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Banerjee A, Mathew S, Naqvi MM, Yilmaz SZ, Zacharopoulou M, Doruker P, Kumita JR, Yang SH, Gur M, Itzhaki LS, Gordon R, Bahar I. Influence of point mutations on PR65 conformational adaptability: Insights from molecular simulations and nanoaperture optical tweezers. SCIENCE ADVANCES 2024; 10:eadn2208. [PMID: 38820156 PMCID: PMC11141623 DOI: 10.1126/sciadv.adn2208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/29/2024] [Indexed: 06/02/2024]
Abstract
PR65 is the HEAT repeat scaffold subunit of the heterotrimeric protein phosphatase 2A (PP2A) and an archetypal tandem repeat protein. Its conformational mechanics plays a crucial role in PP2A function by opening/closing substrate binding/catalysis interface. Using in silico saturation mutagenesis, we identified PR65 "hinge" residues whose substitutions could alter its conformational adaptability and thereby PP2A function, and selected six mutations that were verified to be expressed and soluble. Molecular simulations and nanoaperture optical tweezers revealed consistent results on the specific effects of the mutations on the structure and dynamics of PR65. Two mutants observed in simulations to stabilize extended/open conformations exhibited higher corner frequencies and lower translational scattering in experiments, indicating a shift toward extended conformations, whereas another displayed the opposite features, confirmed by both simulations and experiments. The study highlights the power of single-molecule nanoaperture-based tweezers integrated with in silico approaches for exploring the effect of mutations on protein structure and dynamics.
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Affiliation(s)
- Anupam Banerjee
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Samuel Mathew
- Department of Electrical and Computer Engineering, University of Victoria, Victoria V8P 5C2, Canada
| | - Mohsin M. Naqvi
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Sema Z. Yilmaz
- Department of Mechanical Engineering, Istanbul Technical University, 34437 Istanbul, Turkey
| | - Maria Zacharopoulou
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Janet R. Kumita
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Shang-Hua Yang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Mert Gur
- Department of Mechanical Engineering, Istanbul Technical University, 34437 Istanbul, Turkey
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Laura S. Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Reuven Gordon
- Department of Electrical and Computer Engineering, University of Victoria, Victoria V8P 5C2, Canada
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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Adibnia E, Mansouri-Birjandi MA, Ghadrdan M, Jafari P. A deep learning method for empirical spectral prediction and inverse design of all-optical nonlinear plasmonic ring resonator switches. Sci Rep 2024; 14:5787. [PMID: 38461205 PMCID: PMC10924975 DOI: 10.1038/s41598-024-56522-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/07/2024] [Indexed: 03/11/2024] Open
Abstract
All-optical plasmonic switches (AOPSs) utilizing surface plasmon polaritons are well-suited for integration into photonic integrated circuits (PICs) and play a crucial role in advancing all-optical signal processing. The current AOPS design methods still rely on trial-and-error or empirical approaches. In contrast, recent deep learning (DL) advances have proven highly effective as computational tools, offering an alternative means to accelerate nanophotonics simulations. This paper proposes an innovative approach utilizing DL for spectrum prediction and inverse design of AOPS. The switches employ circular nonlinear plasmonic ring resonators (NPRRs) composed of interconnected metal-insulator-metal waveguides with a ring resonator. The NPRR switching performance is shown using the nonlinear Kerr effect. The forward model presented in this study demonstrates superior computational efficiency when compared to the finite-difference time-domain method. The model analyzes various structural parameters to predict transmission spectra with a distinctive dip. Inverse modeling enables the prediction of design parameters for desired transmission spectra. This model provides a rapid estimation of design parameters, offering a clear advantage over time-intensive conventional optimization approaches. The loss of prediction for both the forward and inverse models, when compared to simulations, is exceedingly low and on the order of 10-4. The results confirm the suitability of employing DL for forward and inverse design of AOPSs in PICs.
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Affiliation(s)
- Ehsan Adibnia
- Faculty of Electrical and Computer Engineering, University of Sistan and Baluchestan (USB), P.O. Box 9816745563, Zahedan, Iran
| | - Mohammad Ali Mansouri-Birjandi
- Faculty of Electrical and Computer Engineering, University of Sistan and Baluchestan (USB), P.O. Box 9816745563, Zahedan, Iran.
| | - Majid Ghadrdan
- Faculty of Electrical and Computer Engineering, University of Sistan and Baluchestan (USB), P.O. Box 9816745563, Zahedan, Iran
| | - Pouria Jafari
- Faculty of Electrical and Computer Engineering, University of Sistan and Baluchestan (USB), P.O. Box 9816745563, Zahedan, Iran
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Roy P, Zhu S, Claude JB, Liu J, Wenger J. Ultraviolet Resonant Nanogap Antennas with Rhodium Nanocube Dimers for Enhancing Protein Intrinsic Autofluorescence. ACS NANO 2023; 17:22418-22429. [PMID: 37931219 PMCID: PMC10690780 DOI: 10.1021/acsnano.3c05008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 09/07/2023] [Indexed: 11/08/2023]
Abstract
Plasmonic optical nanoantennas offer compelling solutions for enhancing light-matter interactions at the nanoscale. However, until now, their focus has been mainly limited to the visible and near-infrared regions, overlooking the immense potential of the ultraviolet (UV) range, where molecules exhibit their strongest absorption. Here, we present the realization of UV resonant nanogap antennas constructed from paired rhodium nanocubes. Rhodium emerges as a robust alternative to aluminum, offering enhanced stability in wet environments and ensuring reliable performance in the UV range. Our results showcase the nanoantenna's ability to enhance the UV autofluorescence of label-free streptavidin and hemoglobin proteins. We achieve significant enhancements of the autofluorescence brightness per protein by up to 120-fold and reach zeptoliter detection volumes, enabling UV autofluorescence correlation spectroscopy (UV-FCS) at high concentrations of several tens of micromolar. We investigate the modulation of fluorescence photokinetic rates and report excellent agreement between the experimental results and numerical simulations. This work expands the applicability of plasmonic nanoantennas to the deep UV range, unlocking the investigation of label-free proteins at physiological concentrations.
