OSA's Digital Library

Journal of the Optical Society of America A

Journal of the Optical Society of America A

| OPTICS, IMAGE SCIENCE, AND VISION

  • Editor: Franco Gori
  • Vol. 30, Iss. 9 — Sep. 1, 2013
  • pp: 1746–1759

Enhanced method for determining the optical response of highly complex biological photonic structures

Andrés E. Dolinko and Diana C. Skigin  »View Author Affiliations


JOSA A, Vol. 30, Issue 9, pp. 1746-1759 (2013)
http://dx.doi.org/10.1364/JOSAA.30.001746


View Full Text Article

Enhanced HTML    Acrobat PDF (1797 KB)





Browse Journals / Lookup Meetings

Browse by Journal and Year


   


Lookup Conference Papers

Close Browse Journals / Lookup Meetings

Article Tools

Share
Citations

Abstract

We present a set of techniques that enhances a previously developed time domain simulation of wave propagation and allows the study of the optical response of a broad range of dielectric photonic structures. This method is particularly suitable for dealing with complex biological structures, especially due to the simple and intuitive way of defining the setup and the photonic structure to be simulated, which can be done via a digital image of the structure. The presented techniques include a direction filter that permits the decoupling of waves traveling simultaneously in different directions, a dynamic differential absorber to cancel the waves reflected at the edges of the simulation space, and a multifrequency excitation scheme. We also show how the simulation can be adapted to apply a near to far field method in order to evaluate the resulting wavefield outside the simulation domain. We validate these techniques, and, as an example, we apply the method to the complex structure of a microorganism called Diachea leucopoda, which exhibits a multicolor iridescent appearance.

© 2013 Optical Society of America

OCIS Codes
(170.1420) Medical optics and biotechnology : Biology
(050.1755) Diffraction and gratings : Computational electromagnetic methods
(350.4238) Other areas of optics : Nanophotonics and photonic crystals
(050.6624) Diffraction and gratings : Subwavelength structures

ToC Category:
Diffraction and Gratings

History
Original Manuscript: March 22, 2013
Revised Manuscript: July 1, 2013
Manuscript Accepted: July 12, 2013
Published: August 6, 2013

Virtual Issues
Vol. 8, Iss. 10 Virtual Journal for Biomedical Optics

Citation
Andrés E. Dolinko and Diana C. Skigin, "Enhanced method for determining the optical response of highly complex biological photonic structures," J. Opt. Soc. Am. A 30, 1746-1759 (2013)
http://www.opticsinfobase.org/josaa/abstract.cfm?URI=josaa-30-9-1746


