Film-Based Transducers: Characterization for Sensing Applications. PLoS One 2015; 10:e0132755. [PMID: 26167853 PMCID: PMC4500498 DOI: 10.1371/journal.pone.0132755] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 06/17/2015] [Indexed: 11/26/2022] Open
Abstract
The performance of sensing surfaces highly relies on nanostructures to enhance their sensitivity and specificity. Herein, nanostructured zinc oxide (ZnO) thin films of various thicknesses were coated on glass and p-type silicon substrates using a sol-gel spin-coating technique. The deposited films were characterized for morphological, structural, and optoelectronic properties by high-resolution measurements. X-ray diffraction analyses revealed that the deposited films have a c-axis orientation and display peaks that refer to ZnO, which exhibits a hexagonal structure with a preferable plane orientation (002). The thicknesses of ZnO thin films prepared using 1, 3, 5, and 7 cycles were measured to be 40, 60, 100, and 200 nm, respectively. The increment in grain size of the thin film from 21 to 52 nm was noticed, when its thickness was increased from 40 to 200 nm, whereas the band gap value decreased from 3.282 to 3.268 eV. Band gap value of ZnO thin film with thickness of 200 nm at pH ranging from 2 to 10 reduces from 3.263eV to 3.200 eV. Furthermore, to evaluate the transducing capacity of the ZnO nanostructure, the refractive index, optoelectric constant, and bulk modulus were analyzed and correlated. The highest thickness (200 nm) of ZnO film, embedded with an interdigitated electrode that behaves as a pH-sensing electrode, could sense pH variations in the range of 2-10. It showed a highly sensitive response of 444 μAmM-1cm-2 with a linear regression of R2 =0.9304. The measured sensitivity of the developed device for pH per unit is 3.72μA/pH.
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Affiliation(s)
- R. Haarindraprasad
- Biomedical Nano Diagnostics Research Group, Institute of Nano Electronic Engineering (INEE), Kangar, Perlis, Malaysia
| | - U. Hashim
- Biomedical Nano Diagnostics Research Group, Institute of Nano Electronic Engineering (INEE), Kangar, Perlis, Malaysia
- * E-mail:
| | - Subash C. B. Gopinath
- Biomedical Nano Diagnostics Research Group, Institute of Nano Electronic Engineering (INEE), Kangar, Perlis, Malaysia
- School of Bioprocess Engineering, University Malaysia Perlis (UniMAP), Kangar, Perlis, Malaysia
| | - Mohd Kashif
- Biomedical Nano Diagnostics Research Group, Institute of Nano Electronic Engineering (INEE), Kangar, Perlis, Malaysia
| | - P. Veeradasan
- Biomedical Nano Diagnostics Research Group, Institute of Nano Electronic Engineering (INEE), Kangar, Perlis, Malaysia
| | - S. R. Balakrishnan
- Biomedical Nano Diagnostics Research Group, Institute of Nano Electronic Engineering (INEE), Kangar, Perlis, Malaysia
| | - K. L. Foo
- Biomedical Nano Diagnostics Research Group, Institute of Nano Electronic Engineering (INEE), Kangar, Perlis, Malaysia
| | - P. Poopalan
- School of Microelectronic Engineering, University Malaysia Perlis (UniMAP), Kuala Perlis, Perlis, Malaysia
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Fathil MFM, Md Arshad MK, Gopinath SCB, Hashim U, Adzhri R, Ayub RM, Ruslinda AR, Nuzaihan M N M, Azman AH, Zaki M, Tang TH. Diagnostics on acute myocardial infarction: Cardiac troponin biomarkers. Biosens Bioelectron 2015; 70:209-20. [PMID: 25841117 DOI: 10.1016/j.bios.2015.03.037] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/05/2015] [Accepted: 03/16/2015] [Indexed: 12/31/2022]
Abstract
Acute myocardial infarction or myocardial infarction (MI) is a major health problem, due to diminished flow of blood to the heart, leads to higher rates of mortality and morbidity. Data from World Health Organization (WHO) accounted 30% of global death annually and expected more than 23 million die annually by 2030. This fatal effects trigger the need of appropriate biomarkers for early diagnosis, thus countermeasure can be taken. At the moment, the most specific markers for cardiac injury are cardiac troponin I (cTnI) and cardiac troponin T (cTnT) which have been considered as 'gold standard'. Due to higher specificity, determination of the level of cardiac troponins became a predominant indicator for MI. Several ways of diagnostics have been formulated, which include enzyme-linked immunosorbent assay, chemiluminescent, fluoro-immunoassays, electrical detections, surface plasmon resonance, and colorimetric protein assay. This review represents and elucidates the strategies, methods and detection levels involved in these diagnostics on cardiac superior biomarkers. The advancement, sensitivity, and limitations of each method are also discussed. In addition, it concludes with a discussion on the point-of care (POC) assay for a fast, accurate and ability of handling small sample measurement of cardiac biomarker.
