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Yoshida S, Kisley L. Super-resolution fluorescence imaging of extracellular environments. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 257:119767. [PMID: 33862370 DOI: 10.1016/j.saa.2021.119767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
The extracellular matrix (ECM) is an important biophysical environment that plays a role in a number of physiological processes. The ECM is highly dynamic, with changes occurring as local, nanoscale, physicochemical variations in physical confinement and chemistry from the perspective of biological molecules. The length and time scale of ECM dynamics are challenging to measure with current spectroscopic techniques. Super-resolution fluorescence microscopy has the potential to probe local, nanoscale, physicochemical variations in the ECM. Here, we review super-resolution imaging and analysis methods and their application to study model nanoparticles and biomolecules within synthetic ECM hydrogels and the brain extracellular space (ECS). We provide a perspective of future directions for the field that can move super-resolution imaging of the ECM towards more biomedically-relevant samples. Overall, super-resolution imaging is a powerful tool that can increase our understanding of extracellular environments at new spatiotemporal scales to reveal ECM processes at the molecular-level.
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Affiliation(s)
- Shawn Yoshida
- Department of Physics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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2
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Gong X, Feng S, Qiao Z, Chen YC. Imaging-Based Optofluidic Biolaser Array Encapsulated with Dynamic Living Organisms. Anal Chem 2021; 93:5823-5830. [PMID: 33734676 DOI: 10.1021/acs.analchem.1c00020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Optofluidic biolasers have emerged as promising tools for biomedical analysis due to their strong light-matter interactions and miniaturized size. Recent developments in optofluidic lasers have opened a new Frontier in monitoring biological processes. However, most biolasers require precise recording of the lasing spectrum at the single cavity level, which limits its application in high-throughput applications. Herein, a microdroplet laser array encapsulated with living Escherichia coli was printed on highly reflective mirrors, where laser emission images were employed to reflect the dynamic changes in living organisms. The concept of image-based lasing analysis was proposed by quantifying the integrated pixel intensity of the lasing image from whispering-gallery modes. Finally, dynamic interactions between E. coli and antibiotic drugs were compared under fluorescence and laser emission images. The amplification that occurred during laser generation enabled the quantification of tiny biological changes in the gain medium. Laser imaging presented a significant increase in integrated pixel intensity by 2 orders of magnitude. Our findings demonstrate that image-based lasing analysis is more sensitive to dynamic changes than fluorescence analysis, paving the way for high-throughput on-chip laser analysis of living organisms.
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Affiliation(s)
- Xuerui Gong
- School of Electrical and Electronics Engineering, Nanyang Technological University, 50 Nanyang Ave., 639798, Singapore
| | - Shilun Feng
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China
| | - Zhen Qiao
- School of Electrical and Electronics Engineering, Nanyang Technological University, 50 Nanyang Ave., 639798, Singapore
| | - Yu-Cheng Chen
- School of Electrical and Electronics Engineering, Nanyang Technological University, 50 Nanyang Ave., 639798, Singapore.,School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Dr., 639798, Singapore
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3
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Yu Z, Lei Y, Yu W, Cheng J, Xing J, Zheng X, Zhan Z, Wang B, Guo C. Fluorescence enhanced lab-on-a-chip patterned using a hybrid technique of femtosecond laser direct writing and anodized aluminum oxide porous nanostructuring. NANOSCALE ADVANCES 2019; 1:3474-3484. [PMID: 36133573 PMCID: PMC9418693 DOI: 10.1039/c9na00352e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/15/2019] [Indexed: 05/14/2023]
Abstract
A nanoporous array structure detection chip with strong spectral resolution, fabricated by femtosecond laser direct writing and anodized aluminum oxide.