Sort:  Author  |  Year  |  Journal  |  Reset  

References

  1. V. G. Veselago, “The electrodynamics of substances with simultaneously negative values of ε and μ,” Sov. Phys. Usp. 10, 509–514 (1968). [CrossRef]
  2. J. B. Pendry, “Negative refraction makes a perfect lens,” Phys. Rev. Lett. 85, 3966–3969 (2000). [CrossRef]
  3. I. Tsukerman, “Negative refraction and the minimum lattice cell size,” J. Opt. Soc. Am. B 25, 927–936 (2008). [CrossRef]
  4. L. Jensen, Z. Lei, C. T. Chan, and P. Sheng, “Photonic band gap from a stack of positive and negative index materials,” Phys. Rev. Lett. 90, 083901 (2003). [CrossRef]
  5. A. Grbic and G. V. Eleftheriades, “Overcoming the diffraction limit with a planar left-handed transmission-line lens,” Phys. Rev. Lett. 92, 117403 (2004). [CrossRef]
  6. T. Ergin, N. Stenger, P. Brenner, J. B. Pendry, and M. Wegener, “Three-dimensional invisibility cloak at optical wavelengths,” Science 328, 337–339 (2010). [CrossRef]
  7. M. Settle, R. Engelen, M. Salib, A. Michaeli, L. Kuipers, and T. F. Krauss, “Flatband slow light in photonic crystals featuring spatial pulse compression and terahertz bandwidth,” Opt. Express 15, 219–226 (2007). [CrossRef]
  8. D. O’Brien, A. Gomez-Iglesias, M. D. Settle, A. Michaeli, M. Salib, and T. F. Krauss, “Tunable optical delay using photonic crystal heterostructure nanocavities,” Phys. Rev. B 76, 115110 (2007). [CrossRef]
  9. J. Valentine, J. Li, T. Zentgraf, G. Bartal, and X. Zhang, “An optical cloak made of dielectrics,” Nat. Mater. 8, 568–571 (2009). [CrossRef]
  10. J. Joannopoulos, R. Meade, and J. Winn, Photonic Crystals (Princeton University, 1995).
  11. P. Russell, “Photonic crystal fibers,” Science 299, 358–362 (2003). [CrossRef]
  12. S. Huntington, J. Katsifolis, B. Gibson, J. Canning, K. Lyytikainen, J. Zagari, L. Cahill, and J. Love, “Retaining and characterising nano-structure within tapered air-silica structured optical fibers,” Opt. Express 11, 98–104 (2003). [CrossRef]
  13. C. Martelli, J. Canning, B. Gibson, and S. Huntington, “Bend loss in structured optical fibres,” Opt. Express 15, 17639–17644 (2007). [CrossRef]
  14. P. Vukusic and J. R. Sambles, “Photonic structures in biology,” Nature 424, 852–855 (2003). [CrossRef]
  15. S. Kinoshita, Structural Colors in the Realm of Nature (World Scientific, 2008).
  16. S. Berthier, Iridescences, the Physical Colours of Insects (Springer, 2007).
  17. M. Inchaussandague, D. Skigin, C. Carmaran, and S. Rosenfeldt, “Structural color in myxomycetes,” Opt. Express 18, 16055–16063 (2010). [CrossRef]
  18. A. E. Luna, D. C. Skigin, M. Inchaussandague, and A. R. Alsina, “Structural color in beetles of South America,” Proc. SPIE 7782, 778205 (2010). [CrossRef]
  19. J. R. Andrewartha, J. R. Fox, and I. J. Wilson, “Resonance anomalies in the lamellar grating,” Opt. Acta 26, 69–89 (1979). [CrossRef]
  20. D. C. Skigin and R. A. Depine, “The multilayer modal method for electromagnetic scattering from surfaces with several arbitrarily shaped grooves,” J. Mod. Opt. 44, 1023–1036 (1997). [CrossRef]
  21. R. A. Depine and D. C. Skigin, “Multilayer modal method for diffraction from dielectric inhomogeneous apertures,” J. Opt. Soc. Am. A 15, 675–683 (1998). [CrossRef]
  22. M. G. Moharam and T. K. Gaylord, “Rigorous coupled-wave analysis of planar-grating diffraction,” J. Opt. Soc. Am. A 71, 811–818 (1981). [CrossRef]
  23. J. Chandezon, M. Dupuis, G. Cornet, and D. Maystre, “Multicoated gratings: a differential formalism applicable in the entire optical region,” J. Opt. Soc. Am. 72, 839–846 (1982). [CrossRef]
  24. R. A. Depine and M. E. Inchaussandague, “Corrugated diffraction gratings in uniaxial crystals,” J. Opt. Soc. Am. A 11, 173–180 (1994). [CrossRef]
