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Article ; Online: Ultrasensitive tapered optical fiber refractive index glucose sensor.

Ujah, Erem / Lai, Meimei / Slaughter, Gymama

2023 Volume 13, Issue 1, Page(s) 4495

Abstract: Refractive index (RI) sensors are of great interest for label-free optical biosensing. A tapered optical fiber (TOF) RI sensor with micron-sized waist diameters can dramatically enhance sensor sensitivity by reducing the mode volume over a long distance. ...

Abstract	Refractive index (RI) sensors are of great interest for label-free optical biosensing. A tapered optical fiber (TOF) RI sensor with micron-sized waist diameters can dramatically enhance sensor sensitivity by reducing the mode volume over a long distance. Here, a simple and fast method is used to fabricate highly sensitive refractive index sensors based on localized surface plasmon resonance (LSPR). Two TOFs (l = 5 mm) with waist diameters of 5 µm and 12 µm demonstrated sensitivity enhancement at λ = 1559 nm for glucose sensing (5-45 wt%) at room temperature. The optical power transmission decreased with increasing glucose concentration due to the interaction of the propagating light in the evanescent field with glucose molecules. The coating of the TOF with gold nanoparticles (AuNPs) as an active layer for glucose sensing generated LSPR through the interaction of the evanescent wave with AuNPs deposited at the tapered waist. The results indicated that the TOF (Ø = 5 µm) exhibited improved sensing performance with a sensitivity of 1265%/RIU compared to the TOF (Ø = 12 µm) at 560%/RIU towards glucose. The AuNPs were characterized using scanning electron microscopy and ultraviolent-visible spectroscopy. The AuNPs-decorated TOF (Ø = 12 µm) demonstrated a high sensitivity of 2032%/RIU toward glucose. The AuNPs-decorated TOF sensor showed a sensitivity enhancement of nearly 4 times over TOF (Ø = 12 µm) with RI ranging from 1.328 to 1.393. The fabricated TOF enabled ultrasensitive glucose detection with good stability and fast response that may lead to next-generation ultrasensitive biosensors for real-world applications, such as disease diagnosis.
Language	English
Publishing date	2023-03-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-31127-4
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Article ; Online: First Probe of Sub-GeV Dark Matter beyond the Cosmological Expectation with the COHERENT CsI Detector at the SNS.

Akimov, D / An, P / Awe, C / Barbeau, P S / Becker, B / Belov, V / Bernardi, I / Blackston, M A / Bock, C / Bolozdynya, A / Browning, J / Cabrera-Palmer, B / Chernyak, D / Conley, E / Daughhetee, J / Detwiler, J / Ding, K / Durand, M R / Efremenko, Y /

Elliott, S R / Fabris, L / Febbraro, M / Gallo Rosso, A / Galindo-Uribarri, A / Green, M P / Heath, M R / Hedges, S / Hoang, D / Hughes, M / Johnson, T / Khromov, A / Konovalov, A / Kozlova, E / Kumpan, A / Li, L / Link, J M / Liu, J / Mann, K / Markoff, D M / Mastroberti, J / Mueller, P E / Newby, J / Parno, D S / Penttila, S I / Pershey, D / Rapp, R / Raybern, J / Razuvaeva, O / Reyna, D / Rich, G C / Ross, J / Rudik, D / Runge, J / Salvat, D J / Salyapongse, A M / Sander, J / Scholberg, K / Shakirov, A / Simakov, G / Sinev, G / Snow, W M / Sosnovtsev, V / Suh, B / Tayloe, R / Tellez-Giron-Flores, K / Tolstukhin, I / Ujah, E / Vanderwerp, J / Varner, R L / Virtue, C J / Visser, G / Wongjirad, T / Yen, Y-R / Yoo, J / Yu, C-H / Zettlemoyer, J

Physical review letters

2023 Volume 130, Issue 5, Page(s) 51803

Abstract: The COHERENT Collaboration searched for scalar dark matter particles produced at the Spallation Neutron Source with masses between 1 and 220 MeV/c^{2} using a CsI[Na] scintillation detector sensitive to nuclear recoils above 9 keV_{nr}. No evidence for ...

