Application of plasmonic devices in spectroscopy and biomedical studies

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2020-12
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Monshat, Hosein
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Lu, Meng
Mina, Mani
Pranav, Shrotriya
Wang, Xinwei
Biswas, Rana
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Mechanical Engineering
Abstract
This report covers more than three years of my academic journey toward earning my Ph.D. in Mechanical Engineering. I have had opportunity to conduct different research related to the application of plasmonic structure in both photonics and biomedical branches. We designed, fabricated and characterized a novel freestanding gold membrane emitter that shows a narrowband infrared emission the near-IR and mid-IR wavelength ranges from 2.5 µm to 5.5 µm. The Au-membrane device shows a transmission coefficient as high as 76.8% and an absorption coefficient of 23.1%. The plasmonic gold-membrane device can be used as a low-cost, lightweight narrowband infrared light source, biomolecular sensor and thermal detector. We also designed and fabricated a narrowband thermoelectric detector by integrating a guided-mode absorbing filter and an on-chip thermocouple which works based on the Seebeck coefficient phenomena. The guided-mode filter exhibits a narrowband optical absorption with a resonant absorption coefficient of 85.4% and a full-width-half-maximum of 14.8 nm in the visible wavelength range. The device also exhibits a responsivity and noise equivalent power of 0.26 V W-1 and 7.5 nW Hz-1/2, respectively. The thermoelectric device can be implemented to provide spectral information during an analysis. In terms of biomedical applications of plasmonic structures, we designed and fabricated an optical-based quantitative polymer chain reaction device to amplify nucleic acids. The device is fully automated and controlled by a simple Arduino Uno R3 micro-controller. A 3W 808 µm laser source is used to heat up the PCR solution. A customized plasmonic chip is designed to absorb the incident light and convert it into heat. The plasmonic chip is also equipped with an on-chip thermocouple which allows us to do real-time temperature monitoring. We successfully amplified different genes with 155 to 722 bp product length using our device, with an efficiency of 98%. We also designed an AMR gene analyzer which allows us to study antimicrobial resistant genes using DNA microarrays. The designed apparatus consists of several sub-assemblies including a thermal management unit, a xyz- motion control sub-system, fluorescence imaging unit, illumination sub-system and a main controller which syncs all the sub-assemblies. An asymmetric PCR has been employed to replicate Cy3-labeled single strand target DNAs’ concentration. The amplification step has been followed by a constant hybridization temperature and finally with a melting test which allow us to detect genomic mutation using melting curve analysis. The device has a 120W heating and cooling module with an average 5°C/sec heating and cooling rate and 0.1°C resolution. A 532nm laser beam with a 500mW output power were used to excite Cy3-labeled target genes. A 5-megapixcel CMOS camera has been used to capture fluorescence signals of hybridized excited target genes. The device successfully amplified 8 different AMR genes extracted from Acinetobacter baumannii, Klebsiella pneumonia, Escherichia coli, and Campylobacter. The mutation study successfully detected a 1.5 °C melting temperature difference between wild-type and mutant-type gyrA genes of Campylobacter jejuni.
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