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Affiliation(s)
- Prithu Roy
- Aix
Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, AMUTech, 13013 Marseille, France
| | - Siyuan Zhu
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jean-Benoît Claude
- Aix
Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, AMUTech, 13013 Marseille, France
| | - Jie Liu
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jérôme Wenger
- Aix
Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, AMUTech, 13013 Marseille, France
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Bahar I, Banerjee A, Mathew S, Naqvi M, Yilmaz S, Zachoropoulou M, Doruker P, Kumita J, Yang SH, Gur M, Itzhaki L, Gordon R. Influence of Point Mutations on PR65 Conformational Adaptability: Insights from Nanoaperture Optical Tweezer Experiments and Molecular Simulations. RESEARCH SQUARE 2023:rs.3.rs-3599809. [PMID: 38014259 PMCID: PMC10680943 DOI: 10.21203/rs.3.rs-3599809/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
PR65 is the HEAT-repeat scaffold subunit of the heterotrimeric protein phosphatase 2A (PP2A) and an archetypal tandem-repeat protein, forming a spring-like architecture. PR65 conformational mechanics play a crucial role in PP2A function by opening/closing the substrate-binding/catalysis interface. Using in-silico saturation mutagenesis we identified "hinge" residues of PR65, whose substitutions are predicted to restrict its conformational adaptability and thereby disrupt PP2A function. Molecular simulations revealed that a subset of hinge mutations stabilized the extended/open conformation, whereas another had the opposite effect. By trapping in nanoaperture optical tweezer, we characterized PR65 motion and showed that the former mutants exhibited higher corner frequencies and lower translational scattering, indicating a shift towards extended conformations, whereas the latter showed the opposite behavior. Thus, experiments confirm the conformations predicted computationally. The study highlights the utility of nanoaperture-based tweezers for exploring structure and dynamics, and the power of integrating this single-molecule method with in silico approaches.
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Liang F, Li M, Xu M, Zhang Y, Dong Y, Soriano SG, McCann ME, Yang G, Xie Z. Sevoflurane anaesthesia induces cognitive impairment in young mice through sequential tau phosphorylation. Br J Anaesth 2023; 131:726-738. [PMID: 37537117 PMCID: PMC10541551 DOI: 10.1016/j.bja.2023.06.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND The volatile anaesthetic sevoflurane induces time (single or multiple exposures)-dependent effects on tau phosphorylation and cognitive function in young mice. The underlying mechanism for this remains largely undetermined. METHODS Mice received 3% sevoflurane for 0.5 h or 2 h daily for 3 days on postnatal day (P) 6, 9, and 12. Another group of mice received 3% sevoflurane for 0.5 h or 1.5 h (3 × 0.5) on P6. We investigated effects of sevoflurane anaesthesia on tau phosphorylation on P6 or P12 mice, on cognitive function from P31 to P37, and on protein interactions, using in vivo studies, in vitro phosphorylation assays, and nanobeam single-molecule level interactions in vitro. RESULTS An initial sevoflurane exposure induced CaMKIIα phosphorylation (132 [11]% vs 100 [6]%, P<0.01), leading to tau phosphorylation at serine 262 (164 [7]% vs 100 [26]%, P<0.01) and tau detachment from microtubules. Subsequent exposures to the sevoflurane induced GSK3β activation, which phosphorylated detached or free tau (tau phosphorylated at serine 262) at serine 202 and threonine 205, resulting in cognitive impairment in young mice. In vitro phosphorylation assays also demonstrated sequential tau phosphorylation. Nanobeam analysis of molecular interactions showed different interactions between tau or free tau and CaMKIIα or GSK3β, and between tau and tubulin at a single-molecule level. CONCLUSIONS Multiple exposures to sevoflurane can induce sequential tau phosphorylation, leading to cognitive impairment in young mice, highlighting the need to investigate the underlying mechanisms of anaesthesia-induced tau phosphorylation in developing brain.
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Affiliation(s)
- Feng Liang
- Department of Anaesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Mengzhu Li
- Department of Anaesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA; Department of Anesthesiology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Miao Xu
- Department of Anaesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA; Department of Anesthesiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yiying Zhang
- Department of Anaesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Yuanlin Dong
- Department of Anaesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Sulpicio G Soriano
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Mary Ellen McCann
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Guang Yang
- Department of Anesthesiology, Columbia University Medical Center, New York, NY, USA
| | - Zhongcong Xie
- Department of Anaesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.
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Babaei E, Wright D, Gordon R. Fringe Dielectrophoresis Nanoaperture Optical Trapping with Order of Magnitude Speed-Up for Unmodified Proteins. NANO LETTERS 2023; 23:2877-2882. [PMID: 36999922 DOI: 10.1021/acs.nanolett.3c00208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Single molecule analysis of proteins in an aqueous environment without modification (e.g., labels or tethers) elucidates their biophysics and interactions relevant to drug discovery. By combining fringe-field dielectrophoresis with nanoaperture optical tweezers we demonstrate an order of magnitude faster time-to-trap for proteins when the counter electrode is outside of the solution. When the counter electrode is inside the solution (the more common configuration found in the literature), electrophoresis speeds up the trapping of polystyrene nanospheres, but this was not effective for proteins in general. Since time-to-trap is critical for high-thoughput analysis, these findings are a major advancement to the nanoaperture optical trapping technique for protein analysis.
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Affiliation(s)
- Elham Babaei
- Department of Electrical and Computer Engineering, University of Victoria, 3800 Finnerty Road, Victoria, BC, Canada V8P5C2
| | - Demelza Wright
- Department of Electrical and Computer Engineering, University of Victoria, 3800 Finnerty Road, Victoria, BC, Canada V8P5C2
| | - Reuven Gordon
- Department of Electrical and Computer Engineering, University of Victoria, 3800 Finnerty Road, Victoria, BC, Canada V8P5C2
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Khosravi B, Gordon R. Reflection mode optical trapping using polarization symmetry breaking from tilted double nanoholes. OPTICS EXPRESS 2023; 31:2621-2627. [PMID: 36785271 DOI: 10.1364/oe.480802] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/26/2022] [Indexed: 06/18/2023]
Abstract
We demonstrate reflection geometry optical trapping using double nanoholes in a metal film. Symmetry breaking of the double nanohole allows for selecting the scattered trapping laser light of orthogonal polarization to the incident beam. This orthogonal polarization light shows a few percent increase when the nanoparticle (e.g., a 20 nm polystyrene particle, or protein bovine serum albumin) is trapped. The reflection geometry simplifies the optical setup and frees up one side of the trap, which has great potential for adding microfluidics to the other side or working with opaque or highly scattering samples.