Abstract	The COHERENT Collaboration searched for scalar dark matter particles produced at the Spallation Neutron Source with masses between 1 and 220 MeV/c^{2} using a CsI[Na] scintillation detector sensitive to nuclear recoils above 9 keV_{nr}. No evidence for dark matter is found and we thus place limits on allowed parameter space. With this low-threshold detector, we are sensitive to coherent elastic scattering between dark matter and nuclei. The cross section for this process is orders of magnitude higher than for other processes historically used for accelerator-based direct-detection searches so that our small, 14.6 kg detector significantly improves on past constraints. At peak sensitivity, we reject the flux consistent with the cosmologically observed dark-matter concentration for all coupling constants α_{D}<0.64, assuming a scalar dark-matter particle. We also calculate the sensitivity of future COHERENT detectors to dark-matter signals which will ambitiously test multiple dark-matter spin scenarios.
Language	English
Publishing date	2023-02-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.130.051803
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Article ; Online: Measurement of the Coherent Elastic Neutrino-Nucleus Scattering Cross Section on CsI by COHERENT.

Elliott, S R / Fabris, L / Febbraro, M / Gallo Rosso, A / Galindo-Uribarri, A / Green, M P / Heath, M R / Hedges, S / Hoang, D / Hughes, M / Johnson, T / Khromov, A / Konovalov, A / Kozlova, E / Kumpan, A / Li, L / Link, J M / Liu, J / Mann, K / Markoff, D M / Mastroberti, J / Mueller, P E / Newby, J / Parno, D S / Penttila, S I / Pershey, D / Rapp, R / Ray, H / Raybern, J / Razuvaeva, O / Reyna, D / Rich, G C / Ross, J / Rudik, D / Runge, J / Salvat, D J / Salyapongse, A M / Scholberg, K / Shakirov, A / Simakov, G / Sinev, G / Snow, W M / Sosnovstsev, V / Suh, B / Tayloe, R / Tellez-Giron-Flores, K / Tolstukhin, I / Ujah, E / Vanderwerp, J / Varner, R L / Virtue, C J / Visser, G / Wongjirad, T / Yen, Y-R / Yoo, J / Yu, C-H / Zettlemoyer, J

Physical review letters

2022 Volume 129, Issue 8, Page(s) 81801

Abstract: We measured the cross section of coherent elastic neutrino-nucleus scattering (CEvNS) using a CsI[Na] scintillating crystal in a high flux of neutrinos produced at the Spallation Neutron Source at Oak Ridge National Laboratory. New data collected before ... ...

Abstract	We measured the cross section of coherent elastic neutrino-nucleus scattering (CEvNS) using a CsI[Na] scintillating crystal in a high flux of neutrinos produced at the Spallation Neutron Source at Oak Ridge National Laboratory. New data collected before detector decommissioning have more than doubled the dataset since the first observation of CEvNS, achieved with this detector. Systematic uncertainties have also been reduced with an updated quenching model, allowing for improved precision. With these analysis improvements, the COHERENT Collaboration determined the cross section to be (165_{-25}^{+30})×10^{-40} cm^{2}, consistent with the standard model, giving the most precise measurement of CEvNS yet. The timing structure of the neutrino beam has been exploited to compare the CEvNS cross section from scattering of different neutrino flavors. This result places leading constraints on neutrino nonstandard interactions while testing lepton flavor universality and measures the weak mixing angle as sin^{2}θ_{W}=0.220_{-0.026}^{+0.028} at Q^{2}≈(50 MeV)^{2}.
Language	English
Publishing date	2022-05-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.129.081801
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Article ; Online: Measurement of Electron-Neutrino Charged-Current Cross Sections on ^{127}I with the COHERENT NaIνE Detector.