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Affiliation(s)
- Zhi Yu
- The Guo China-US Photonics Laboratory
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Yuhao Lei
- The Guo China-US Photonics Laboratory
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Weili Yu
- The Guo China-US Photonics Laboratory
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Jinluo Cheng
- The Guo China-US Photonics Laboratory
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Jun Xing
- The Guo China-US Photonics Laboratory
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Xin Zheng
- The Guo China-US Photonics Laboratory
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Zhibing Zhan
- The Institute of Optics
- University of Rochester
- Rochester
- USA
| | - Bin Wang
- The Guo China-US Photonics Laboratory
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Chunlei Guo
- The Guo China-US Photonics Laboratory
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
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5
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Ozcelik D, Jain A, Stambaugh A, Stott MA, Parks JW, Hawkins A, Schmidt H. Scalable Spatial-Spectral Multiplexing of Single-Virus Detection Using Multimode Interference Waveguides. Sci Rep 2017; 7:12199. [PMID: 28939852 PMCID: PMC5610187 DOI: 10.1038/s41598-017-12487-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/06/2017] [Indexed: 11/09/2022] Open
Abstract
Simultaneous detection of multiple pathogens and samples (multiplexing) is one of the key requirements for diagnostic tests in order to enable fast, accurate and differentiated diagnoses. Here, we introduce a novel, highly scalable, photonic approach to multiplex analysis with single virus sensitivity. A solid-core multimode interference (MMI) waveguide crosses multiple fluidic waveguide channels on an optofluidic chip to create multi-spot excitation patterns that depend on both the wavelength and location of the channel along the length of the MMI waveguide. In this way, joint spectral and spatial multiplexing is implemented that encodes both spatial and spectral information in the time dependent fluorescence signal. We demonstrate this principle by using two excitation wavelengths and three fluidic channels to implement a 6x multiplex assay with single virus sensitivity. High fidelity detection and identification of six different viruses from a standard influenza panel is reported. This multimodal multiplexing strategy scales favorably to large numbers of targets or large numbers of clinical samples. Further, since single particles are detected unbound in flow, the technique can be broadly applied to direct detection of any fluorescent target, including nucleic acids and proteins.
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Affiliation(s)
- Damla Ozcelik
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Aadhar Jain
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Alexandra Stambaugh
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Matthew A Stott
- ECEn Department, 459 Clyde Building, Brigham Young University, Provo, UT, 84602, USA
| | - Joshua W Parks
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Aaron Hawkins
- ECEn Department, 459 Clyde Building, Brigham Young University, Provo, UT, 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.
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6
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Wang H, Xu A, Wang S, Chughtai S. Cross domain adaptation by learning partially shared classifiers and weighting source data points in the shared subspaces. Neural Comput Appl 2016. [DOI: 10.1007/s00521-016-2541-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Testa G, Persichetti G, Bernini R. Liquid Core ARROW Waveguides: A Promising Photonic Structure for Integrated Optofluidic Microsensors. MICROMACHINES 2016; 7:mi7030047. [PMID: 30407419 PMCID: PMC6190334 DOI: 10.3390/mi7030047] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/29/2016] [Accepted: 03/07/2016] [Indexed: 12/11/2022]
Abstract
In this paper, we introduce a liquid core antiresonant reflecting optical waveguide (ARROW) as a novel optofluidic device that can be used to create innovative and highly functional microsensors. Liquid core ARROWs, with their dual ability to guide the light and the fluids in the same microchannel, have shown great potential as an optofluidic tool for quantitative spectroscopic analysis. ARROWs feature a planar architecture and, hence, are particularly attractive for chip scale integrated system. Step by step, several improvements have been made in recent years towards the implementation of these waveguides in a complete on-chip system for highly-sensitive detection down to the single molecule level. We review applications of liquid ARROWs for fluids sensing and discuss recent results and trends in the developments and applications of liquid ARROW in biomedical and biochemical research. The results outlined show that the strong light matter interaction occurring in the optofluidic channel of an ARROW and the versatility offered by the fabrication methods makes these waveguides a very promising building block for optofluidic sensor development.
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Affiliation(s)
- Genni Testa
- Istituto per il Rilevamento Elettromagnetico dell'Ambiente, Consiglio Nazionale delle Ricerche (IREA-CNR), Via Diocleziano 328, 80124 Naples, Italy.
| | - Gianluca Persichetti
- Istituto per il Rilevamento Elettromagnetico dell'Ambiente, Consiglio Nazionale delle Ricerche (IREA-CNR), Via Diocleziano 328, 80124 Naples, Italy.
| | - Romeo Bernini
- Istituto per il Rilevamento Elettromagnetico dell'Ambiente, Consiglio Nazionale delle Ricerche (IREA-CNR), Via Diocleziano 328, 80124 Naples, Italy.
