Abstract

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

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    [Crossref]
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2011 (5)

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. Photonics 5, 230–233 (2011).
[Crossref]

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. Lett 36, 3173–3175 (2011).
[Crossref] [PubMed]

Y. Dumeige, “Quasi-phase-matching and second-harmonic generation enhancement in a semiconductor microresonator array using slow-light effects,” Phys Rev A 83, 045802 (2011).
[Crossref]

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 Express 19, 7094–7105 (2011).
[Crossref] [PubMed]

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 II 8074, 807417 (2011).

2010 (4)

M. Notomi, “Manipulating light with strongly modulated photonic crystals,” Rep. Prog. Phys. 73, 096501 (2010).
[Crossref]

A. C. Selden, “Practical tests for distinguishing slow light from saturable absorption,” Opt. Express 18, 13204–13211 (2010).
[Crossref] [PubMed]

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]

V. S. Zapasskii and G. G. Kozlov, “On two models of light pulse delay in saturable absorber,” Opt. Spectrosc. 109, 407–412 (2010).
[Crossref]

2009 (4)

R. W. Boyd, “Slow and fast light: fundamentals and applications,” J. Mod. Opt. 56, 1908–1915 (2009).
[Crossref]

R. W. Boyd and D. J. Gauthier, “Controlling the velocity of light pulses,” Science 326, 1074–1077 (2009).
[Crossref] [PubMed]

G. S. Agarwal and T. N. Dey, “Non-electromagnetically induced transparency mechanisms for slow light,” Laser Photonics Rev 3, 287–300 (2009).
[Crossref]

A. C. Selden, “Slow light and saturable absorption,” Opt. Spectrosc. 106, 881–888 (2009).
[Crossref]

2008 (5)

B. Macke and B. Segard, “Slow light in saturable absorbers,” Phys Rev A 78, 013817 (2008).
[Crossref]

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. Express 16, 3844–3852 (2008).
[Crossref] [PubMed]

L. Thevenaz, “Slow and fast light in optical fibres,” Nat. Photonics 2, 474–481 (2008).
[Crossref]

L. V. Hau, “Optical information processing in Bose-Einstein condensates,” Nat. Photonics 2, 451–453 (2008).
[Crossref]

T. Baba, “Slow light in photonic crystals,” Nat. Photonics 2, 465–473 (2008).
[Crossref]

2007 (6)

R. M. Camacho, C. J. Broadbent, I. Ali-Khan, and J. C. Howell, “All-optical delay of images using slow light,” Phys Rev Lett 98, 043902 (2007).
[Crossref]

Z. Shi, R. W. Boyd, R. M. Camacho, P. K. Vudyasetu, and J. C. Howell, “Slow-light fourier transform interferometer.” Phys Rev Lett 99, 240801(1–4) (2007).
[Crossref]

F. N. Xia, L. Sekaric, and Y. Vlasov, “Ultracompact optical buffers on a silicon chip,” Nat. Photonics 1, 65–71 (2007).
[Crossref]

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]

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]

P. Acebal, L. Carretero, S. Blaya, A. Murciano, and A. Fimia, “Theoretical approach to photoinduced inhomogeneous anisotropy in bacteriorhodopsin films,” Phys Rev E 76, 016608 (2007).
[Crossref]

2006 (2)

V. S. Zapasskii and G. G. Kozlov, “A saturable absorber, coherent population oscillations, and slow light,” Opt. Spectrosc. 100, 419–424 (2006).
[Crossref]

R. M. Camacho, M. V. Pack, and J. C. Howell, “Low-distortion slow light using two absorption resonances,” Phys Rev A 73, 063812 (2006).
[Crossref]

2005 (5)

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,” Nature 438, 65–69 (2005).
[Crossref] [PubMed]

J. B. Khurgin, “Optical buffers based on slow light in electromagnetically induced transparent media and coupled resonator structures: comparative analysis,” J. Opt. Soc Am B 22, 1062–1074 (2005).
[Crossref]

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]

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 B 4A–4B, 1–4 (2005).