An, P / Awe, C / Barbeau, P S / Becker, B / Belov, V / Bernardi, I / Bock, C / Bolozdynya, A / Bouabid, R / Brown, A / Browning, J / Cabrera-Palmer, B / Cervantes, M / Conley, E / Daughhetee, J / Detwiler, J / Ding, K / Durand, M R / Efremenko, Y /

Elliott, S R / Fabris, L / Febbraro, M / Gallo Rosso, A / Galindo-Uribarri, A / Germer, A C / Green, M P / Hakenmüller, J / Heath, M R / Hedges, S / Hughes, M / Johnson, B A / Johnson, T / Khromov, A / Konovalov, A / Kozlova, E / Kumpan, A / Kyzylova, O / Li, L / Link, J M / Liu, J / Mahoney, M / Major, A / Mann, K / Markoff, D M / Mastroberti, J / Mattingly, J / Mueller, P E / Newby, J / Parno, D S / Penttila, S I / Pershey, D / Prior, C G / Rapp, R / Ray, H / Raybern, J / Razuvaeva, O / Reyna, D / Rich, G C / Ross, J / Rudik, D / Runge, J / Salvat, D J / Sander, J / Scholberg, K / Shakirov, A / Simakov, G / Sinev, G / Skuse, C / Snow, W M / Sosnovtsev, V / Subedi, T / Suh, B / Tayloe, R / Tellez-Giron-Flores, K / Tsai, Y-T / Ujah, E / Vanderwerp, J / van Nieuwenhuizen, E E / Varner, R L / Virtue, C J / Visser, G / Walkup, K / Ward, E M / Wongjirad, T / Yoo, J / Yu, C-H / Zawada, A / Zettlemoyer, J / Zderic, A

Physical review letters

2023 Volume 131, Issue 22, Page(s) 221801

Abstract: Using an 185-kg NaI[Tl] array, COHERENT has measured the inclusive electron-neutrino charged-current cross section on ^{127}I with pion decay-at-rest neutrinos produced by the Spallation Neutron Source at Oak Ridge National Laboratory. Iodine is one the ... ...

Abstract	Using an 185-kg NaI[Tl] array, COHERENT has measured the inclusive electron-neutrino charged-current cross section on ^{127}I with pion decay-at-rest neutrinos produced by the Spallation Neutron Source at Oak Ridge National Laboratory. Iodine is one the heaviest targets for which low-energy (≤50 MeV) inelastic neutrino-nucleus processes have been measured, and this is the first measurement of its inclusive cross section. After a five-year detector exposure, COHERENT reports a flux-averaged cross section for electron neutrinos of 9.2_{-1.8}^{+2.1}×10^{-40} cm^{2}. This corresponds to a value that is ∼41% lower than predicted using the MARLEY event generator with a measured Gamow-Teller strength distribution. In addition, the observed visible spectrum from charged-current scattering on ^{127}I has been measured between 10 and 55 MeV, and the exclusive zero-neutron and one-or-more-neutron emission cross sections are measured to be 5.2_{-3.1}^{+3.4}×10^{-40} and 2.2_{-0.5}^{+0.4}×10^{-40} cm^{2}, respectively.
Language	English
Publishing date	2023-12-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.131.221801
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Book ; Online: Measurement of scintillation response of CsI[Na] to low-energy nuclear recoils by COHERENT

Akimov, D. / An, P. / Awe, C. / Barbeau, P. S. / Becker, B. / Belov, V. / Bernardi, I. / Blackston, M. A. / Bock, C. / Bolozdynya, A. / Browning, J. / Cabrera-Palmer, B. / Chernyak, D. / Conley, E. / Daughhetee, J. / Detwiler, J. / Ding, K. / Durand, M. R. / Efremenko, Y. /

Elliott, S. R. / Fabris, L. / Febbraro, M. / Rosso, A. Gallo / Galindo-Uribarri, A. / Green, M. P. / Heath, M. R. / Hedges, S. / Hoang, D. / Hughes, M. / Johnson, T. / Khromov, A. / Konovalov, A. / Kozlova, E. / Kumpan, A. / Li, L. / Link, J. M. / Liu, J. / Mann, K. / Markoff, D. M. / Mastroberti, J. / Melikyan, Y. A. / Mueller, P. E. / Newby, J. / Parno, D. S. / Penttila, S. I. / Pershey, D. / Rapp, R. / Ray, H. / Raybern, J. / Razuvaeva, O. / Reyna, D. / Rich, G. C. / Ross, J. / Rudik, D. / Runge, J. / Salvat, D. J. / Salyapongse, A. M. / Scholberg, K. / Shakirov, A. / Simakov, G. / Sinev, G. / Snow, W. M. / Sosnovstsev, V. / Suh, B. / Tayloe, R. / Tellez-Giron-Flores, K. / Tolstukhin, I. / Ujah, E. / Vanderwerp, J. / Varner, R. L. / Virtue, C. J. / Visser, G. / Wongjirad, T. / Yen, Y. -R. / Yoo, J. / Yu, C. -H. / Zettlemoyer, J.

