OSA's Digital Library

Virtual Journal for Biomedical Optics

Virtual Journal for Biomedical Optics


  • Editors: Andrew Dunn and Anthony Durkin
  • Vol. 7, Iss. 12 — Dec. 19, 2012

Rigorous analysis of the propagation of sinusoidal pulses in bacteriorhodopsin films

Pablo Acebal, Salvador Blaya, Luis Carretero, R. F. Madrigal, and A. Fimia  »View Author Affiliations

Optics Express, Vol. 20, Issue 23, pp. 25497-25512 (2012)

View Full Text Article

Enhanced HTML    Acrobat PDF (1061 KB) Open Access

Browse Journals / Lookup Meetings

Browse by Journal and Year


Lookup Conference Papers

Close Browse Journals / Lookup Meetings

Article Tools



The propagation of sinusoidal pulses in bacteriorhodopsin films has been theoretically analyzed using a complete study of the photoinduced processes that take into account all the physical parameters, the coupling of rate equations with the energy transfer equation and the temperature change during the experiment. The theoretical approach was compared to experimental data and a good concordance was observed. This theoretical treatment, can be widely applied, i.e when arbitrary pump and/or signal is used or in the case of the pump and signal beams have different wavelengths. Due to we have performed a rigorous analysis, from this treatment the corresponding two level approximation has also been analyzed for these systems.

© 2012 OSA

OCIS Codes
(190.4710) Nonlinear optics : Optical nonlinearities in organic materials
(190.5530) Nonlinear optics : Pulse propagation and temporal solitons
(160.1435) Materials : Biomaterials

ToC Category:
Nonlinear Optics

Original Manuscript: August 27, 2012
Revised Manuscript: October 1, 2012
Manuscript Accepted: October 1, 2012
Published: October 25, 2012

Virtual Issues
Vol. 7, Iss. 12 Virtual Journal for Biomedical Optics

Pablo Acebal, Salvador Blaya, Luis Carretero, R. F. Madrigal, and A. Fimia, "Rigorous analysis of the propagation of sinusoidal pulses in bacteriorhodopsin films," Opt. Express 20, 25497-25512 (2012)

