{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/113352"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/113352","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Photonic crystal enhanced excitation, directional extraction, and blinking suppression for single quantum dot digital resolution biosensing","abstract":"The student, Yanyu Xiong, submitted this Thesis for approval on 2021-07-23 at 12:53.","abstract_html":"The student, Yanyu Xiong, submitted this Thesis for approval on 2021-07-23 at 12:53.","abstract_has_math":false,"creators":["Xiong, Yanyu"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Electrical & Computer Engr","degree_department":null,"school":null,"contributors":["Cunningham, Brian T"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-01-12T22:56:16Z","date_published":"2022-01-12T22:56:16Z","updated_at":"2026-07-22T22:24:53Z","subjects":["Photonic Crystal","Fluorescence Microscopy","Quantum Dot","Biosensor","miRNA Assay"],"languages":["en"],"rights":["Copyright 2021 Yanyu Xiong"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/113352","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Cunningham, Brian T"]},{"key":"dc:creator","label":"Author","values":["Xiong, Yanyu"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2022-01-12T22:56:16Z","2024-01-12T22:56:20Z","2021-07-23","2021-08"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Electrical & Computer Engr"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Photonic Crystal","Fluorescence Microscopy","Quantum Dot","Biosensor","miRNA Assay"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2021 Yanyu Xiong"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/113352"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["The student, Yanyu Xiong, submitted this Thesis for approval on 2021-07-23 at 12:53.","This Thesis was approved for publication on 2021-07-23 at 13:12.","DSpace SAF Submission Ingestion Package generated from Vireo submission #17086 on 2022-01-12 at 13:05:34","While nanoscale quantum emitters are effective tags for measuring biomolecular interactions, their utility for applications that demand single-unit observations are limited by the requirements for large numerical aperture (NA) objectives, fluorescence intermittency (blinking) and poor photon collection efficiency resulted from omnidirectional emission. Here, we report a nearly 3,000-fold signal enhancement achieved through the multiplicative effects of enhanced excitation, highly directional extraction, quantum efficiency improvement and blinking suppression through a photonic crystal (PC) surface. The approach achieves single Quantum Dot (QD) sensitivity with high signal-to-noise (~59), even with a low NA lens (NA = 0.5, 50X), and inexpensive optical setup without total internal reflection fluorescence (TIRF) or high gain electron-multiplying camera. The blinking suppression capability of the PC improves the QDs “on-time” from 15% to 85%, providing a novel method to ameliorate signal intermittency issues encountered during ultrasensitive measurements and fast motion tracking at the single particle level. As a representative molecular diagnostic application that requires ultrasensitive detection limits achieved through digital resolution counting of target biomarkers, we developed a QD-tagged “bridge” assay for cancer-associated miRNA biomarkers from a 45 ul sample volume with single-molecule resolution, single-base mutation selectivity, 10 aM (10^-17 Molar) detection limit, and linear dose-response over a 9-log concentration range with a single step, room temperature workflow. Additionally, we clearly observe differential surface motion trajectories of individual QDs when their surface attachment stringency is altered by changing a single base in the target miRNA sequence. Experimental characterization is supported by electromagnetic numerical simulations to show that the synergistic properties of the PC-QD system achieves its overall enhancement from the independent contributions of enhanced excitation, enhanced extraction (including both photon extraction rate improvement and quantum efficiency change via the Purcell effect) and enhanced collection efficiency. The approach presented here demonstrates a path toward digital resolution detection of a broad range of biomolecular analyte classes for ultrasensitive quantitative analysis that combines robust point-of-care instrumentation with simple assay protocols that do not require enzymatic amplification.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2023-08-01","The student, Yanyu Xiong, accepted the attached license on 2021-07-23 at 12:32.","Made available in DSpace on 2022-01-12T22:56:16Z (GMT). No. of bitstreams: 2 XIONG-THESIS-2021.pdf: 12588073 bytes, checksum: e97bf1250743afd169de33270b8e417d (MD5) LICENSE.txt: 4208 bytes, checksum: 3f2a54fe90dc30ab10f887e851ef15e8 (MD5) Previous issue date: 2021-07-23","Embargo set by: Seth Robbins for item 121281 Lift date: 2024-01-12T22:56:20Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Author requested closed access (OA after 2yrs) in Vireo ETD system","Limited"]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Photonic crystal enhanced excitation, directional extraction, and blinking suppression for single quantum dot digital resolution biosensing"]}]}],"canonical_facts":{"dc:contributor":["Cunningham, Brian T"],"dc:creator":["Xiong, Yanyu"],"dc:date":["2022-01-12T22:56:16Z","2024-01-12T22:56:20Z","2021-07-23","2021-08"],"dc:description":["The student, Yanyu Xiong, submitted this Thesis for approval on 2021-07-23 at 12:53.","This Thesis was approved for publication on 2021-07-23 at 13:12.","DSpace SAF Submission Ingestion Package generated from Vireo submission #17086 on 2022-01-12 at 13:05:34","While nanoscale quantum emitters are effective tags for measuring biomolecular interactions, their utility for applications that demand single-unit observations are limited by the requirements for large numerical aperture (NA) objectives, fluorescence intermittency (blinking) and poor photon collection efficiency resulted from omnidirectional emission. Here, we report a nearly 3,000-fold signal enhancement achieved through the multiplicative effects of enhanced excitation, highly directional extraction, quantum efficiency improvement and blinking suppression through a photonic crystal (PC) surface. The approach achieves single Quantum Dot (QD) sensitivity with high signal-to-noise (~59), even with a low NA lens (NA = 0.5, 50X), and inexpensive optical setup without total internal reflection fluorescence (TIRF) or high gain electron-multiplying camera. The blinking suppression capability of the PC improves the QDs “on-time” from 15% to 85%, providing a novel method to ameliorate signal intermittency issues encountered during ultrasensitive measurements and fast motion tracking at the single particle level. As a representative molecular diagnostic application that requires ultrasensitive detection limits achieved through digital resolution counting of target biomarkers, we developed a QD-tagged “bridge” assay for cancer-associated miRNA biomarkers from a 45 ul sample volume with single-molecule resolution, single-base mutation selectivity, 10 aM (10^-17 Molar) detection limit, and linear dose-response over a 9-log concentration range with a single step, room temperature workflow. Additionally, we clearly observe differential surface motion trajectories of individual QDs when their surface attachment stringency is altered by changing a single base in the target miRNA sequence. Experimental characterization is supported by electromagnetic numerical simulations to show that the synergistic properties of the PC-QD system achieves its overall enhancement from the independent contributions of enhanced excitation, enhanced extraction (including both photon extraction rate improvement and quantum efficiency change via the Purcell effect) and enhanced collection efficiency. The approach presented here demonstrates a path toward digital resolution detection of a broad range of biomolecular analyte classes for ultrasensitive quantitative analysis that combines robust point-of-care instrumentation with simple assay protocols that do not require enzymatic amplification.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2023-08-01","The student, Yanyu Xiong, accepted the attached license on 2021-07-23 at 12:32.","Made available in DSpace on 2022-01-12T22:56:16Z (GMT). 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