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8
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Dey S, Dolci M, Zijlstra P. Single-Molecule Optical Biosensing: Recent Advances and Future Challenges. ACS PHYSICAL CHEMISTRY AU 2023; 3:143-156. [PMID: 36968450 PMCID: PMC10037498 DOI: 10.1021/acsphyschemau.2c00061] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023]
Abstract
In recent years, the sensitivity and specificity of optical sensors has improved tremendously due to improvements in biochemical functionalization protocols and optical detection systems. As a result, single-molecule sensitivity has been reported in a range of biosensing assay formats. In this Perspective, we summarize optical sensors that achieve single-molecule sensitivity in direct label-free assays, sandwich assays, and competitive assays. We describe the advantages and disadvantages of single-molecule assays and summarize future challenges in the field including their optical miniaturization and integration, multimodal sensing capabilities, accessible time scales, and compatibility with real-life matrices such as biological fluids. We conclude by highlighting the possible application areas of optical single-molecule sensors that include not only healthcare but also the monitoring of the environment and industrial processes.
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Affiliation(s)
- Swayandipta Dey
- Eindhoven University of Technology, Department of Applied Physics, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven, 5600 MB, The Netherlands
- Eindhoven Hendrik Casimir Institute, Eindhoven, 5600 MB, The Netherlands
| | - Mathias Dolci
- Eindhoven University of Technology, Department of Applied Physics, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven, 5600 MB, The Netherlands
- Eindhoven Hendrik Casimir Institute, Eindhoven, 5600 MB, The Netherlands
| | - Peter Zijlstra
- Eindhoven University of Technology, Department of Applied Physics, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven, 5600 MB, The Netherlands
- Eindhoven Hendrik Casimir Institute, Eindhoven, 5600 MB, The Netherlands
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9
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Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
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Watanabe K, Wu HY, Xavier J, Joshi LT, Vollmer F. Single Virus Detection on Silicon Photonic Crystal Random Cavities. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107597. [PMID: 35218293 DOI: 10.1002/smll.202107597] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/08/2022] [Indexed: 06/14/2023]
Abstract
On-chip silicon microcavity sensors are advantageous for the detection of virus and biomolecules due to their compactness and the enhanced light-matter interaction with the analyte. While their theoretical sensitivity is at the single-molecule level, the fabrication of high quality (Q) factor silicon cavities and their integration with optical couplers remain as major hurdles in applications such as single virus detection. Here, label-free single virus detection using silicon photonic crystal random cavities is proposed and demonstrated. The sensor chips consist of free-standing silicon photonic crystal waveguides and do not require pre-fabricated defect cavities or optical couplers. Residual fabrication disorder results in Anderson-localized cavity modes which are excited by a free space beam. The Q ≈105 is sufficient for observing discrete step-changes in resonance wavelength for the binding of single adenoviruses (≈50 nm radius). The authors' findings point to future applications of CMOS-compatible silicon sensor chips supporting Anderson-localized modes that have detection capabilities at the level of single nanoparticles and molecules.
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Affiliation(s)
- Keisuke Watanabe
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK
| | - Hsin-Yu Wu
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK
| | - Jolly Xavier
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK
| | - Lovleen Tina Joshi
- School of Biomedical Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Frank Vollmer
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK
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Single-molecule optofluidic microsensor with interface whispering gallery modes. Proc Natl Acad Sci U S A 2022; 119:2108678119. [PMID: 35115398 PMCID: PMC8832994 DOI: 10.1073/pnas.2108678119] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2021] [Indexed: 12/23/2022] Open
Abstract
Optical microresonators have emerged as promising platforms for label-free detection of molecules. However, approaching optimum sensitivity is hindered due to the weak tail of evanescent fields. Here, we report the implementation of the interface modes for ultrasensitive sensing in a microbubble resonator. With the electromagnetic field peaked at the interface between the optical resonator and the analyte solution, interface modes enable sensing of biomolecules with a detection limit of 0.3 pg/cm2. Single-molecule detection is further demonstrated using the plasmonic-enhanced interface modes. In addition, intrinsically integrated into a microfluidic channel, the sensor exhibits ultrasmall sample consumption down to 10 pL, providing an automatic platform for biomedical analysis. Label-free sensors are highly desirable for biological analysis and early-stage disease diagnosis. Optical evanescent sensors have shown extraordinary ability in label-free detection, but their potentials have not been fully exploited because of the weak evanescent field tails at the sensing surfaces. Here, we report an ultrasensitive optofluidic biosensor with interface whispering gallery modes in a microbubble cavity. The interface modes feature both the peak of electromagnetic-field intensity at the sensing surface and high-Q factors even in a small-sized cavity, enabling a detection limit as low as 0.3 pg/cm2. The sample consumption can be pushed down to 10 pL due to the intrinsically integrated microfluidic channel. Furthermore, detection of single DNA with 8 kDa molecular weight is realized by the plasmonic-enhanced interface mode.
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Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications. Int J Mol Sci 2022; 23:ijms23031484. [PMID: 35163407 PMCID: PMC8835741 DOI: 10.3390/ijms23031484] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 12/24/2022] Open
Abstract
Nanoscale biosensors, a highly promising technique in clinical analysis, can provide sensitive yet label-free detection of biomolecules. The spatial and chemical specificity of the surface coverage, the proper immobilization of the bioreceptor as well as the underlying interfacial phenomena are crucial elements for optimizing the performance of a biosensor. Due to experimental limitations at the microscopic level, integrated cross-disciplinary approaches that combine in silico design with experimental measurements have the potential to present a powerful new paradigm that tackles the issue of developing novel biosensors. In some cases, computational studies can be seen as alternative approaches to assess the microscopic working mechanisms of biosensors. Nonetheless, the complex architecture of a biosensor, associated with the collective contribution from "substrate-receptor-analyte" conjugate in a solvent, often requires extensive atomistic simulations and systems of prohibitive size which need to be addressed. In silico studies of functionalized surfaces also require ad hoc force field parameterization, as existing force fields for biomolecules are usually unable to correctly describe the biomolecule/surface interface. Thus, the computational studies in this field are limited to date. In this review, we aim to introduce fundamental principles that govern the absorption of biomolecules onto functionalized nanomaterials and to report state-of-the-art computational strategies to rationally design nanoscale biosensors. A detailed account of available in silico strategies used to drive and/or optimize the synthesis of functionalized nanomaterials for biosensing will be presented. The insights will not only stimulate the field to rationally design functionalized nanomaterials with improved biosensing performance but also foster research on the required functionalization to improve biomolecule-surface complex formation as a whole.