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Affiliation(s)
- M F M Fathil
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia
| | - M K Md Arshad
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia; School of Microelectronic Engineering (SOME), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia.
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia
| | - U Hashim
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia; School of Microelectronic Engineering (SOME), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia
| | - R Adzhri
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia
| | - R M Ayub
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia; School of Microelectronic Engineering (SOME), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia
| | - A R Ruslinda
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia
| | - M Nuzaihan M N
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia
| | - A H Azman
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia
| | - M Zaki
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia
| | - Thean-Hock Tang
- Advance Medical & Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Kepala Batas, Penang, Malaysia
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Adam T, Hashim U. Highly sensitive silicon nanowire biosensor with novel liquid gate control for detection of specific single-stranded DNA molecules. Biosens Bioelectron 2014; 67:656-61. [PMID: 25453738 DOI: 10.1016/j.bios.2014.10.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/19/2014] [Accepted: 10/01/2014] [Indexed: 01/16/2023]
Abstract
The study demonstrates the development of a liquid-based gate-control silicon nanowire biosensor for detection of specific single-stranded DNA (ssDNA) molecules. The sensor was fabricated using conventional photolithography coupled with an inductively coupled plasma dry etching process. Prior to the application of DNA to the device, its linear response to pH was confirmed by serial dilution from pH 2 to pH 14. Then, the sensor surface was silanized and directly aminated with (3-aminopropyl) triethoxysilane to create a molecular binding chemistry for biofunctionalization. The resulting Si‒O‒Si‒ components were functionalized with receptor ssDNA, which interacted with the targeted ssDNA to create a field across the silicon nanowire and increase the current. The sensor shows selectivity for the target ssDNA in a linear range from target ssDNA concentrations of 100 pM to 25 nM. With its excellent detection capabilities, this sensor platform is promising for detection of specific biomarkers and other targeted proteins.
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Affiliation(s)
- Tijjani Adam
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), 01000 Kangar, Perlis, Malaysia.
| | - U Hashim
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis (UniMAP), 01000 Kangar, Perlis, Malaysia.
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Liu WW, Chai SP, Mohamed AR, Hashim U. Synthesis and characterization of graphene and carbon nanotubes: A review on the past and recent developments. J IND ENG CHEM 2014. [DOI: 10.1016/j.jiec.2013.08.028] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abd HR, Al-Douri Y, Ahmed NM, Hashim U. Alternative-Current Electrochemical Etching of Uniform Porous Silicon for Photodetector Applications. INT J ELECTROCHEM SC 2013; 8:11461-11473. [DOI: 10.1016/s1452-3981(23)13197-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Husnen RA, Naser MA, Al-Douri Y, Hashim U. Influence of Current Density on Porous Silicon Characteristics. AMR 2013; 795:219-222. [DOI: 10.4028/www.scientific.net/amr.795.219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Porous silicon structures have been fabricated by electrochemical etching using different current density. From field emission scanning electron microscope images (FE-SEM) it was observed that more uniform distribution of pores is obtained when the current density was increased from 20mA/cm2to30 mA/cm2. The porosity is estimated based on the analysis of FE-SEM and gravimetric analysis, the results were confirmed by reflectivity measurements which show that the high current density and porous samples have low reflection for wide spectrum. Results show good improvement in the solar cell efficiency.