  25. A. A. Maradudin, T. R. Michel, A. R. McGurn, and E. R. Méndez, “Enhanced backscattering of light from a random grating,” Ann. Phys. 203, 255–307 (1990). [CrossRef]
  26. M. Lester, D. C. Skigin, and R. A. Depine, “Blaze produced by a dual-period array of subwavelength cylinders,” J. Opt. A 11, 045705 (2009). [CrossRef]
  27. G. Schmidt and B. H. Kleemann, “Integral equation methods from grating theory to photonics: an overview and new approaches for conical diffraction,” J. Mod. Opt. 58, 407–423 (2011). [CrossRef]
  28. A. Taflove and S. C. Hagness, Computational Electrodynamics: The Finite-Difference Time-Domain Method, 3rd ed. (Artech, 2005).
  29. K. Yee, “Numerical solution of initial boundary value problems involving Maxwell’s equations in isotropic media,” IEEE Trans. Antennas Propag. 14, 302–307 (1966).
  30. A. F. Oskooi, D. Roundy, M. Ibanescu, P. Bermel, J. D. Joannopoulos, and S. G. Johnson, “MEEP: a flexible free-software package for electromagnetic simulations by the FDTD method,” Comput. Phys. Commun. 181, 687–702 (2010). [CrossRef]
  31. M. Kolle, Photonic Structures Inspired by Nature (Springer-Verlag, 2011).
  32. M. F. Su, I. El-Kady, D. A. Bader, and S. Lin, “A novel FDTD application featuring OpenMP-MPI hybrid parallelization,” in Proceedings of the 33rd International Conference on Parallel Processing (ICPP), Montreal, 2004, pp. 373–379.
  33. A. E. Dolinko, “From Newton’s second law to Huygens’s principle: visualizing waves in a large array of masses joined by springs,” Eur. J. Phys. 30, 1217–1228 (2009). [CrossRef]
  34. T.-H. Pei and Y.-T. Huang, “Effective refractive index of the photonic crystal deduced from the oscillation model of the membrane,” J. Opt. Soc. Am. B 29, 2334–2338 (2012). [CrossRef]
  35. C. E. Shannon, “Communication in the presence of noise,” Proc. Inst. Radio Eng. 37, 10–21 (1949). [CrossRef]
  36. R. Courant, K. Friedrichs, and H. Lewy, “Über die partiellen Differenzengleichungen der mathematischen Physik,” Math. Ann. 100, 32–74 (1928). [CrossRef]
  37. P. J. Cobelli, A. Maurel, V. Pagneux, and P. Petitjeans, “Global measurement of water waves by Fourier transform profilometry,” Exp. Fluids 46, 1037–1047 (2009). [CrossRef]
  38. J. Berenger, “A perfectly matched layer for the absorption of electromagnetic waves,” J. Comp. Physiol. 114, 185–200 (1994).
  39. B. Engquist and A. Majda, “Numerical absorbing boundary conditions for the wave equation,” Commun. Pure Appl. Math 32, 313–357 (1979). [CrossRef]
  40. R. L. Higdon, “Absorbing boundary conditions for difference approximations to the multi-dimensional wave equation,” Math. Comp. 47, 437–459 (1986).
  41. R. L. Higdon, “Numerical absorbing boundary conditions for the wave equation,” Math. Comp. 49, 65–90 (1987).
  42. B. Hennelly and J. T. Sheridan, “Generalizing, optimizing, and inventing numerical algorithms for the fractional Fourier, Fresnel, and linear canonical transforms,” J. Opt. Soc. Am. A 22, 917–927 (2005). [CrossRef]
  43. J. D. Jackson, Classical Electrodynamics, 3rd ed. (Wiley, 1998).
  44. A. Dolinko, D. Skigin, M. Inchaussandague, and C. Carmaran, “Photonic simulation method applied to the study of structural color in myxomycetes,” Opt. Express 20, 15139–15148 (2012). [CrossRef]

Cited By

Alert me when this paper is cited

OSA is able to provide readers links to articles that cite this paper by participating in CrossRef's Cited-By Linking service. CrossRef includes content from more than 3000 publishers and societies. In addition to listing OSA journal articles that cite this paper, citing articles from other participating publishers will also be listed.


« Previous Article  |  Next Article »

OSA is a member of CrossRef.

CrossCheck Deposited