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13
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Yang Y, Liang F, Gao J, Dong Y, Zhang Y, Yang G, Soriano SG, Feng HJ, Xie Z. Testosterone attenuates sevoflurane-induced tau phosphorylation and cognitive impairment in neonatal male mice. Br J Anaesth 2021; 127:929-941. [PMID: 34686310 DOI: 10.1016/j.bja.2021.08.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/14/2021] [Accepted: 08/26/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Sevoflurane anaesthesia induces phosphorylation of the microtubule-associated protein tau and cognitive impairment in neonatal, but not adult, mice. The underlying mechanisms remain largely to be determined. Sex hormones can be neuroprotective, but little is known about the influence of testosterone on age-dependent anaesthesia effects. METHODS Six- and 60-day-old male mice received anaesthesia with sevoflurane 3% for 2 h daily for 3 days. Morris water maze, immunoassay, immunoblotting, co-immunoprecipitation, nanobeam technology, and electrophysiology were used to assess cognition; testosterone concentrations; tau phosphorylation; glycogen synthase kinase-3β (GSK3β) activation; binding or interaction between tau and GSK3β; and neuronal activation in mice, cells, and neurones. RESULTS Compared with 60-day-old male mice, 6-day-old male mice had lower testosterone concentrations (3.03 [0.29] vs 0.44 [0.12] ng ml-1; P<0.01), higher sevoflurane-induced tau phosphorylation in brain (133 [20]% vs 100 [6]% in 6-day-old mice, P<0.01; 103 [8]% vs 100 [13]% in 60-day-old mice, P=0.77), and sevoflurane-induced cognitive impairment. Testosterone treatment increased brain testosterone concentrations (1.76 [0.10] vs 0.39 [0.05] ng ml-1; P<0.01) and attenuated the sevoflurane-induced tau phosphorylation and cognitive impairment in neonatal male mice. Testosterone inhibited the interaction between tau and GSK3β, and attenuated sevoflurane-induced inhibition of excitatory postsynaptic currents in hippocampal neurones. CONCLUSIONS Lower brain testosterone concentrations in neonatal compared with adult male mice contributed to age-dependent tau phosphorylation and cognitive impairment after sevoflurane anaesthesia. Testosterone might attenuate the sevoflurane-induced tau phosphorylation and cognitive impairment by inhibiting the interaction between tau and GSK3β.
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Affiliation(s)
- Yongyan Yang
- Department of Anesthesia, Tianjin Medical University General Hospital, Tianjin, People's Republic of China; Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Feng Liang
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Jie Gao
- Department of Anesthesiology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, People's Republic of China; Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yuanlin Dong
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Yiying Zhang
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Guang Yang
- Department of Anesthesiology, Columbia University Medical Center, New York, NY, USA
| | - Sulpicio G Soriano
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hua-Jun Feng
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhongcong Xie
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.
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Du G, Bao X, Lin S, Pang H, Bannur Nanjunda S, Bao Q. Infrared Polaritonic Biosensors Based on Two-Dimensional Materials. Molecules 2021; 26:molecules26154651. [PMID: 34361804 PMCID: PMC8347072 DOI: 10.3390/molecules26154651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022] Open
Abstract
In recent years, polaritons in two-dimensional (2D) materials have gained intensive research interests and significant progress due to their extraordinary properties of light-confinement, tunable carrier concentrations by gating and low loss absorption that leads to long polariton lifetimes. With additional advantages of biocompatibility, label-free, chemical identification of biomolecules through their vibrational fingerprints, graphene and related 2D materials can be adapted as excellent platforms for future polaritonic biosensor applications. Extreme spatial light confinement in 2D materials based polaritons supports atto-molar concentration or single molecule detection. In this article, we will review the state-of-the-art infrared polaritonic-based biosensors. We first discuss the concept of polaritons, then the biosensing properties of polaritons on various 2D materials, then lastly the impending applications and future opportunities of infrared polaritonic biosensors for medical and healthcare applications.
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Affiliation(s)
- Guangyu Du
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225009, China; (G.D.); (H.P.)
- Songshan Lake Materials Laboratory, Dongguan 523808, China;
| | - Xiaozhi Bao
- Joint Key Laboratory of the Ministry of Education, Institute of Applied Physics and Materials Engineering, University of Macau, Macau, China;
| | - Shenghuang Lin
- Songshan Lake Materials Laboratory, Dongguan 523808, China;
| | - Huan Pang
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225009, China; (G.D.); (H.P.)
| | - Shivananju Bannur Nanjunda
- Department of Electrical Engineering, Centre of Excellence in Biochemical Sensing and Imaging Technologies (Cen-Bio-SIM), Indian Institute of Technology Madras, Chennai 600036, India
- Correspondence: (S.B.N.); (Q.B.)
| | - Qiaoliang Bao
- Shenzhen Exciton Science and Technology Ltd., Shenzhen 518052, China
- Correspondence: (S.B.N.); (Q.B.)
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15
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Microfluidics-Based Plasmonic Biosensing System Based on Patterned Plasmonic Nanostructure Arrays. MICROMACHINES 2021; 12:mi12070826. [PMID: 34357236 PMCID: PMC8303257 DOI: 10.3390/mi12070826] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/27/2021] [Accepted: 07/12/2021] [Indexed: 11/18/2022]
Abstract
This review aims to summarize the recent advances and progress of plasmonic biosensors based on patterned plasmonic nanostructure arrays that are integrated with microfluidic chips for various biomedical detection applications. The plasmonic biosensors have made rapid progress in miniaturization sensors with greatly enhanced performance through the continuous advances in plasmon resonance techniques such as surface plasmon resonance (SPR) and localized SPR (LSPR)-based refractive index sensing, SPR imaging (SPRi), and surface-enhanced Raman scattering (SERS). Meanwhile, microfluidic integration promotes multiplexing opportunities for the plasmonic biosensors in the simultaneous detection of multiple analytes. Particularly, different types of microfluidic-integrated plasmonic biosensor systems based on versatile patterned plasmonic nanostructured arrays were reviewed comprehensively, including their methods and relevant typical works. The microfluidics-based plasmonic biosensors provide a high-throughput platform for the biochemical molecular analysis with the advantages such as ultra-high sensitivity, label-free, and real time performance; thus, they continue to benefit the existing and emerging applications of biomedical studies, chemical analyses, and point-of-care diagnostics.