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Gan CL, Hashim U. Reliability Assessment and Activation Energy Study of Au and Pd-Coated Cu Wires Post High Temperature Aging in Nanoscale Semiconductor Packaging. J Electron Packag 2013; 135:0210101-210107. [PMID: 24891811 PMCID: PMC3994760 DOI: 10.1115/1.4024013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 02/24/2013] [Indexed: 06/03/2023]
Abstract
Wearout reliability and high temperature storage life (HTSL) activation energy of Au and Pd-coated Cu (PdCu) ball bonds are useful technical information for Cu wire deployment in nanoscale semiconductor device packaging. This paper discusses the influence of wire type on the wearout reliability performance of Au and PdCu wire used in fine pitch BGA package after HTSL stress at various aging temperatures. Failure analysis has been conducted to identify the failure mechanism after HTSL wearout conditions for Au and PdCu ball bonds. Apparent activation energies (Eaa) of both wire types are investigated after HTSL test at 150 °C, 175 °C and 200 °C aging temperatures. Arrhenius plot has been plotted for each ball bond types and the calculated Eaa of PdCu ball bond is 0.85 eV and 1.10 eV for Au ball bond in 110 nm semiconductor device. Obviously Au ball bond is identified with faster IMC formation rate with IMC Kirkendall voiding while PdCu wire exhibits equivalent wearout and or better wearout reliability margin compare to conventional Au wirebond. Lognormal plots have been established and its mean to failure (t50) have been discussed in this paper.
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Affiliation(s)
- C L Gan
- Spansion (Penang) Sdn Bhd., Phase II Free Industrial Zone, 11900 Bayan Lepas, Penang, Malaysia; Institute of Nano Electronic Engineering (INEE) , Universiti Malaysia Perlis, 01000 Kangar, Perlis, Malaysia e-mail:
| | - U Hashim
- Institute of Nano Electronic Engineering (INEE) , Universiti Malaysia Perlis, 01000 Kangar , Perlis , Malaysia
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Adam T, Hashim U, Dhahi TS, Foo KL, Leow PL, Chee PS. Polysilicon Nanowire Fabrication as a Transducer for Fast Reaction Assays in Nano Lab-on-Chip Domain. ACTA ACUST UNITED AC 2013. [DOI: 10.1166/sl.2013.2746] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ali ME, Hashim U, Kashif M, Mustafa S, Che Man YB, Abd Hamid SB. Development of swine-specific DNA markers for biosensor-based halal authentication. Genet Mol Res 2012; 11:1762-72. [PMID: 22843053 DOI: 10.4238/2012.june.29.9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The pig (Sus scrofa) mitochondrial genome was targeted to design short (15-30 nucleotides) DNA markers that would be suitable for biosensor-based hybridization detection of target DNA. Short DNA markers are reported to survive harsh conditions in which longer ones are degraded into smaller fragments. The whole swine mitochondrial-genome was in silico digested with AluI restriction enzyme. Among 66 AluI fragments, five were selected as potential markers because of their convenient lengths, high degree of interspecies polymorphism and intraspecies conservatism. These were confirmed by NCBI blast analysis and ClustalW alignment analysis with 11 different meat-providing animal and fish species. Finally, we integrated a tetramethyl rhodamine-labeled 18-nucleotide AluI fragment into a 3-nm diameter citrate-tannate coated gold nanoparticle to develop a swine-specific hybrid nanobioprobe for the determination of pork adulteration in 2.5-h autoclaved pork-beef binary mixtures. This hybrid probe detected as low as 1% pork in deliberately contaminated autoclaved pork-beef binary mixtures and no cross-species detection was recorded, demonstrating the feasibility of this type of probe for biosensor-based detection of pork adulteration of halal and kosher foods.
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Affiliation(s)
- M E Ali
- Institute of Nano Electronic Engineering, Universiti Malaysia, Kangar, Perlis, Malaysia.