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Liu S, Hawkins AR, Schmidt H. Optofluidic devices with integrated solid-state nanopores. Mikrochim Acta 2016; 183:1275-1287. [PMID: 27046940 DOI: 10.1007/s00604-016-1758-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This review (with 90 refs.) covers the state of the art in optofluidic devices with integrated solid-state nanopores for use in detection and sensing. Following an introduction into principles of optofluidics and solid-state nanopore technology, we discuss features of solid-state nanopore based assays using optofluidics. This includes the incorporation of solid-state nanopores into optofluidic platforms based on liquid-core anti-resonant reflecting optical waveguides (ARROWs), methods for their fabrication, aspects of single particle detection and particle manipulation. We then describe the new functionalities provided by solid-state nanopores integrated into optofluidic chips, in particular acting as smart gates for correlated electro-optical detection and discrimination of nanoparticles. This enables the identification of viruses and λ-DNA, particle trajectory simulations, enhancing sensitivity by tuning the shape of nanopores. The review concludes with a summary and an outlook.
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Affiliation(s)
- Shuo Liu
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Aaron R Hawkins
- ECEn Department, 459 Clyde Building, Brigham Young University, Provo, UT 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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Wan W, Zhu MQ, Tian Z, Li ADQ. Antiphase dual-color correlation in a reactant-product pair imparts ultrasensitivity in reaction-linked double-photoswitching fluorescence imaging. J Am Chem Soc 2015; 137:4312-5. [PMID: 25774573 DOI: 10.1021/jacs.5b01007] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A pair of reversible photochemical reactions correlates their reactant and product specifically, and such a correlation uniquely distinguishes their correlated signal from others that are not linked by this reversible reaction. Here a nanoparticle-shielded fluorophore is photodriven to undergo structural dynamics, alternating between a green-fluorescence state and a red-fluorescence state. As time elapses, the fluorophore can be in either state but not both at the same time. Thus, the red fluorescence is maximized while the green fluorescence is minimized and vice versa. Such an antiphase dual-color (AD) corelationship between the red and green fluorescence maxima as well as between their minima can be exploited to greatly improve the signal-to-noise ratio, thus enhancing the ultimate detection limit. Potential benefits of this correlation include elimination of all interferences originating from single-color dyes and signal amplification of AD photoswitching molecules by orders of magnitude.
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Affiliation(s)
- Wei Wan
- †Department of Chemistry and Center for Materials Research, Washington State University, Pullman, Washington 99164, United States
| | - Ming-Qiang Zhu
- ‡Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Zhiyuan Tian
- §School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Alexander D Q Li
- †Department of Chemistry and Center for Materials Research, Washington State University, Pullman, Washington 99164, United States
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Parks JW, Cai H, Zempoaltecatl L, Yuzvinsky TD, Leake K, Hawkins AR, Schmidt H. Hybrid optofluidic integration. LAB ON A CHIP 2013; 13:4118-23. [PMID: 23969694 PMCID: PMC3818110 DOI: 10.1039/c3lc50818h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Complete integration of microfluidic and optical functions in a single lab-on-chip device is one goal of optofluidics. Here, we demonstrate the hybrid integration of a PDMS-based fluid handling layer with a silicon-based optical detection layer in a single optofluidic system. The optical layer consists of a liquid-core antiresonant reflecting optical waveguide (ARROW) chip that is capable of single particle detection and interfacing with optical fiber. Integrated devices are reconfigurable and able to sustain high pressures despite the small dimensions of the liquid-core waveguide channels. We show the combination of salient sample preparation capabilities-particle mixing, distribution, and filtering-with single particle fluorescence detection. Specifically, we demonstrate fluorescent labelling of λ-DNA, followed by flow-based single-molecule detection on a single device. This points the way towards amplification-free detection of nucleic acids with low-complexity biological sample preparation on a chip.
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Affiliation(s)
- Joshua W Parks
- School of Engineering, University of CA Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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Persichetti G, Testa G, Bernini R. High sensitivity UV fluorescence spectroscopy based on an optofluidic jet waveguide. OPTICS EXPRESS 2013; 21:24219-24230. [PMID: 24104332 DOI: 10.1364/oe.21.024219] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A novel spectroscopic sensor based on an optofluidic liquid jet waveguide is presented. In this device, a liquid jet waveguide is generated with the solution under analysis. This stream, exploiting total internal reflection, acts as an optical waveguide confining the autofluorescence light produced by chemical or biological samples when opportunely excited. Using a self-aligned configuration, the liquid jet is directly coupled with a multimode optical fiber collecting the fluorescence towards the detection system. Experimental measurements have been performed using an UV excitation source on water solutions containing representative water pollutants as aromatic hydrocarbons or bacteria showing very low limit of detection.