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16
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Dong Y, Liang F, Huang L, Fang F, Yang G, Tanzi RE, Zhang Y, Quan Q, Xie Z. The anesthetic sevoflurane induces tau trafficking from neurons to microglia. Commun Biol 2021; 4:560. [PMID: 33980987 PMCID: PMC8115254 DOI: 10.1038/s42003-021-02047-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/29/2021] [Indexed: 01/08/2023] Open
Abstract
Accumulation and spread of tau in Alzheimer's disease and other tauopathies occur in a prion-like manner. However, the mechanisms and downstream consequences of tau trafficking remain largely unknown. We hypothesized that tau traffics from neurons to microglia via extracellular vesicles (EVs), leading to IL-6 generation and cognitive impairment. We assessed mice and neurons treated with anesthetics sevoflurane and desflurane, and applied nanobeam-sensor technology, an ultrasensitive method, to measure tau/p-tau amounts. Sevoflurane, but not desflurane, increased tau or p-tau amounts in blood, neuron culture medium, or EVs. Sevoflurane increased p-tau amounts in brain interstitial fluid. Microglia from tau knockout mice took up tau and p-tau when treated with sevoflurane-conditioned neuron culture medium, leading to IL-6 generation. Tau phosphorylation inhibitor lithium and EVs generation inhibitor GW4869 attenuated tau trafficking. GW4869 mitigated sevoflurane-induced cognitive impairment in mice. Thus, tau trafficking could occur from neurons to microglia to generate IL-6, leading to cognitive impairment.
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Affiliation(s)
- Yuanlin Dong
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Feng Liang
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Lining Huang
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Department of Anesthesiology, the Second Hospital of Hebei Medical University, Shijiazhuang, P.R. China
| | - Fang Fang
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Department of Anesthesia, Zhongshan Hospital, Fudan University, Shanghai, P. R. China
| | - Guang Yang
- Department of Anesthesiology, Columbia University Medical Center, New York, NY, USA
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Yiying Zhang
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Qimin Quan
- Rowland Institute at Harvard University, Cambridge, MA, USA
- NanoMosaic, Woburn, MA, USA
| | - Zhongcong Xie
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.
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17
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Toropov N, Cabello G, Serrano MP, Gutha RR, Rafti M, Vollmer F. Review of biosensing with whispering-gallery mode lasers. LIGHT, SCIENCE & APPLICATIONS 2021; 10:42. [PMID: 33637696 PMCID: PMC7910454 DOI: 10.1038/s41377-021-00471-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/04/2021] [Accepted: 01/09/2021] [Indexed: 05/04/2023]
Abstract
Lasers are the pillars of modern optics and sensing. Microlasers based on whispering-gallery modes (WGMs) are miniature in size and have excellent lasing characteristics suitable for biosensing. WGM lasers have been used for label-free detection of single virus particles, detection of molecular electrostatic changes at biointerfaces, and barcode-type live-cell tagging and tracking. The most recent advances in biosensing with WGM microlasers are described in this review. We cover the basic concepts of WGM resonators, the integration of gain media into various active WGM sensors and devices, and the cutting-edge advances in photonic devices for micro- and nanoprobing of biological samples that can be integrated with WGM lasers.
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Affiliation(s)
- Nikita Toropov
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.
| | - Gema Cabello
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK
| | - Mariana P Serrano
- Departamento de Química, Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - Rithvik R Gutha
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK
| | - Matías Rafti
- Departamento de Química, Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - Frank Vollmer
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.
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18
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Qian J, Zhu Z, Yuan J, Liu Y, Liu B, Zhao X, Jiang L. Selectively enhanced Raman/fluorescence spectra in photonic-plasmonic hybrid structures. NANOSCALE ADVANCES 2020; 2:4682-4688. [PMID: 36132894 PMCID: PMC9418944 DOI: 10.1039/d0na00625d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/12/2020] [Indexed: 06/16/2023]
Abstract
The manipulation of the interaction between molecules and photonic-plasmonic hybrid structures is critical for the application of surface-enhanced spectroscopy (SES). Herein, we report a study on the mode coupling mechanism and SES performance in a typical optoplasmonic system constructed with a polystyrene microsphere (PS MS) resonator and gold nanoparticles (Au NPs). The mode coupling mechanism was found to be closely dependent on the relative positions of PS MS, Au NPs, and molecules in the optoplasmonic system, based on which selectively enhanced Raman and fluorescence signals of molecules can be realized via the collaboration of enhancement and quenching channels of the PS MS and Au NPs. We demonstrate two arrangements of the photonic-plasmonic hybrid structure, which can support fluorescence signals with sharp whispering-gallery modes and apparently enhanced Raman signals with relatively low detection limits and good robustness, respectively.
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Affiliation(s)
- Jisong Qian
- Institute of Micro-nano Photonic & Beam Steering, School of Science, Nanjing University of Science and Technology Nanjing 210094 China
| | - Zebin Zhu
- Institute of Micro-nano Photonic & Beam Steering, School of Science, Nanjing University of Science and Technology Nanjing 210094 China
| | - Jing Yuan
- Institute of Micro-nano Photonic & Beam Steering, School of Science, Nanjing University of Science and Technology Nanjing 210094 China
| | - Ying Liu
- Institute of Micro-nano Photonic & Beam Steering, School of Science, Nanjing University of Science and Technology Nanjing 210094 China
| | - Bing Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Nanjing 210009 China
| | - Xiangwei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Nanjing 210009 China
| | - Liyong Jiang
- Institute of Micro-nano Photonic & Beam Steering, School of Science, Nanjing University of Science and Technology Nanjing 210094 China
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19
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Huang Q, Li N, Zhang H, Che C, Sun F, Xiong Y, Canady TD, Cunningham BT. Critical Review: digital resolution biomolecular sensing for diagnostics and life science research. LAB ON A CHIP 2020; 20:2816-2840. [PMID: 32700698 PMCID: PMC7485136 DOI: 10.1039/d0lc00506a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
One of the frontiers in the field of biosensors is the ability to quantify specific target molecules with enough precision to count individual units in a test sample, and to observe the characteristics of individual biomolecular interactions. Technologies that enable observation of molecules with "digital precision" have applications for in vitro diagnostics with ultra-sensitive limits of detection, characterization of biomolecular binding kinetics with a greater degree of precision, and gaining deeper insights into biological processes through quantification of molecules in complex specimens that would otherwise be unobservable. In this review, we seek to capture the current state-of-the-art in the field of digital resolution biosensing. We describe the capabilities of commercially available technology platforms, as well as capabilities that have been described in published literature. We highlight approaches that utilize enzymatic amplification, nanoparticle tags, chemical tags, as well as label-free biosensing methods.
