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Source Code and Simulation Results: Chiral and directional optical emission from a dipole source coupled to a helical plasmonic antenna
<h3>Summary</h3> <p>This publication supplements the article "Chiral and directional optical emission from a dipole source coupled to a helical plasmonic antenna" with tabulated data and Matlab code that allows the reproduction of the results. Within the article, the chiral behavior of single and double plasmonic nano antennas made from silver is numerically investigated with a focus on the coupling of a linear polarized dipole as an excitation source to the helix.</p> <h3>Simulation Setup - FEM Simulations</h3> <p>The script "run_wavlengthscan.m" allows to reproduce all simulations of the article. It can be chosen between the single and double helices, by specifying the keys parameter "keys.doppelhelix" where 0 gives a single and 1 a double helix. The number of turns can be specified by choosing "keys.case". The dipol is located within a 20nm thick hBN substrate layer, on glass (BK7). Results of the Purcell enhancement can be plotted using the scripts "display_results_single_helix.m" and "display_results_doublehelix.m" in the folder "results". The far-field plots can be reproduced using the scripts "display_farfiel_polarization_single_helix.m" and "display_farfiel_polarization_double_helix.m" of the folder "FunctionsAndScripts".</p> <p>The template for the mesh is contained in the folder "generate_grid_file", where the parameters of the helix (for example: radius, tube radius, and pitch height) can be modified.</p> <p>Within the folder "project3D" all required .jcm files are stored. Copy the "grid.jcm" file with the geometry of interest to this folder to perform simulations.</p> <p>All required keys parameters for the JCM template files (.jcmt, jcmpt) are set within the functions "set_numerical_parameter.m" and "set_physical_parameters.m", contained in the folder "FunctionsAndScripts". Therein, the function "set_sources.m" specifies the parameters for the dipole excitation, such as the position, and the strength (equivalent to the polarization).</p> <h3>Semi-Analytical Model</h3> <p>The Jupyter notebook "Semi_Analytical_Plasmonic_Helix.ipynb" contains the commented Python script for the semi-analytical design tool used to obtain far-field radiation patterns of the single helix. This semi-analytical design tool is based on an analytical model developed in [4]. The script can be divided into three parts. First, the single helix is defined, and a linear wavelength scaling law [5] is used to determine the illuminating wavelengths at which Fabry-Pérot resonances occur. Second, the overlap integral between the mode current on the helix and the incident electric field is evaluated for a given direction of incident light. Thirdly, the direction of incidence is varied to obtain the far-field radiation patterns. The script allows for the radiation patterns to be exported as a .csv file. Alternatively, the radiation patterns can be plotted directly using the provided single_plot functions.</p> <h3>Material</h3> <p>The material data has been taken from the <a href="https://refractiveindex.info/" target="_blank" rel="noopener">refractiveindex.info</a> database. For silver the data is taken from tabulated data from Johnson and Christy [1] . The dispersion relation for hBN comes from [2] and tabulated data for glass (BK7) from [3]. The MATLAB script "material_properties_plot.m" plots the material fits above the wavelengths of interest. The required tabulated data is given in the folder "material_data".</p> <p>With 'material_properties_plot.m' the fits to the material data can be reproduced and plotted.</p> <h3>Usage</h3> <p>The .zip folder Helix_FEM contains all data and scripts to reproduce the plots from the 3D FEM simulations.</p> <p>The Jupyter Notebook Semi_Analytical_Plasmonic_Helix reprouces the results from the semi-analytical model.</p> <h3>Requirements</h3> <ul> <li>JCMsuite (at least 5.4.0)</li> <li>MATLAB (tested with version R2023b)</li> <li>Python (tested with Version 3.10.9)</li> <li>Jupyter Notebook (tested with 6.5.2) </li> </ul> <p>To run the simulations with JCMsuite you must replace corresponding placeholders with a path to your installation of JCMsuite. Free trial licenses are available, please refer to the homepage of <a href="https://jcmwave.com/">JCMwave</a>.</p> <h3>References</h3> <p>[1] P. B. Johnson and R.-W. Christy, “Optical constants of the noble metals,” Phys. Rev. B 6, 4370 (1972).</p> <p>[2] S.-Y. Lee, T.-Y. Jeong, S. Jung, and K.-J. Yee, “Refractive index dispersion of hexagonal boron nitride in the visible and near-infrared,” Phys. Status Solidi B 256, 1800417 (2019).</p> <p>[3] “SCHOTT Zemax catalogue 2017-01-20b,” (2017).</p> <div>[4] K. Höflich et al., "Resonant behavior of a single plasmonic helix." Optica 6, 1098(2019).</div> <div> </div> <div>[5]L. Novotny, "Effective wavelength scaling for optical antennas", Phys. Rev. Lett. 98,266802 (2007).</div>
Рис. 3. Αичинка T. ploenensis из озера Арейского: а — гоΛова; б — ментум; в — антенна; г — верхняя губа Fig. 3. Larva of T. ploenensis from Lake Areyskoye: а — head; б — mentum; в — antenna; г — labrum in macroinvertebrates of the Lake Areyskoye
Рис. 3. Αичинка T. ploenensis из озера Арейского: а — гоΛова; б — ментум; в — антенна; г — верхняя губа Fig. 3. Larva of T. ploenensis from Lake Areyskoye: а — head; б — mentum; в — antenna; г — labrum
Figs 1–4. Antenna. 1 in Taxonomic study of Ufens Girault from Xinjiang, China (Hymenoptera: Trichogrammatidae)
Figs 1–4. Antenna. 1. Ufens similis (Kryger), ♂. 2. U. similis (Kryger), ♀. 3. U. pallidus Owen, ♂. 4. U. foersteri (Kryger), ♂.
