Tunability and Sensing Properties of Plasmonic/1D Photonic Crystal

Shaban, Mohamed; Ahmed, Ashour M.; Abdel‐Rahman, Ehab; Hamdy, Hany

doi:10.1038/srep41983

Cited by 100 publications

(39 citation statements)

References 47 publications

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“…These observations confirm that NR molecules preferentially bind to surfaces of β -sheets with their transition dipoles parallel to the fibril backbones (Fig. 2(b) inset), similar to the binding behavior of Thioflavin T [30, 31]. NR may bind transiently to grooves formed by adjacent amino acid side chains [32].…”

Section: Resolving Structural Heterogeneities Within Amyloid Fiberssupporting

confidence: 73%

Single-molecule orientation localization microscopy for resolving structural heterogeneities between amyloid fibrils

Ding

Mazidi

et al. 2020

Preprint

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5Simultaneous measurements of single-molecule positions and orientations provide critical insight 6 into a variety of biological and chemical processes. Various engineered point spread functions (PSFs) 7 have been introduced for measuring the orientation and rotational diffusion of dipole-like emitters, 8 but the widely used Cramér-Rao bound only evaluates performance for one specific orientation at 9 a time. Here, we report a performance metric, termed variance upper bound (VUB), that yields 10 a global maximum CRB for all possible molecular orientations, thereby enabling the measurement 11 performance of any PSF to be computed efficiently (~1000 times faster than calculating average 12 CRB). Our VUB reveals that the simple polarized standard PSF provides robust and precise ori-13 entation measurements if emitters are near a refractive index interface. Using the polarized PSF, 14 we measure the orientations and positions of Nile red (NR) molecules transiently bound to amy-15 loid aggregates. Our super-resolved images reveal the main binding mode of NR to amyloid fibers, 16 as well as structural heterogeneities within amyloid fibrillar networks, that cannot be resolved by 17 single-molecule localization alone. 19A key strength of single-molecule localization mi-20 croscopy (SMLM) is its ability to measure the full distri-21 bution of the phenomena under study and avoid ensemble 22 averaging. Going beyond standard SMLM to measure 23 SM position and orientation simultaneously is critical 24 for understanding a variety of nanoscale biological and 25 chemical processes, such as the motions of molecular mo-26 tors [1-3], the complex higher-order structures of DNA 27 [4, 5], and reaction kinetics within catalytic nanoparti-28 cles [6]. To perform these measurements, molecular po-29 sition and orientation must be encoded within the shape 30 of the image produced by a microscope, i.e., its point-31 spread function (PSF). However, balancing the need to 32 resolve various orientations unambiguously with the need 33 to detect SMs efficiently with high signal-to-background 34 ratio (SBR) remains a challenge that limits the adoption 35 of Single-Molecule Orientation Localization Microscopy 36 (SMOLM) for biological and chemical applications; exist-37 ing techniques either cannot discriminate between similar 38 types of molecular motions or cannot detect weak fluo-39 rescent emitters. 40 In order to design a PSF for measuring molecular ori-41 entation, one must have a figure of merit for compari-42 son. The Cramér-Rao bound (CRB), which is the best-43 possible precision achievable by an unbiased estimator, 44 has been used extensively for evaluating [7] and opti-45 mizing [8, 9] SMLM techniques. However, since CRB 46 quantifies measurement performance locally, in the sense 47 65 tection channels, exhibiting a polarized (standard) PSF, 66 provides superior measurement precision when molecules 67 are near a refractive index interface, especially when they 68 lie perpendicular to the optical axis, even under low SBR. 69 ...