Sort:  Author  |  Year  |  Journal  |  Reset  


  1. J. B. Khurgin, “Optical buffers based on slow light in electromagnetically induced transparent media and coupled resonator structures: comparative analysis,” J. Opt. Soc Am B22, 1062–1074 (2005). [CrossRef]
  2. F. N. Xia, L. Sekaric, and Y. Vlasov, “Ultracompact optical buffers on a silicon chip,” Nat. Photonics1, 65–71 (2007). [CrossRef]
  3. M. A. Anton and F. Carreno, “Quantum memory and all-optical switching in positive charged quantum dots via Zeeman coherent oscillations,” J. Opt.12, 104006 (2010). [CrossRef]
  4. N. Akopian, L. Wang, A. Rastelli, O. G. Schmidt, and V. Zwiller, “Hybrid semiconductor-atomic interface: slowing down single photons from a quantum dot rid f-4017-2010,” Nat. Photonics5, 230–233 (2011). [CrossRef]
  5. Z. Shi, R. W. Boyd, R. M. Camacho, P. K. Vudyasetu, and J. C. Howell, “Slow-light fourier transform interferometer.” Phys Rev Lett99, 240801(1–4) (2007). [CrossRef]
  6. J. F. Wang, Y. D. Zhang, X. N. Zhang, H. Tian, H. Wu, Y. X. Cai, J. Zhang, and P. Yuan, “Enhancing the sensitivity of fiber Mach-Zehnder interferometers using slow and fast light,” Opt. Lett36, 3173–3175 (2011). [CrossRef] [PubMed]
  7. Y. Dumeige, “Quasi-phase-matching and second-harmonic generation enhancement in a semiconductor microresonator array using slow-light effects,” Phys Rev A83, 045802 (2011). [CrossRef]
  8. R. W. Boyd, “Slow and fast light: fundamentals and applications,” J. Mod. Opt.56, 1908–1915 (2009). [CrossRef]
  9. R. W. Boyd and D. J. Gauthier, “Controlling the velocity of light pulses,” Science326, 1074–1077 (2009). [CrossRef] [PubMed]
  10. G. S. Agarwal and T. N. Dey, “Non-electromagnetically induced transparency mechanisms for slow light,” Laser Photonics Rev3, 287–300 (2009). [CrossRef]
  11. A. Kasapi, M. Jain, G. Y. Yin, and S. E. Harris, “Electromagnetically induced transparency - propagation dynamics,” Phys Rev Lett74, 2447–2450 (1995). [CrossRef] [PubMed]
  12. M. D. Lukin, “Colloquium: Trapping and manipulating photon states in atomic ensembles,” Rev Mod Phys75, 457–472 (2003). [CrossRef]
  13. L. V. Hau, “Optical information processing in Bose-Einstein condensates,” Nat. Photonics2, 451–453 (2008). [CrossRef]
  14. M. S. Bigelow, N. N. Lepeshkin, and R. W. Boyd, “Superluminal and slow light propagation in a room-temperature solid,” Science301, 200–202 (2003). [CrossRef] [PubMed]
  15. M. S. Bigelow, N. N. Lepeshkin, and R. W. Boyd, “Observation of ultraslow light propagation in a ruby crystal at room temperature,” Phys Rev Lett90, 113903 (2003). [CrossRef] [PubMed]
  16. R. M. Camacho, M. V. Pack, and J. C. Howell, “Low-distortion slow light using two absorption resonances,” Phys Rev A73, 063812 (2006). [CrossRef]
  17. R. M. Camacho, C. J. Broadbent, I. Ali-Khan, and J. C. Howell, “All-optical delay of images using slow light,” Phys Rev Lett98, 043902 (2007). [CrossRef]
  18. Y. A. Vlasov, M. O’Boyle, H. F. Hamann, and S. J. McNab, “Active control of slow light on a chip with photonic crystal waveguides,” Nature438, 65–69 (2005). [CrossRef] [PubMed]
  19. T. Baba, “Slow light in photonic crystals,” Nat. Photonics2, 465–473 (2008). [CrossRef]
  20. M. Notomi, “Manipulating light with strongly modulated photonic crystals,” Rep. Prog. Phys.73, 096501 (2010). [CrossRef]
  21. A. Yariv, Y. Xu, R. K. Lee, and A. Scherer, “Coupled-resonator optical waveguide: a proposal and analysis,” Opt. Lett24, 711–713 (1999). [CrossRef]
  22. D. D. Smith, H. Chang, K. A. Fuller, A. T. Rosenberger, and R. W. Boyd, “Coupled-resonator-induced transparency,” Phys Rev A69, 063804(1–6) (2004). [CrossRef]
  23. L. Carretero, S. Blaya, P. Acebal, A. Fimia, R. Madrigal, and A. Murciano, “Coupled wave analysis of holographically induced transparency (HIT) generated by two multiplexed volume gratings,” Opt Express19, 7094–7105 (2011). [CrossRef] [PubMed]
  24. L. Carretero, S. Blaya, A. Murciano, P. Acebal, A. Fimia, and R. Madrigal, “Coupled-wave theory analysis of holographic structures for slow-light applications,” Holography: Advances and Modern Trends II8074, 807417 (2011).
  25. Z. M. Zhu, A. M. C. Dawes, D. J. Gauthier, L. Zhang, and A. E. Willner, “Broadband SBS slow light in an optical fiber,” J. Lightwave Technol.25, 201–206 (2007). [CrossRef]
  26. L. Thevenaz, “Slow and fast light in optical fibres,” Nat. Photonics2, 474–481 (2008). [CrossRef]