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Rahman MM, Ali ME, Khan AA, Akanda AM, Uddin MK, Hashim U, Abd Hamid SB. Isolation, characterization, and identification of biological control agent for potato soft rot in Bangladesh. ScientificWorldJournal 2012; 2012:723293. [PMID: 22645446 PMCID: PMC3356727 DOI: 10.1100/2012/723293] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Accepted: 02/12/2012] [Indexed: 12/03/2022] Open
Abstract
A total of 91 isolates of probable antagonistic bacteria of potato soft rot bacterium Erwinia carotovora subsp. carotovora (Ecc) were extracted from rhizospheres and endophytes of various crop plants, different soil varieties, and atmospheres in the potato farming areas of Bangladesh. Antibacterial activity of the isolated probable antagonistic bacteria was tested in vitro against the previously identified most common and most virulent soft rot causing bacterial strain Ecc P-138. Only two isolates E-45 and E-65 significantly inhibited the in vitro growth of Ecc P-138. Physiological, biochemical, and carbon source utilization tests identified isolate E-65 as a member of the genus Bacillus and the isolate E-45 as Lactobacillus sp. The stronger antagonistic activity against Ecc P-138 was found in E-65 in vitro screening and storage potatoes. E-65 reduced the soft rot infection to 22-week storage potatoes of different varieties by 32.5–62.5% in model experiment, demonstrating its strong potential to be used as an effective biological control agent for the major pectolytic bacteria Ecc. The highest (62.5%) antagonistic effect of E-65 was observed in the Granola and the lowest (32.7%) of that was found in the Cardinal varieties of the Bangladeshi potatoes. The findings suggest that isolate E-65 could be exploited as a biocontrol agent for potato tubers.
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Affiliation(s)
- M M Rahman
- Department of Plant Pathology, Bangabadhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
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Ali ME, Hashim U, Dhahi TS, Mustafa S, Man YBC, Latif MA. Analysis of Pork Adulteration in Commercial Burgers Targeting Porcine-Specific Mitochondrial Cytochrome B Gene by TaqMan Probe Real-Time Polymerase Chain Reaction. FOOD ANAL METHOD 2011. [DOI: 10.1007/s12161-011-9311-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ali ME, Hashim U, Mustafa S, Che Man YB. Swine-Specific PCR-RFLP Assay Targeting Mitochondrial Cytochrome B Gene for Semiquantitative Detection of Pork in Commercial Meat Products. FOOD ANAL METHOD 2011. [DOI: 10.1007/s12161-011-9290-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Ali ME, Hashim U, Mustafa S, Man YBC, Yusop MHM, Bari MF, Islam KN, Hasan MF. Nanoparticle sensor for label free detection of swine DNA in mixed biological samples. Nanotechnology 2011; 22:195503. [PMID: 21430321 DOI: 10.1088/0957-4484/22/19/195503] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We used 40 ± 5 nm gold nanoparticles (GNPs) as colorimetric sensor to visually detect swine-specific conserved sequence and nucleotide mismatch in PCR-amplified and non-amplified mitochondrial DNA mixtures to authenticate species. Colloidal GNPs changed color from pinkish-red to gray-purple in 2 mM PBS. Visually observed results were clearly reflected by the dramatic reduction of surface plasmon resonance peak at 530 nm and the appearance of new features in the 620-800 nm regions in their absorption spectra. The particles were stabilized against salt-induced aggregation upon the adsorption of single-stranded DNA. The PCR products, without any additional processing, were hybridized with a 17-base probe prior to exposure to GNPs. At a critical annealing temperature (55 °C) that differentiated matched and mismatched base pairing, the probe was hybridized to pig PCR product and dehybridized from the deer product. The dehybridized probe stuck to GNPs to prevent them from salt-induced aggregation and retained their characteristic red color. Hybridization of a 27-nucleotide probe to swine mitochondrial DNA identified them in pork-venison, pork-shad and venison-shad binary admixtures, eliminating the need of PCR amplification. Thus the assay was applied to authenticate species both in PCR-amplified and non-amplified heterogeneous biological samples. The results were determined visually and validated by absorption spectroscopy. The entire assay (hybridization plus visual detection) was performed in less than 10 min. The LOD (for genomic DNA) of the assay was 6 µg ml(-1) swine DNA in mixed meat samples. We believe the assay can be applied for species assignment in food analysis, mismatch detection in genetic screening and homology studies between closely related species.
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Affiliation(s)
- M E Ali
- Institute of Nano Electronic Engineering (INNE), Universiti Malaysia Perlis, Kangar, Perlis, Malaysia
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Hashim U, Abd Rahman SF, A. Shohini ME. Design and Fabrication of Nanowire-Based Conductance Biosensor Using Spacer Patterning Techniq. Biosensors 2010. [DOI: 10.5772/7203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Rahman SFA, Hashim U, Nor MNM, Nuri AMM, Shohini MEA, Salleh S, Rusop M, Soga T. Nanowire Formation Using Electron Beam Lithography. AIP Conference Proceedings 2009. [DOI: 10.1063/1.3160194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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