2021

Abstract: We present results of several measurements of CsI[Na] scintillation response to 3-60 keV energy nuclear recoils performed by the COHERENT collaboration using tagged neutron elastic scattering experiments and an endpoint technique. Earlier results, used ... ...

Abstract	We present results of several measurements of CsI[Na] scintillation response to 3-60 keV energy nuclear recoils performed by the COHERENT collaboration using tagged neutron elastic scattering experiments and an endpoint technique. Earlier results, used to estimate the coherent elastic neutrino-nucleus scattering (CEvNS) event rate for the first observation of this process achieved by COHERENT at the Spallation Neutron Source (SNS), have been reassessed. We discuss corrections for the identified systematic effects and update the respective uncertainty values. The impact of updated results on future precision tests of CEvNS is estimated. We scrutinize potential systematic effects that could affect each measurement. In particular we confirm the response of the H11934-200 Hamamatsu photomultiplier tube (PMT) used for the measurements presented in this study to be linear in the relevant signal scale region.
Keywords	Physics - Instrumentation and Detectors
Subject code	621
Publishing date	2021-11-03
Publishing country	us
Document type	Book ; Online
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Article: Use of graph theory for secondary structure recognition and sequential assignment in heteronuclear (13C, 15N) NMR spectra: application to HU protein from Bacillus stearothermophilus.

van Geerestein-Ujah, E C / Mariani, M / Vis, H / Boelens, R / Kaptein, R

Biopolymers

1996 Volume 39, Issue 5, Page(s) 691–707

Abstract: A computer-assisted procedure, based upon a branch of mathematics known as graph theory, has been developed to recognize secondary structure elements in proteins from their corresponding nuclear Overhauser effect spectroscopy (NOESY)-type spectra and to ... ...

Abstract	A computer-assisted procedure, based upon a branch of mathematics known as graph theory, has been developed to recognize secondary structure elements in proteins from their corresponding nuclear Overhauser effect spectroscopy (NOESY)-type spectra and to carry out their sequential assignment. In the method, NOE connectivity templates characteristic of regular secondary structures are identified in the spectra. Resonance assignment is then achieved by connecting these NOE patterns of secondary structure together, and thereby matching connected spin systems to specific parts of the primary sequence. The range of NOE-graph templates of secondary structure motifs, incorporating alpha-helices and beta-strand motifs, has been examined for reliability and extent of secondary structure identification in a data base composed of the high resolution structures of 20 proteins. The analysis identified several robust NOE-graph templates and supports the implementation of an ordered search strategy. The method, known as SERENDIPITY, has been applied to the analysis of nuclear Overhauser effect data from a three-dimensional time-shared nuclear Overhauser effect spectroscopy (13C, 15N) heteronuclear single quantum correlation spectrum of the (alpha + beta) type protein HU from Bacillus stearothermophilus. The arrangement of the elucidated elements of secondary structure is very similar to that of the x-ray and nmr structures of HU. In addition, our analysis revealed a pattern of interstrand nuclear Overhauser effect in the beta-arm region (residues 53-76) of HU, which suggest irregularities, not reported in the x-ray structure, in both strands of the beta-arm at Ala57 and Pro72, respectively. At these residues, both strands of the beta-arm appear to flip inside out before continuing as a regular antiparallel beta-sheet.
MeSH term(s)	Amino Acid Sequence ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Biopolymers/chemistry ; Carbon Isotopes ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/genetics ; Geobacillus stearothermophilus/chemistry ; Geobacillus stearothermophilus/genetics ; Magnetic Resonance Spectroscopy ; Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Nitrogen Isotopes ; Protein Structure, Secondary
Chemical Substances	Bacterial Proteins ; Biopolymers ; Carbon Isotopes ; DNA-Binding Proteins ; Nitrogen Isotopes ; histone-like protein HU, bacteria
Language	English
Publishing date	1996-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1123-x
ISSN	1097-0282 ; 0006-3525
ISSN (online)	1097-0282
ISSN	0006-3525
DOI	10.1002/(sici)1097-0282(199611)39:5<691::aid-bip8>3.0.co;2-r
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Article: Graph-theoretical assignment of secondary structure in multidimensional protein NMR spectra: application to the lac repressor headpiece.