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 E 72, 011909 (2005).
[Crossref]

2004 (3)

D. D. Smith, H. Chang, K. A. Fuller, A. T. Rosenberger, and R. W. Boyd, “Coupled-resonator-induced transparency,” Phys Rev A 69, 063804(1–6) (2004).
[Crossref]

M. S. Bigelow, N. N. Lepeshkin, and R. W. Boyd, “Ultra-slow and superluminal light propagation in solids at room temperature,” J. Phys-Cond Mat 16, R1321–R1340 (2004).
[Crossref]

G. S. Agarwal and T. N. Dey, “Sub- and superluminal propagation of intense pulses in media with saturated and reverse absorption,” Phys Rev Lett 92, 203901 (2004).
[Crossref] [PubMed]

2003 (3)

M. S. Bigelow, N. N. Lepeshkin, and R. W. Boyd, “Superluminal and slow light propagation in a room-temperature solid,” Science 301, 200–202 (2003).
[Crossref] [PubMed]

M. S. Bigelow, N. N. Lepeshkin, and R. W. Boyd, “Observation of ultraslow light propagation in a ruby crystal at room temperature,” Phys Rev Lett 90, 113903 (2003).
[Crossref] [PubMed]

M. D. Lukin, “Colloquium: Trapping and manipulating photon states in atomic ensembles,” Rev Mod Phys 75, 457–472 (2003).
[Crossref]

2002 (1)

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]

2000 (1)

E. Korchemskaya, D. Stepanchikov, and T. Dyukova, “Photoinduced anisotropy in chemically-modified films of bacteriorhodopsin and its genetic mutants,” Opt. Mater 14, 185–191 (2000).
[Crossref]

1999 (1)

A. Yariv, Y. Xu, R. K. Lee, and A. Scherer, “Coupled-resonator optical waveguide: a proposal and analysis,” Opt. Lett 24, 711–713 (1999).
[Crossref]

1996 (1)

1995 (1)

A. Kasapi, M. Jain, G. Y. Yin, and S. E. Harris, “Electromagnetically induced transparency - propagation dynamics,” Phys Rev Lett 74, 2447–2450 (1995).
[Crossref] [PubMed]

1993 (1)

1992 (1)

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]

1989 (1)

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]

1969 (1)

1967 (1)

A. C. Selden, “Pulse transmission through a saturable absorber,” Brit. J. Appl. Phys. 18, 743–748 (1967).
[Crossref]

1935 (1)

H. Eyring, “The activated complex and the absolute rate of chemical reactions,” Chem. Rev. 17, 65–77 (1935).
[Crossref]

Acebal, P.

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 Express 19, 7094–7105 (2011).
[Crossref] [PubMed]

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 II 8074, 807417 (2011).

P. Acebal, L. Carretero, S. Blaya, A. Murciano, and A. Fimia, “Theoretical approach to photoinduced inhomogeneous anisotropy in bacteriorhodopsin films,” Phys Rev E 76, 016608 (2007).
[Crossref]

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 B 4A–4B, 1–4 (2005).

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 E 72, 011909 (2005).
[Crossref]

Adamo, C.

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.

Agarwal, G. S.

G. S. Agarwal and T. N. Dey, “Non-electromagnetically induced transparency mechanisms for slow light,” Laser Photonics Rev 3, 287–300 (2009).
[Crossref]

G. S. Agarwal and T. N. Dey, “Sub- and superluminal propagation of intense pulses in media with saturated and reverse absorption,” Phys Rev Lett 92, 203901 (2004).
[Crossref] [PubMed]

Akopian, N.

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. Photonics 5, 230–233 (2011).
[Crossref]

Ali-Khan, I.

R. M. Camacho, C. J. Broadbent, I. Ali-Khan, and J. C. Howell, “All-optical delay of images using slow light,” Phys Rev Lett 98, 043902 (2007).
[Crossref]

Al-Laham, M. A.

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.

Andres, J. L.

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.

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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.

Baba, T.

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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.

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M. S. Bigelow, N. N. Lepeshkin, and R. W. Boyd, “Ultra-slow and superluminal light propagation in solids at room temperature,” J. Phys-Cond Mat 16, R1321–R1340 (2004).
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Birge, R. R.