Fig. 12 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 12. Enlarged labial palp (lef) showing sensillum chaeticum (C) and sensillum styloconicum (S); and enlarged apical maxillary palp (right) showing apical sensilla basiconica (A1, A2, A3), medial sensilla basiconica (M1, M2, M3), and lateral sensilla basiconica (L1, L2).
Fig. 11 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 11. Apical maxillary palp showing apical sensilla basiconica (A1, A2, A3), medial sensilla basiconica (M1, M2, M3), and lateral sensilla basiconica (L1, L2) in 4 species of Lepidoptera: A) Spodoptera litura, B) Chilo partellus, C) Plutella xylostella, and D) Maruca vitrata.
Fig. 8 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 8. Labrum (L) showing distribution and number of sensilla chaetica (C1–C15) in 4 species of Lepidoptera: A) Spodoptera litura, B) Chilo partellus, C) Plutella xylostella, and D) Maruca vitrata.
Fig. 7 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 7. Ventral and lateral view of larval mouthparts showing labrum (L), mandible (M), maxillae (MX), labium (LI), antennae (A), stemma (ST), and long tactile setae (LTS) in 4 species of Lepidoptera: A) Spodoptera litura, B) Chilo partellus, C) Plutella xylostella, and D) Maruca vitrata.
Fig. 4 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 4. SEM images of larval antennae of Plutella xylostella at different instars: A) 1st instar, B) 2nd instar, C) 3rd instar, and D) 4th instar.
Fig. 15 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 15. Multiple sequence alignment of the partialsequence of the Or83b gene in Spodoptera litura, Chilo partellus, Plutella xylostella, and Maruca vitrata with the reference sequence of Spodoptera litura Or83b (Accession No. JQ811935) using ClustalW sofware. Grey shades represent completely conserved bases. Primer sequences used for amplification of the partial Or83b gene are underlined.
Fig. 1 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 1. Dorsal surface of the larval head showing short tactile setae (STS) and long tactile setae (LTS) in 4 species of Lepidoptera: A) Spodoptera litura, B) Chilo partellus, C) Plutella xylostella, and D) Maruca vitrata.
Fig. 6 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 6. Antenna is segmented (I–III), showing the presence of sensilla styloconica (S1, S2), sensilla basiconica (B1, B2, B3), and sensillum chaeticum (C) in 4 species of Lepidoptera: A) Spodoptera litura, B) Chilo partellus, C) Plutella xylostella, and D) Maruca vitrata.
Fig. 3 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 3. SEM images of larval antennae of Chilo partellus at different instars: A) 1st instar, B) 2nd instar, C) 3rd instar, D) 4th instar, E) 5th instar, and F) 6th instar.
Fig. 5 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 5. SEM images of larval antennae of Maruca vitrata at different instars: A) 1st instar, B) 2nd instar, C) 3rd instar, D) 4th instar, and E) 5th instar.
Fig. 2 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 2. SEM images of larval antennae of Spodoptera litura at different instars: A) 1st instar, B) 2nd instar, C) 3rd instar, D) 4th instar, and E) 5th instar.
Fig. 10 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 10. Enlarged maxillae (MX) showing maxillary palp (MP), galea (G), stipes (ST), and cardo (CA), with galea showing the distribution of sensilla styloconica (S1–S4) and sensilla chaetica (C) in 4 species of Lepidoptera: A) Spodoptera litura, B) Chilo partellus, C) Plutella xylostella, and D) Maruca vitrata.
Fig. 16 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 16. Multiple sequence alignment of the deduced amino acid sequence of the partial Or83b gene of Spodoptera litura, Chilo partellus, Plutella xylostella, and Maruca vitrata with the reference sequence of Spodoptera litura Or83b (Accession No. AFN22085) using ClustalW sofware. Grey shades represent completely conserved residues.
Fig. 14 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 14. Phylogenetic tree produced for the Or83b amino acid sequences of lepidopteran species collected from the NCBI database and Or83b amino acid sequences of Spodoptera litura, Chilo partellus, Plutella xylostella, and Maruca vitrata generated in this study, analyzed using MEGA6 sofware. The rectangular boxes indicate the template sequences generated in this study.
Fig. 9 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 9. Mandible (M) showing sensilla chaetica (C1, C2) in 4 species of Lepidoptera: A) Spodoptera litura, B) Chilo partellus, C) Plutella xylostella, and D) Maruca vitrata.
Fig. 13 in Comparison of sensory structures present on larval antennae and mouthparts of lepidopteran crop pests
Fig. 13. Ventral labium (LI) surface of mouthparts showing hypopharynx (H), labial palp (LP), spinneret (SP), sensilla chaetica (C), and sensilla styloconica (S) in 4 species of Lepidoptera: A) Spodoptera litura, B) Chilo partellus, C) Plutella xylostella, and D) Maruca vitrata.
Fig. 1. Right antenna. A in Garypus sanasai Lin, Huang & Chang 2022, sp. nov.
Fig. 1. Right antenna. A, Lysiosquilla maculata (Fabricius, 1793) (formerly Lysiosquillina), male, TL 162 mm, Queensland, Australia, AM P14919; B, Lysiosquilla lisa (Ahyong & Randall, 2001) comb. nov. (formerly Lysiosquillina), male holotype, TL 295 mm, Bali, Indonesia, MZB Cru1444; C, Lysiosquilla suthersi Ahyong, 2001, male holotype, TL 150 mm, Queensland, Australia, QM W24225; D, Lysiosquilla scabricauda (Lamarck, 1818), male TL 210 mm, Key West Florida, AM P45739. Scale: A = 7.0 mm, B = 3.5 mm, C = 12.0 mm, D = 5.0 mm. Abbreviations: mesial papilla (mp), anteromesial lobe (aml).
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