van Geerestein-Ujah, E C / Slijper, M / Boelens, R / Kaptein, R

Journal of biomolecular NMR

1995 Volume 6, Issue 1, Page(s) 67–78

Abstract: A novel procedure is presented for the automatic identification of secondary structures in proteins from their corresponding NOE data. The method uses a branch of mathematics known as graph theory to identify prescribed NOE connectivity patterns ... ...

Abstract	A novel procedure is presented for the automatic identification of secondary structures in proteins from their corresponding NOE data. The method uses a branch of mathematics known as graph theory to identify prescribed NOE connectivity patterns characteristic of the regular secondary structures. Resonance assignment is achieved by connecting these patterns of secondary structure together, thereby matching the connected spin systems to specific segments of the protein sequence. The method known as SERENDIPITY refers to a set of routines developed in a modular fashion, where each program has one or several well-defined tasks. NOE templates for several secondary structure motifs have been developed and the method has been successfully applied to data obtained from NOESY-type spectra. The present report describes the application of the SERENDIPITY protocol to a 3D NOESY-HMQC spectrum of the 15N-labelled lac repressor headpiece protein. The application demonstrates that, under favourable conditions, fully automated identification of secondary structures and semi-automated assignment are feasible.
MeSH term(s)	Amino Acid Sequence ; Computer Graphics ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Protein Structure, Secondary ; Repressor Proteins/chemistry ; Repressor Proteins/genetics ; Software
Chemical Substances	Repressor Proteins
Language	English
Publishing date	1995-07
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1081696-3
ISSN	0925-2738
ISSN	0925-2738
DOI	10.1007/bf00417493
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Article: Identification of beta-sheet motifs, of psi-loops, and of patterns of amino acid residues in three-dimensional protein structures using a subgraph-isomorphism algorithm

Artymiuk, P.J / Grindley, H.M / Poirrette, A.R / Rice, D.W / Ujah, E.C / Willett, P

Journal of chemical information and computer sciences. Jan/Feb 1994. v. 34 (1)

1994

Abstract: This paper discusses the use of graph-theoretical techniques for the representation and searching of 3-D protein structures that are represented by labeled graphs. Two types of graph are considered. The nodes in the first type of chemical graph describe ... ...

Abstract	This paper discusses the use of graph-theoretical techniques for the representation and searching of 3-D protein structures that are represented by labeled graphs. Two types of graph are considered. The nodes in the first type of chemical graph describe the secondary-structure elements and the edges the geometric relationships between pairs of these elements. The use of Ullmann's subgraph isomorphism algorithm with these representations permits the identification of all occurrences of all possible beta-sheet motifs in a 114-protein subset of the Protein Data Bank. A binary notation is used to describe the parallel or antiparallel characters of adjacent strands in a sheet, and it is shown that very few of the possible types of sheet are found to occur in practice. Similar conclusions are obtained using a more detailed notation that includes the sheets' topological connectivities. The latter notation enables searches to be carried out for psi-loops and allows the identification of 20 proteins that had not previously been known to contain this type of loop. The nodes in the second type of protein graph describe the amino acid residues in protein structures and the edges the geometric relationships between pairs of these residues. The use of the Ullmann algorithm with these representations permits the identification of the occurrences of patterns of residues. The identification process is illustrated by means of searches for the two aspartate groups that are known to be involved in the catalytic mechanism of the aspartic proteinases.
Keywords	databases ; proteins ; molecular conformation ; amino acid sequences ; algorithms ; protein conformation
Language	English
Dates of publication	1994-01
Size	p. 54-62.
Document type	Article
ZDB-ID	190019-5
ISSN	0095-2338
ISSN	0095-2338
Database	NAL-Catalogue (AGRICOLA)

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