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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 Express 19, 7094–7105 (2011).
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P. Acebal, L. Carretero, S. Blaya, A. Murciano, and A. Fimia, “Theoretical approach to photoinduced inhomogeneous anisotropy in bacteriorhodopsin films,” Phys Rev E 76, 016608 (2007).
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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 B 4A–4B, 1–4 (2005).

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 E 72, 011909 (2005).
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Blumer, R.

Boyd, R. W.

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Z. Shi, R. W. Boyd, R. M. Camacho, P. K. Vudyasetu, and J. C. Howell, “Slow-light fourier transform interferometer.” Phys Rev Lett 99, 240801(1–4) (2007).
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D. D. Smith, H. Chang, K. A. Fuller, A. T. Rosenberger, and R. W. Boyd, “Coupled-resonator-induced transparency,” Phys Rev A 69, 063804(1–6) (2004).
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M. S. Bigelow, N. N. Lepeshkin, and R. W. Boyd, “Ultra-slow and superluminal light propagation in solids at room temperature,” J. Phys-Cond Mat 16, R1321–R1340 (2004).
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M. S. Bigelow, N. N. Lepeshkin, and R. W. Boyd, “Superluminal and slow light propagation in a room-temperature solid,” Science 301, 200–202 (2003).
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M. S. Bigelow, N. N. Lepeshkin, and R. W. Boyd, “Observation of ultraslow light propagation in a ruby crystal at room temperature,” Phys Rev Lett 90, 113903 (2003).
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Broadbent, C. J.

R. M. Camacho, C. J. Broadbent, I. Ali-Khan, and J. C. Howell, “All-optical delay of images using slow light,” Phys Rev Lett 98, 043902 (2007).
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Bruchle, C.

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).
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Burant, J. C.

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.

Cai, Y. X.

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. Lett 36, 3173–3175 (2011).
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Camacho, R. M.

Z. Shi, R. W. Boyd, R. M. Camacho, P. K. Vudyasetu, and J. C. Howell, “Slow-light fourier transform interferometer.” Phys Rev Lett 99, 240801(1–4) (2007).
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R. M. Camacho, C. J. Broadbent, I. Ali-Khan, and J. C. Howell, “All-optical delay of images using slow light,” Phys Rev Lett 98, 043902 (2007).
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R. M. Camacho, M. V. Pack, and J. C. Howell, “Low-distortion slow light using two absorption resonances,” Phys Rev A 73, 063812 (2006).
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Cammi, R.

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.

Carreno, F.

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).
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Carretero, L.

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 Express 19, 7094–7105 (2011).
[Crossref] [PubMed]

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 II 8074, 807417 (2011).

P. Acebal, L. Carretero, S. Blaya, A. Murciano, and A. Fimia, “Theoretical approach to photoinduced inhomogeneous anisotropy in bacteriorhodopsin films,” Phys Rev E 76, 016608 (2007).
[Crossref]

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 B 4A–4B, 1–4 (2005).

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 E 72, 011909 (2005).
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Challacombe, M.

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.

Chang, H.

D. D. Smith, H. Chang, K. A. Fuller, A. T. Rosenberger, and R. W. Boyd, “Coupled-resonator-induced transparency,” Phys Rev A 69, 063804(1–6) (2004).
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Cheeseman, J. R.

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.

Chen, W.

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.

Chen, Z.

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).
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Cioslowski, J.

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.

Clifford, S.

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.

Cossi, M.

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.

Cui, Q.

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.

Daniels, A. D.

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Dapprich, S.

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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.

Liu, G.

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.

Lukin, M. D.

M. D. Lukin, “Colloquium: Trapping and manipulating photon states in atomic ensembles,” Rev Mod Phys 75, 457–472 (2003).
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Macke, B.

B. Macke and B. Segard, “Slow light in saturable absorbers,” Phys Rev A 78, 013817 (2008).
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Madrigal, R.

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 Express 19, 7094–7105 (2011).
[Crossref] [PubMed]

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 II 8074, 807417 (2011).