  27. P. F. Wu and D. V. G. L. N. Rao, “Controllable snail-paced light in biological bacteriorhodopsin thin film,” Phys Rev Lett.95, 253601 (2005). [CrossRef] [PubMed]
  28. C. S. Yelleswarapu, R. Philip, F. J. Aranda, B. R. Kimball, and D. V. G. L. N. Rao, “Slow light in bacteriorhodopsin solution using coherent population oscillations,” Opt. Lett.32, 1788–1790 (2007). [CrossRef] [PubMed]
  29. C. S. Yelleswarapu, S. Laoui, R. Philip, and D. V. G. L. N. Rao, “Coherent population oscillations and superluminal light in a protein complex,” Opt. Express16, 3844–3852 (2008). [CrossRef] [PubMed]
  30. V. S. Zapasskii and G. G. Kozlov, “A saturable absorber, coherent population oscillations, and slow light,” Opt. Spectrosc.100, 419–424 (2006). [CrossRef]
  31. B. Macke and B. Segard, “Slow light in saturable absorbers,” Phys Rev A78, 013817 (2008). [CrossRef]
  32. A. C. Selden, “Slow light and saturable absorption,” Opt. Spectrosc.106, 881–888 (2009). [CrossRef]
  33. A. C. Selden, “Practical tests for distinguishing slow light from saturable absorption,” Opt. Express18, 13204–13211 (2010). [CrossRef] [PubMed]
  34. A. C. Selden, “Pulse transmission through a saturable absorber,” Brit. J. Appl. Phys.18, 743–748 (1967). [CrossRef]
  35. M. S. Bigelow, N. N. Lepeshkin, and R. W. Boyd, “Ultra-slow and superluminal light propagation in solids at room temperature,” J. Phys-Cond Mat16, R1321–R1340 (2004). [CrossRef]
  36. G. S. Agarwal and T. N. Dey, “Sub- and superluminal propagation of intense pulses in media with saturated and reverse absorption,” Phys Rev Lett92, 203901 (2004). [CrossRef] [PubMed]
  37. P. Acebal, L. Carretero, S. Blaya, A. Murciano, and A. Fimia, “Theoretical approach to photoinduced inhomogeneous anisotropy in bacteriorhodopsin films,” Phys Rev E76, 016608 (2007). [CrossRef]
  38. N. Hampp, A. Popp, C. Bruchle, and D. Oesterhelt, “Diffraction efficiency of bacteriorhodopsin films for holography containing bacteriorhodopsin wildtype BRWT and its variants BRD85E and BRD96N,” J. Phys. Chem. pp. 4679–4685 (1992). [CrossRef]
  39. J. D. Downie and D. T. Smithey, “Measurements of holographic properties of bacteriorhodopsin films,” Appl. Opt.35, 5780–5789 (1996). [CrossRef] [PubMed]
  40. Q. W. Song, C. Zhang, R. Blumer, R. B. Gross, Z. Chen, and R. Birge, “Chemically enhanced bacteriorhodopsin thin-film spatial light modulator,” Opt. Lett.18, 1373–1375 (1993). [CrossRef] [PubMed]
  41. E. Korchemskaya, D. Stepanchikov, and T. Dyukova, “Photoinduced anisotropy in chemically-modified films of bacteriorhodopsin and its genetic mutants,” Opt. Mater14, 185–191 (2000). [CrossRef]
  42. H. Eyring, “The activated complex and the absolute rate of chemical reactions,” Chem. Rev.17, 65–77 (1935). [CrossRef]
  43. V. May and O. Khn, Charge and energy transfer dynamics in molecular system (Wiley-VCH, 2000).
  44. C. Penney, “Light scattering in term of oscillator strenghts and refractive indices,” J. Opt. Soc. Am.59, 34–42 (1969). [CrossRef]
  45. J. Y. Huang, Z. Chen, and A. Lewis, “Second-harmonic generation in purple membrane-poly(vinyl alcohol) films: probing the dipolar characteristics of the bacteriorhodopsin chromophore in bR570 and M412,” J. Phys. Chem.93, 3314–3320 (1989). [CrossRef]
  46. J. A. Stuart, D. L. Marcy, K. J. Wise, and R. R. Birge, “Volumetric optical memory based on bacterirhodopsin,” Synth. Met.127, 3–15 (2002). [CrossRef]
  47. P. Acebal, L. Carretero, S. Blaya, R. F. Madrigal, A. Murciano, and A. Fimia, “Simulation of diffraction efficiency in oriented bacteriorhodopsin films,” Advances in Computational Methods in Sciences and Engineering 2005, Vols 4 A & 4 B4A–4B, 1–4 (2005).
  48. P. Acebal, S. Blaya, L. Carretero, and A. Fimia, Upper limits of dielectric permittivity modulation in bacteriorhodopsin films “Upper limits of dielectric permittivity modulation in bacteriorhodopsin films,” Phys Rev E72, 011909 (2005). [CrossRef]
  49. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Menucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petereson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P. M. W. Gill, B. G. Johnson, W. Chen, M. W. Wong, J. L. Andres, M. Head-Gordon, E. S. Replogle, and J. A. Pople, GAUSSIAN 98, Revision A.7, Gaussian, Inc, Pittsburg PA, 1998.
  50. V. S. Zapasskii and G. G. Kozlov, “On two models of light pulse delay in saturable absorber,” Opt. Spectrosc.109, 407–412 (2010). [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