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Affiliation(s)
- Qinglan Huang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Nantao Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Hanyuan Zhang
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Congnyu Che
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Fu Sun
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Taylor D. Canady
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Brian T. Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Illinois Cancer Center, University of Illinois at Urbana-Champaign Urbana, IL 61801
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20
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Photonic Crystal Nanobeam Cavities for Nanoscale Optical Sensing: A Review. MICROMACHINES 2020; 11:mi11010072. [PMID: 31936559 PMCID: PMC7019810 DOI: 10.3390/mi11010072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 12/22/2022]
Abstract
The ability to detect nanoscale objects is particular crucial for a wide range of applications, such as environmental protection, early-stage disease diagnosis and drug discovery. Photonic crystal nanobeam cavity (PCNC) sensors have attracted great attention due to high-quality factors and small-mode volumes (Q/V) and good on-chip integrability with optical waveguides/circuits. In this review, we focus on nanoscale optical sensing based on PCNC sensors, including ultrahigh figure of merit (FOM) sensing, single nanoparticle trapping, label-free molecule detection and an integrated sensor array for multiplexed sensing. We believe that the PCNC sensors featuring ultracompact footprint, high monolithic integration capability, fast response and ultrahigh sensitivity sensing ability, etc., will provide a promising platform for further developing lab-on-a-chip devices for biosensing and other functionalities.
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21
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Jin X, Hapsari ND, Lee S, Jo K. DNA binding fluorescent proteins as single-molecule probes. Analyst 2020; 145:4079-4095. [DOI: 10.1039/d0an00218f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA binding fluorescent proteins are useful probes for a broad range of biological applications.
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Affiliation(s)
- Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
- Chemistry Education Program
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
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22
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You M, Lin Z, Wang F, Bai Y, Li X, Su Y, Liu J. Chip-scale humidity sensor based on a silicon nanobeam cavity. OPTICS LETTERS 2019; 44:5322-5325. [PMID: 31674998 DOI: 10.1364/ol.44.005322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 09/25/2019] [Indexed: 06/10/2023]
Abstract
In this Letter, a novel humidity sensor based on a chip-scale silicon nanobeam cavity with polymethyl methacrylate (PMMA) cladding is demonstrated. This sensor is easy to fabricate and compatible with CMOS technology. It shows a humidity sensing with a linear wavelength dependence of 22.9 pm/% relative humidity (RH) in a wide range of RH from 10% to 85%, an ultra-fast response time of 540 ms, and high stability. After annealing, the sensor exhibits high reversibility, repeatability, and temperature insensitivity at the range of 25°C-40°C. To the best of our knowledge, this is the first application of integrated photonics in high performance humidity detection. It provides a new way for the chip-scale sensor to integrate with photonic devices and optical systems.
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23
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Badman RP, Ye F, Wang MD. Towards biological applications of nanophotonic tweezers. Curr Opin Chem Biol 2019; 53:158-166. [PMID: 31678712 DOI: 10.1016/j.cbpa.2019.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 02/07/2023]
Abstract
Optical trapping (synonymous with optical tweezers) has become a core biophysical technique widely used for interrogating fundamental biological processes on size scales ranging from the single-molecule to the cellular level. Recent advances in nanotechnology have led to the development of 'nanophotonic tweezers,' an exciting new class of 'on-chip' optical traps. Here, we describe how nanophotonic tweezers are making optical trap technology more broadly accessible and bringing unique biosensing and manipulation capabilities to biological applications of optical trapping.
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Affiliation(s)
- Ryan P Badman
- Department of Physics & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Fan Ye
- Department of Physics & LASSP, Cornell University, Ithaca, NY 14853, USA; Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA
| | - Michelle D Wang
- Department of Physics & LASSP, Cornell University, Ithaca, NY 14853, USA; Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA.
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24
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Bano K, Bajwa SZ, Bassous NJ, Webster TJ, Shaheen A, Taj A, Hameed S, Tehseen B, Dai Z, Iqbal MZ, Khan WS. Development of biocompatible 1D CuO nanoneedles and their potential for sensitive, mass-based detection of anti-tuberculosis drugs. APPLIED NANOSCIENCE 2019. [DOI: 10.1007/s13204-019-01003-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Subramanian S, Wu HY, Constant T, Xavier J, Vollmer F. Label-Free Optical Single-Molecule Micro- and Nanosensors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1801246. [PMID: 30073717 DOI: 10.1002/adma.201801246] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/23/2018] [Indexed: 05/12/2023]
Abstract
Label-free optical sensor systems have emerged that exhibit extraordinary sensitivity for detecting physical, chemical, and biological entities at the micro/nanoscale. Particularly exciting is the detection and analysis of molecules, on miniature optical devices that have many possible applications in health, environment, and security. These micro- and nanosensors have now reached a sensitivity level that allows for the detection and analysis of even single molecules. Their small size enables an exceedingly high sensitivity, and the application of quantum optical measurement techniques can allow the classical limits of detection to be approached or surpassed. The new class of label-free micro- and nanosensors allows dynamic processes at the single-molecule level to be observed directly with light. By virtue of their small interaction length, these micro- and nanosensors probe light-matter interactions over a dynamic range often inaccessible by other optical techniques. For researchers entering this rapidly advancing field of single-molecule micro- and nanosensors, there is an urgent need for a timely review that covers the most recent developments and that identifies the most exciting opportunities. The focus here is to provide a summary of the recent techniques that have either demonstrated label-free single-molecule detection or claim single-molecule sensitivity.
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Affiliation(s)
- Sivaraman Subramanian
- Living Systems Institute, Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QD, UK
| | - Hsin-Yu Wu
- Living Systems Institute, Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QD, UK
| | - Tom Constant
- Living Systems Institute, Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QD, UK
| | - Jolly Xavier
- Living Systems Institute, Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QD, UK
| | - Frank Vollmer
- Living Systems Institute, Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QD, UK
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Abstract
Absorption microscopy is a promising alternative to fluorescence microscopy for single-molecule imaging. So far, molecular absorption has been probed optically via the attenuation of a probing laser or via photothermal effects. The sensitivity of optical probing is not only restricted by background scattering but it is fundamentally limited by laser shot noise, which minimizes the achievable single-molecule signal-to-noise ratio. Here, we present nanomechanical photothermal microscopy, which overcomes the scattering and shot-noise limit by detecting the photothermal heating of the sample directly with a temperature-sensitive substrate. We use nanomechanical silicon nitride drums, whose resonant frequency detunes with local heating. Individual Au nanoparticles with diameters from 10 to 200 nm and single molecules (Atto 633) are scanned with a heating laser with a peak irradiance of 354 ± 45 µW/µm2 using 50× long-working-distance objective. With a stress-optimized drum we reach a sensitivity of 16 fW/Hz1/2 at room temperature, resulting in a single-molecule signal-to-noise ratio of >70. The high sensitivity combined with the inherent wavelength independence of the nanomechanical sensor presents a competitive alternative to established tools for the analysis and localization of nonfluorescent single molecules and nanoparticles.