Madrigal, R. F.

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 B 4A–4B, 1–4 (2005).

Malick, D. K.

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.

Marcy, D. L.

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).
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Martin, R. L.

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.

May, V.

V. May and O. Khn, Charge and energy transfer dynamics in molecular system (Wiley-VCH, 2000).

McNab, S. J.

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,” Nature 438, 65–69 (2005).
[Crossref] [PubMed]

Menucci, B.

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.

Millam, J. M.

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.

Montgomery, J. A.

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.

Morokuma, K.

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.

Murciano, A.

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 II 8074, 807417 (2011).

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 Express 19, 7094–7105 (2011).
[Crossref] [PubMed]

P. Acebal, L. Carretero, S. Blaya, A. Murciano, and A. Fimia, “Theoretical approach to photoinduced inhomogeneous anisotropy in bacteriorhodopsin films,” Phys Rev E 76, 016608 (2007).
[Crossref]

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 B 4A–4B, 1–4 (2005).

Nanayakkara, A.

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.

Notomi, M.

M. Notomi, “Manipulating light with strongly modulated photonic crystals,” Rep. Prog. Phys. 73, 096501 (2010).
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O’Boyle, M.

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,” Nature 438, 65–69 (2005).
[Crossref] [PubMed]

Ochterski, J.

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.

Oesterhelt, D.

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).
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Ortiz, J. V.

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.

Pack, M. V.

R. M. Camacho, M. V. Pack, and J. C. Howell, “Low-distortion slow light using two absorption resonances,” Phys Rev A 73, 063812 (2006).
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Peng, C. Y.

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.

Penney, C.

Petereson, G. A.

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.

Philip, R.

Piskorz, P.

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.

Pomelli, C.

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.

Pople, J. A.

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.

Popp, A.

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).
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Rabuck, A. D.

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Figures (10)

Fig. 1
Fig. 1

Schematic representation of the bacteriorhodopsin structure and its photocycles.

Fig. 2
Fig. 2

The experimental setup used to analyze the propagation of sinusoidal pulses in bacteriorhodopsin film.

Fig. 3
Fig. 3

Temporal variation of the pump beam with an intensity of 2650 W/m2 and a wavelength of 532 nm. The points are the experimental data, the blue line represents the results obtained by the rigorous theory and the red one corresponds to the two level approximation, where it has been used the parameters shown in table 1

Fig. 4
Fig. 4

Temporal variation of the sinusoidal modulated beam (signal) with an intensity of 84 W/m2 and a wavelength of 532 nm. The points are the experimental data, the blue line represents the results obtained by the rigorous theory and the red one corresponds to the two level approximation, where it has been used the parameters shown in table 1

Fig. 5
Fig. 5

Temporal variation of different peaks of the sinusoidal modulated beam (signal) with an intensity of 84 W/m2 and a wavelength of 532 nm. The yellow line is the experimental reference beam, the blue line represents the results obtained by the rigorous theory and the red one corresponds to the two level approximation, where it has been used the parameters shown in table 1

Fig. 6
Fig. 6

Temporal variation of the normalized population densities (nX) at different layers of the bacteriorhodopsin film obtained by the rigorous model. It has been analyzed the case of a pump beam intensity of 2650 W/m2 and sinusoidal modulated beam (signal) with an intensity of 84 W/m2. As before, the wavelength of both beams were 532 nm and it has been used the parameters shown in table 1.

Fig. 7
Fig. 7

Theoretical variation of the delay of sinusoidal modulated beam (signal) as a function of the modulation frequency obtained by the rigorous model. It has been analyzed the case of a signal intensity of 84 W/m2 and pump of 2650 W/m2 with wavelength of 532 nm both. As before, it has been used the parameters shown in table 1.

Fig. 8
Fig. 8

Theoretical and experimental variation of the delay of sinusoidal modulated beam (signal) as a function of the pump intensity obtained by the rigorous model. It has been analyzed the case of a signal intensity of 5 % of the pump beam and the wavelength of both beams were 532 nm. As before, it has been used the parameters shown in table 1.