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12
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Cuennet JG, Vasdekis AE, Psaltis D. Optofluidic-tunable color filters and spectroscopy based on liquid-crystal microflows. LAB ON A CHIP 2013; 13:2721-2726. [PMID: 23752198 DOI: 10.1039/c3lc50501d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The integration of color filters with microfluidics has attracted substantial attention in recent years, for on-chip absorption, fluorescence, or Raman analysis. We describe such tunable filters based on the micro-flow of liquid crystals. The filter operation is based on the wavelength-dependent liquid crystal birefringence that can be tuned by modifying the flow velocity field in the microchannel. The latter is possible both temporally and spatially by varying the inlet pressure and the channel geometry, respectively. We explored the use of these optofluidic filters for on-chip absorption spectroscopy in poly(dimethylsiloxane) microfluidic systems; by integrating the distance-dependent color filter with a dye-filled micro-channel, the absorption spectrum of a dye could be measured. Liquid crystal microflows substantially simplify the optofluidic integration, actuation and tuning of color filters for lab-on-a-chip spectroscopic applications.
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Affiliation(s)
- J G Cuennet
- Optics Laboratory, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Switzerland
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Persichetti G, Testa G, Bernini R. Optofluidic jet waveguide for laser-induced fluorescence spectroscopy. OPTICS LETTERS 2012; 37:5115-5117. [PMID: 23258023 DOI: 10.1364/ol.37.005115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
An optofluidic water-jet waveguide on chip for fluorescence analysis is presented. A high-speed water stream produced by means of a microchannel acts at the same time as the solution to analyze and as the collecting optical waveguide. The absence of solid walls and the very optically smooth surface of the liquid stream permits a strong increase of the signal-to-noise ratio. The device layout allows a self-alignment direct coupling of a water-jet waveguide with a multimode optical fiber connected to the detector. The performances of the integrated system are tested on Cy5 water solutions. For a 4.5 mm long water-jet waveguide, the measured limit of detection (LOD) is 2.56 nM and filter-free detection is possible with an LOD of 6.11 nM.
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Su X, Xiao X, Zhang C, Zhao M. Nucleic acid fluorescent probes for biological sensing. APPLIED SPECTROSCOPY 2012; 66:1249-1262. [PMID: 23146180 DOI: 10.1366/12-06803] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Nucleic acid fluorescent probes are playing increasingly important roles in biological sensing in recent years. In addition to the conventional functions of single-stranded DNA/RNA to hybridize with their complementary strands, affinity nucleic acids (aptamers) with specific target binding properties have also been developed, which has greatly broadened the application of nucleic acid fluorescent probes to the detection of a large variety of analytes, including small molecules, proteins, ions, and even whole cells. Another chemical property of nucleic acids is to act as substrates for various nucleic acid enzymes. This property can be utilized not only to detect those enzymes and screen their inhibitors, but also employed to develop effective signal amplification systems, which implies extensive applications. This review mainly covers the biosensing methods based on the above three types of nucleic acid fluorescent probes. The most widely used intensity-based biosensing assays are covered first, including nucleic acid probe-based signal amplification methods. Then fluorescence lifetime, fluorescence anisotropy, and fluorescence correlation spectroscopy assays are introduced, respectively. As a rapidly developing field, fluorescence imaging approaches are also briefly summarized.
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Affiliation(s)
- Xin Su
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, China
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Fan X, White IM. Optofluidic Microsystems for Chemical and Biological Analysis. NATURE PHOTONICS 2011; 5:591-597. [PMID: 22059090 PMCID: PMC3207487 DOI: 10.1038/nphoton.2011.206] [Citation(s) in RCA: 403] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Optofluidics - the synergistic integration of photonics and microfluidics - has recently emerged as a new analytical field that provides a number of unique characteristics for enhanced sensing performance and simplification of microsystems. In this review, we describe various optofluidic architectures developed in the past five years, emphasize the mechanisms by which optofluidics enhances bio/chemical analysis capabilities, including sensing and the precise control of biological micro/nanoparticles, and envision new research directions to which optofluidics leads.
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Affiliation(s)
- Xudong Fan
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI 48109, USA
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