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Section: Resolving Structural Heterogeneities Within Amyloid Fiberssupporting

confidence: 73%

Single-molecule orientation localization microscopy for resolving structural heterogeneities between amyloid fibrils

Ding

Mazidi

et al. 2020

Preprint

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“…The transfer matrix method (TMM) is a suitable method for calculating the reflection of the multilayer structure 1–5 . From the TMM we obtain the reflectance of electromagnetic waves through metal/PSi-1DPC as follows 43 :where M 11 , M 22 , M 12 and M 21 are the elements of the total transfer matrix of the proposed structure.…”

Section: Resultsmentioning

confidence: 99%

“…As shown in this Figure, wide photonic band gaps appeared for each n v value. These gaps resulted from the constructive interference of electromagnetic waves at the interface between each two layers 1,5,12 , since the width of the band gap increases with increasing the mismatch between the constituent materials 10–12 . With increasing the refractive index of the void, the photonic band gap decreases due to decrement the contrast of the refractive indices between the PSi and Si substance.…”

Section: Discussionmentioning

confidence: 99%

Ultra-high sensitive 1D porous silicon photonic crystal sensor based on the coupling of Tamm/Fano resonances in the mid-infrared region

Ahmed

Mehaney

2019

Sci Rep

Self Cite

167

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Porous silicon one-dimensional photonic crystals (PSi-1DPCs) are capable of sensing solutions and liquids based on the smallest variation of the refractive indices. In the present work, we present a novel metal/PSi-1DPC as a liquid sensor based on Tamm/Fano resonances. The operating wavelength range is from 6.35 to 9.85 μm in the mid-infrared (MIR) spectral region. Different metals (Al, Ag, Au, and Pt) are attached to the top surface of the PSi-1DPCs structure to show Tamm/Fano resonances more clearly. To the best of our knowledge, it is the first time that Tamm/Fano resonances exhibit simultaneously in PSi-1DPCs within the same structure. The reflection spectra were calculated for the metal/PSi-1DPC structure by using the transfer matrix method (TMM) and the Bruggeman’s effective medium approximation (BEMA). The simulations show that the Tamm/Fano resonances are red-shifted towards the higher wavelengths with increasing the refractive index of the pores. The Ag/PSi-1DPC sensor showed the highest performance. Its sensitivity can be reached to the value 5018 nm/RIU with a high-quality factor of about 2149.27. We predict the proposed sensors can be easily fabricated and we expect them to show higher performance than other reported sensors of this type. Therefore, it will be of interest in the field of optical sensing in different fields.

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“…"Fabrication"techniques" Various' techniques' have' been' employed' to' 1D' photonic' crystals' where' reproducible' deposition' of' thin' layers,' is' mandatory' to' achieve' a' high' optical' quality.' Processes' like' ion' implanting' [113],' sol-gel' [114,115],' electronJbeam' evaporation' [116],' Pulsed' Laser' Deposition' [117,118],' PECVD' [119]' and' sputtering' [120][121][122][123]' can' be' successfully' employed' for'the'fabrication'of'microcavities'based.' Anyway' the' deposition' protocols' have' to' careful' be' tailored' on' the' particular' materials' employed' and' possible' application' of' the' fabricated' system.'…”

Section: Number Of Bilayersmentioning

confidence: 99%

“…Anyway' the' deposition' protocols' have' to' careful' be' tailored' on' the' particular' materials' employed' and' possible' application' of' the' fabricated' system.' More' in' detail' semiconductor' materials' are' successfully' employed' for' the' fabrication' of' 1D' periodic' photonic' crystals' but' also'dielectric'materials'could'be'used'and'recent'works'demonstrate'as'the'addition'of'metal' layers' allow' to' combine' 1DJPC' with' the' surface' plasmon' resonance' (SPR)' to' realize' optical' sensors' [119].' OxideJbased' dielectric' materials' are' particularly' suitable' for' fabricating' photonic' band' gap' (PBG)' structures' because' they' have' wide' transparency' from' the' ultraviolet' to' the' near' infrared' (NIR).'…”

Section: Number Of Bilayersmentioning

confidence: 99%

Optical properties of periodic, quasi-periodic, and disordered one-dimensional photonic structures

Bellingeri¹,

et al. 2017

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Tunability and Sensing Properties of Plasmonic/1D Photonic Crystal

Cited by 100 publications

References 47 publications

Single-molecule orientation localization microscopy for resolving structural heterogeneities between amyloid fibrils

Single-molecule orientation localization microscopy for resolving structural heterogeneities between amyloid fibrils

Ultra-high sensitive 1D porous silicon photonic crystal sensor based on the coupling of Tamm/Fano resonances in the mid-infrared region

Optical properties of periodic, quasi-periodic, and disordered one-dimensional photonic structures

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