Fig. 9
Fig. 9

Theoretical variation of the delay of sinusoidal modulated beam (signal) as a function of the pump intensity obtained by the rigorous model. It has been analyzed the case of a signal intensity of 84 W/m2 and the wavelength of both beams were 532 nm. As before, it has been used the parameters shown in table 1.

Fig. 10
Fig. 10

Temporal variation of the normalized population densities (nX) at different layers of the bacteriorhodopsin film obtained by the rigorous model. It has been analyzed the case of a modulation frequency of 0.3 π Hz and sinusoidal modulated beam (signal) with an intensity of 5% of the pump beam. As before, the wavelength of both beams were 532 nm and it has been used the parameters shown in Table 1.

Tables (1)

Tables Icon

Table 1 Values for the microscopic optical properties of the different states of bR (μ1g and λ1g from references [45, 46]). γ=Γ/2.355=2×1014s−1, α0=2.76×10−26m3 and rate constants at 293 K are: kkl=2300 s−1, klm=169 s−1, kmn=0.98 s−1, kno=110 s−1, kob=5.2 s−1, klk=230 s−1, kml=64.6 s−1, knm=40 s−1, kon=0.1 s−1.

Equations (20)

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I a ( ζ , t ) ζ = ( β a a ( ζ , t ) + β a a R ( ζ , t ) ) I a ( ζ , t )
β a a ( ω , ζ , t ) = κ i 3 N i a κ ( ζ , t ) σ i i κ ( ω )
β a a R ( ω , ζ , t ) = κ i 3 N i a κ ( ζ , t ) σ i i , R κ ( ω ) + i 3 N i a m σ i i , R m
B = A n ia
A = ( Φ i a B Φ i a K Φ i a L 0 Φ i a N k o b Φ i a B ( Φ i a K + k k l ) k l k 0 0 0 0 k k l ( Φ i a L + k l k + k l m ) k m l 0 0 0 0 k l m ( k m l + k m n ) k n m 0 0 0 0 k m n ( Φ i a N + k n m + k n o ) k o n 1 1 1 1 1 1 )
Φ i a κ = ϕ κ h ¯ ω σ i i κ I a
k 1 = K B T 1 h ( h k 0 K B T 0 ) T 0 / T 1
T = T 0 + a i n ( 1 i b i e c i t ) a d e ( 1 i h i e g i t )
σ i i κ ( ω ) = ω ( μ e g , i κ ) 2 c h ¯ ε 0 Exp [ ( ω ω e g κ ) 2 2 γ 2 ] 2 π γ
σ i i , R κ ( ω ) = 24 π ( α i i κ ( ω ) ) 2 ω 4 9 c 4
α ^ κ = α 0 . I ^ + α ^ C κ
α i i C κ ( ω ) e , e 1 α i i , e C κ ( 0 ) + α i i , 1 C κ ( 0 ) Ω 1 C κ ( ω ; ω )
α i i , e C κ ( 0 ) = 2 ( μ e g , i κ ) 2 h ¯ ε 0 ω e g κ
Ω 1 C κ ( ω ; ω ) = ( ω 1 g κ ) 2 ( ( ω 1 g κ ) 2 ω 2 ) ( ( ω 1 g κ ) 2 ω 2 ) 2 + Γ 2 ω 2
I a [ j ] = I a [ j 1 ] e ( κ i 3 N i a κ ( j , t ) ( σ i i κ ( ω ) + σ i i , R κ ( ω ) ) + i 3 N i a m σ i i , R m ) Δ ζ
I a = I a 0 + I a 1 Sin ( δ t ) 2
n i a B t = ξ B n i a B + ξ M n i a M
1 = n i a B + n i a M
ξ B = k k l k l m Φ i a B k l k Φ i a K + ( k k l + Φ i a K ) ( k l m + Φ i a L )
ξ M = k m l + k m n k m n k n m ( k o b + k o n ) k n o k o b + k n m ( k o b + k o n ) + ( k o b + k o n ) Φ i a N k l m k m l ( k k l + Φ i a K ) k l k Φ i a K + ( k k l + Φ i a K ) ( k l m + Φ i a L )

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