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27
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Yang D, Chen X, Zhang X, Lan C, Zhang Y. High-Q, low-index-contrast photonic crystal nanofiber cavity for high sensitivity refractive index sensing. APPLIED OPTICS 2018; 57:6958-6965. [PMID: 30129584 DOI: 10.1364/ao.57.006958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 07/20/2018] [Indexed: 06/08/2023]
Abstract
We present the design of simultaneous high-quality (Q)-factor and high-sensitivity (S) photonic crystal nanofiber cavities (PCNFCs) made of single silica nanofiber that have a low-index contrast (ratio=1.45). By using the three-dimensional finite-difference time-domain method, two different resonant modes, dielectric mode (DM) and air mode (AM), are designed and optimized to achieve an ultrahigh figure of merit (FOM), respectively. Numerical simulations are performed to study the Q-factors and sensitivities of the proposed PCNFCs. It shows that for both DM- and AM-based PCNFCs, respectively, the Q-factors and sensitivities of Q∼1.1×107, S=563.6 nm/RIU and Q∼2.1×105, S=736.8 nm/RIU can be estimated, resulting in FOMs as high as 4.31×106 and 1.13×105, respectively. To the best of our knowledge, this is the first silica nanofiber cavity geometry that simultaneously features high Q and high S for both DM and AM in PCNFCs. Compared with the state of the art of nanofiber-based cavities, the cavity Q-factor to mode volume (V) ratio (Q/V) in this work has been improved more than two orders of magnitude. The demonstration of a high Q/V cavity in low-index-contrast nanofibers can open up versatile applications using a broad range of functional and flexible fibers. Moreover, due to the extended evanescent field and small mode volumes, the proposed PCNFCs are ideal platforms for remote ultra-sensitive refractive-index-based gas sensing without the need for complicated coupling systems.
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Sun J, Maeno K, Aki S, Sueyoshi K, Hisamoto H, Endo T. Design and Fabrication of a Visible-Light-Compatible, Polymer-Based Photonic Crystal Resonator and Waveguide for Sensing Applications. MICROMACHINES 2018; 9:E410. [PMID: 30424343 PMCID: PMC6187389 DOI: 10.3390/mi9080410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/02/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022]
Abstract
In this paper, we have proposed a polymer-based photonic crystal (PhC) resonator, with multiple sizes of cavities, and a waveguide to be used as highly sensitive optical sensor components. Properties of the proposed PhC were simulated by the finite-difference time-domain method, and the polymer-based PhC resonator and waveguide were fabricated on a photoresist (polymer) by electron beam lithography, which was prepared on an Au-layer-deposited Si substrate. We detected the resonant light that penetrated through the waveguide and was trapped in the PhC resonator. Optical characteristics of the fabricated PhC were evaluated by detecting the polymer layer deposition process by using the layer-by-layer (LbL) method to deposit polymer layers. As a result, by using an optimized design of a polymer-based PhC resonator with a long cavity (equivalent to a defect of three holes), the PhC structure changes caused by LbL deposition lead to changes in resonant light wavelength (peak shift: 5.26 nm/layer). Therefore, we suggest that a PhC resonator and a waveguide is applicable as an optical sensor.
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Affiliation(s)
- Jiayi Sun
- Department of Applied Chemistry, Osaka Prefecture University, Osaka 599-8531, Japan.
| | - Kenichi Maeno
- Department of Applied Chemistry, Osaka Prefecture University, Osaka 599-8531, Japan.
| | - Shoma Aki
- Department of Applied Chemistry, Osaka Prefecture University, Osaka 599-8531, Japan.
| | - Kenji Sueyoshi
- Department of Applied Chemistry, Osaka Prefecture University, Osaka 599-8531, Japan.
| | - Hideaki Hisamoto
- Department of Applied Chemistry, Osaka Prefecture University, Osaka 599-8531, Japan.
| | - Tatsuro Endo
- Department of Applied Chemistry, Osaka Prefecture University, Osaka 599-8531, Japan.
- Japan Science and Technology Agency (JST) Precursory Research for Embryonic Science and Technology (PRESTO), Tokyo 102-8666, Japan.
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Hacohen N, Ip CJX, Gordon R. Analysis of Egg White Protein Composition with Double Nanohole Optical Tweezers. ACS OMEGA 2018; 3:5266-5272. [PMID: 31458737 PMCID: PMC6641915 DOI: 10.1021/acsomega.8b00651] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/03/2018] [Indexed: 05/21/2023]
Abstract
We use a double nanohole optical tweezer to analyze the protein composition of egg white through analysis of many individual protein trapping events. The proteins are grouped by mass based on two metrics: standard deviation of the trapping laser intensity fluctuations from the protein diffusion and the time constant of these fluctuations coming from the autocorrelation. Quantitative analysis is demonstrated for artificial samples, and then, the approach is applied to real egg white. The composition found from real egg white corresponds well to past reports using gel electrophoresis. This approach differs from past works by allowing for individual protein analysis in heterogeneous solutions without the need for denaturing, labeling, or tethering.
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Ding K, Chan CT. An eigenvalue approach to quantum plasmonics based on a self-consistent hydrodynamics method. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:084007. [PMID: 29283109 DOI: 10.1088/1361-648x/aaa43c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Plasmonics has attracted much attention not only because it has useful properties such as strong field enhancement, but also because it reveals the quantum nature of matter. To handle quantum plasmonics effects, ab initio packages or empirical Feibelman d-parameters have been used to explore the quantum correction of plasmonic resonances. However, most of these methods are formulated within the quasi-static framework. The self-consistent hydrodynamics model offers a reliable approach to study quantum plasmonics because it can incorporate the quantum effect of the electron gas into classical electrodynamics in a consistent manner. Instead of the standard scattering method, we formulate the self-consistent hydrodynamics method as an eigenvalue problem to study quantum plasmonics with electrons and photons treated on the same footing. We find that the eigenvalue approach must involve a global operator, which originates from the energy functional of the electron gas. This manifests the intrinsic nonlocality of the response of quantum plasmonic resonances. Our model gives the analytical forms of quantum corrections to plasmonic modes, incorporating quantum electron spill-out effects and electrodynamical retardation. We apply our method to study the quantum surface plasmon polariton for a single flat interface.
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Affiliation(s)
- Kun Ding
- Department of Physics and Institute for Advanced Study, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, People's Republic of China
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Liu C, Deb S, Ferreira VS, Xu E, Baumgart T. Kinetics of PTEN-mediated PI(3,4,5)P3 hydrolysis on solid supported membranes. PLoS One 2018; 13:e0192667. [PMID: 29447222 PMCID: PMC5813967 DOI: 10.1371/journal.pone.0192667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/26/2018] [Indexed: 11/18/2022] Open
Abstract
Phosphatidylinositides play important roles in cellular signaling and migration. Phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P3) is an important phosphatidylinositide because it acts as a secondary messenger to trigger cell movement and proliferation. A high level of PI(3,4,5)P3 at the plasma membrane is known to contribute to tumorigenesis. One key enzyme that regulates PI(3,4,5)P3 levels at the plasma membrane is phosphatase and tensin homologue deleted on chromosome 10 (PTEN), which dephosphorylates PI(3,4,5)P3 through hydrolysis to form phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2). It has been reported that PI(4,5)P2 is involved in positive feedback in the PI(3,4,5)P3 hydrolysis by PTEN. However, how PI(3,4,5)P3 dephosphorylation by PTEN is regulated, is still under debate. How other PI(3,4,5)P3-binding proteins affect the dephosphorylation kinetics catalyzed by PTEN also remains unclear. Here, we develop a fluorescent-protein biosensor approach to study how PI(3,4,5)P3 dephosphorylation is regulated by PTEN as well as its membrane-mediated feedback mechanisms. Our observation of sigmoidal kinetics of the PI(3,4,5)P3 hydrolysis reaction supports the notion of autocatalysis in PTEN function. We developed a kinetic model to describe the observed reaction kinetics, which allowed us to i) distinguish between membrane-recruitment and allosteric activation of PTEN by PI(4,5)P2, ii) account for the influence of the biosensor on the observed reaction kinetics, and iii) demonstrate that all of these mechanisms contribute to the kinetics of PTEN-mediated catalysis.
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Affiliation(s)
- Chun Liu
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sanghamitra Deb
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Vinicius S Ferreira
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Eric Xu
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tobias Baumgart
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Ferreira MFS, Castro-Camus E, Ottaway DJ, López-Higuera JM, Feng X, Jin W, Jeong Y, Picqué N, Tong L, Reinhard BM, Pellegrino PM, Méndez A, Diem M, Vollmer F, Quan Q. Roadmap on optical sensors. JOURNAL OF OPTICS (2010) 2017; 19:083001. [PMID: 29375751 PMCID: PMC5781231 DOI: 10.1088/2040-8986/aa7419] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Sensors are devices or systems able to detect, measure and convert magnitudes from any domain to an electrical one. Using light as a probe for optical sensing is one of the most efficient approaches for this purpose. The history of optical sensing using some methods based on absorbance, emissive and florescence properties date back to the 16th century. The field of optical sensors evolved during the following centuries, but it did not achieve maturity until the demonstration of the first laser in 1960. The unique properties of laser light become particularly important in the case of laser-based sensors, whose operation is entirely based upon the direct detection of laser light itself, without relying on any additional mediating device. However, compared with freely propagating light beams, artificially engineered optical fields are in increasing demand for probing samples with very small sizes and/or weak light-matter interaction. Optical fiber sensors constitute a subarea of optical sensors in which fiber technologies are employed. Different types of specialty and photonic crystal fibers provide improved performance and novel sensing concepts. Actually, structurization with wavelength or subwavelength feature size appears as the most efficient way to enhance sensor sensitivity and its detection limit. This leads to the area of micro- and nano-engineered optical sensors. It is expected that the combination of better fabrication techniques and new physical effects may open new and fascinating opportunities in this area. This roadmap on optical sensors addresses different technologies and application areas of the field. Fourteen contributions authored by experts from both industry and academia provide insights into the current state-of-the-art and the challenges faced by researchers currently. Two sections of this paper provide an overview of laser-based and frequency comb-based sensors. Three sections address the area of optical fiber sensors, encompassing both conventional, specialty and photonic crystal fibers. Several other sections are dedicated to micro- and nano-engineered sensors, including whispering-gallery mode and plasmonic sensors. The uses of optical sensors in chemical, biological and biomedical areas are described in other sections. Different approaches required to satisfy applications at visible, infrared and THz spectral regions are also discussed. Advances in science and technology required to meet challenges faced in each of these areas are addressed, together with suggestions on how the field could evolve in the near future.
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Affiliation(s)
- Mário F S Ferreira
- Department of Physics, I3N-Institute of Nanostructures, Nanomodelling and Nanofabrication, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Enrique Castro-Camus
- Centro de Investigaciones en Optica A.C. Loma del Bosque 115, Lomas del Campestre. Leon, Guanajuato, 37150, Mexico
| | - David J Ottaway
- Department of Physics and Institute of Photonics and Advanced Sensing, The University of Adelaide, Adelaide, South Australia, Australia
| | - José Miguel López-Higuera
- Photonics Engineering Group (GIF), Department TEISA, University of Cantabria, E-39005 Santander, Spain
- CIBER-bbn, Instituto de Salud Carlos III, E-28029 Madrid, Spain
- IDIVAL, Instituto de Investigación Marques Valdecilla, E-39011 Santander, Cantabria, Spain
| | - Xian Feng
- Beijing Engineering Research Center of Applied Laser Technology; Institute of Laser Engineering, Beijing University of Technology, Beijing 100124, People's Republic of China
| | - Wei Jin
- Department of Electrical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Yoonchan Jeong
- Laser Engineering and Applications Laboratory, Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Nathalie Picqué
- Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Str. 1. D-85748 Garching, Germany
| | - Limin Tong
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Björn M Reinhard
- Photonics Center, Boston University, 8 Saint Mary's Street, Boston, Massachusetts 02215, United States of America
- Chemistry Department, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States of America
| | - Paul M Pellegrino
- RDRL-SEE-O, US Army Research Laboratory, 2800 Powder Mill Road, Adelphi, Maryland 20783, United States of America
| | - Alexis Méndez
- MCH Engineering LLC, Alameda, California 94501, United States of America
| | - Max Diem
- Laboratory for Spectral Diagnosis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States of America
- Cireca Theranostics, LLC, Cambridge, Massachusetts 02139, United States of America
| | - Frank Vollmer
- Living Systems Institute, Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QD, United Kingdom
| | - Qimin Quan
- Rowland Institute at Harvard University, Cambridge, Massachusetts 02142, United States of America
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