Abstract

We theoretically analyze the effect of probe beam intensity on all-optical switching based on nonlinear absorption, using the pump-probe configuration. To draw general inferences that are applicable to a wide range of polyatomic molecules, we consider as a typical example, switching in pharaonis phoborhodopsin (ppR) protein and its mutants that exhibit a complex photocycle similar to bacteriorhodopsin (bR), having a number of intermediates with respective absorption spectra spanning the entire visible region. The switching of the transmission of a cw probe beam by a pulsed pump beam has been studied in detail at different wavelength combinations. Interesting consequences emerge from the present analysis. It is shown that by controlling the probe intensity, the switching characteristics can be inverted, switching time can be reduced and the profile of the switched probe beam and the switching contrast can be controlled. For some cases, the switching contrast can also be maximized by optimizing the probe intensity. Increase in probe intensity also leads to increase in switching contrast under certain conditions. At particular spectral and kinetic conditions, the nonlinear optical material appears linear for a given probe intensity and pump-probe wavelengths, respectively. Variation in probe intensity thus provides an effective means to modify the switching characteristics instead of using mutants with different rate constants for a variety of nonlinear absorption based all-optical devices.

© 2012 OSA

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    [CrossRef] [PubMed]

2012 (2)

M. Hari, S. Mathew, B. Nithyaja, S. A. Joseph, V. P. N. Nampoori, and P. Radhakrishnan, “Saturable and reverse saturable absorption in aqueous silver nanoparticles at off-resonant wavelngth,” Opt. Quantum Electron.43(1-5), 49–58 (2012).
[CrossRef]

S. Roy, P. Sethi, J. Topolancik, and F. Vollmer, “All-optical reversible logic gates with bacteriorhodopsin protein coated microresonators,” Adv. Opt. Technol.2012, 727206 (2012).
[CrossRef]

2011 (6)

A. Charas, A. L. Mendonça, J. Clark, L. Bazzana, A. Nocivelli, G. Lanzani, and J. Morgado, “Stimulated emission and ultrafast optical switching in a ter(9,9′-spirobifluorene)-co-methylmethacrylate copolymer,” J. Polym. Sci., B, Polym. Phys.49(1), 52–61 (2011).
[CrossRef]

G. A. Wurtz, R. Pollard, W. Hendren, G. P. Wiederrecht, D. J. Gosztola, V. A. Podolskiy, and A. V. Zayats, “Designed ultrafast optical nonlinearity in a plasmonic nanorod metamaterial enhanced by nonlocality,” Nat. Nanotechnol.6(2), 107–111 (2011).
[CrossRef] [PubMed]

S. Roy and C. Yadav, “All-optical ultrafast logic gates based on saturable to reverse saturable absorption transition in CuPc-doped PMMA thin films,” Opt. Commun.284(19), 4435–4440 (2011).
[CrossRef]

R. R. Dasari, M. M. Sartin, M. Cozzuol, S. Barlow, J. W. Perry, and S. R. Marder, “Synthesis and linear and nonlinear absorption properties of dendronised ruthenium(II) phthalocyanine and naphthalocyanine,” Chem. Commun. (Camb.)47(15), 4547–4549 (2011).
[CrossRef] [PubMed]

G. S. He, J. Zhu, A. Baev, M. Samoć, D. L. Frattarelli, N. Watanabe, A. Facchetti, H. Ågren, T. J. Marks, and P. N. Prasad, “Twisted π-system chromophores for all-optical switching,” J. Am. Chem. Soc.133(17), 6675–6680 (2011).
[CrossRef] [PubMed]

K. Zhang, J. Li, W. Wang, J. Xiao, W. Yin, and L. Yu, “Enhancing the linear absorption and tuning the nonlinearity of TiO2 nanowires through the incorporation of Ag nanoparticles,” Opt. Lett.36(17), 3443–3445 (2011).
[CrossRef] [PubMed]

2010 (7)

D. N. Christodoulides, I. C. Khoo, G. J. Salamo, G. I. Stegeman, and E. W. Van Stryland, “Nonlinear refraction and absorption: mechanisms and magnitudes,” Adv. Opt. Photon.2(1), 60–200 (2010).
[CrossRef]

J. M. Hales, J. Matichak, S. Barlow, S. Ohira, K. Yesudas, J. L. Brédas, J. W. Perry, and S. R. Marder, “Design of polymethine dyes with large third-order optical nonlinearities and loss figures of merit,” Science327(5972), 1485–1488 (2010).
[CrossRef] [PubMed]

X. Chen, J. Tao, G. Zou, W. Su, Q. Zhang, and P. Wang, “Thermosensitive silver/polydiacetylene nanocrystals with tunable nonlinear optical properties,” ChemPhysChem11(17), 3599–3603 (2010).
[CrossRef] [PubMed]

S. A. Haque and J. Nelson, “Physics. Toward organic all-optical switching,” Science327(5972), 1466–1467 (2010).
[CrossRef] [PubMed]

H. Wang, H. Su, H. Qian, Z. Wang, X. Wang, and A. Xia, “Structure-dependent all-optical switching in graphene-nanoribbon-like molecules: fully conjugated tri(perylene bisimides),” J. Phys. Chem. A114(34), 9130–9135 (2010).
[CrossRef] [PubMed]

P. Sharma, “Enhancement of speed of digital operation in bacteriorhodopsin based photonic switches,” Optik (Stuttg.)121(4), 384–388 (2010).
[CrossRef]

S. Roy, M. Prasad, J. Topolancik, and F. Vollmer, “All-optical switching with bacteriorhodopsin protein coated microcavities and its application to low-power computing circuits,” J. Appl. Phys.107(5), 053115 (2010).
[CrossRef]

2008 (3)

P. Sharma, “Fast photonic switching in pharaonis phoborhodopsin protein molecules,” J. Biophotonics1(6), 526–530 (2008).
[CrossRef]

S. Roy and P. Sharma, “Analysis of all-optical light modulation in proteorhodopsin protein molecules,” Optik (Stuttg.)119(4), 192–202 (2008).
[CrossRef]

X. Hu, P. Jiang, C. Ding, H. Yang, and Q. Gong, “Picosecond and low-power all-optical switching based on an organic photonic bandgap microcavity,” Nat. Photonics2(3), 185–189 (2008).
[CrossRef]

2006 (6)

S. F. Mingaleev, A. E. Miroshnichenko, Y. S. Kivshar, and K. Busch, “All-optical switching, bistability, and slow-light transmission in photonic crystal waveguide-resonator structures,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys.74(4), 046603 (2006).
[CrossRef] [PubMed]

J. Topolancik and F. Vollmer, “All-optical switching in the near infrared with bacteriorhodopsin-coated microcavities,” Appl. Phys. Lett.89(18), 184103 (2006).
[CrossRef]

S. Roy, T. Kikukawa, P. Sharma, and N. Kamo, “All-optical switching in Pharaonis phoborhodopsin protein molecules,” IEEE Trans. Nanobioscience5(3), 178–187 (2006).
[CrossRef] [PubMed]

R. Moukhametzianov, J. P. Klare, R. Efremov, C. Baeken, A. Göppner, J. Labahn, M. Engelhard, G. Büldt, and V. I. Gordeliy, “Development of the signal in sensory rhodopsin and its transfer to the cognate transducer,” Nature440(7080), 115–119 (2006).
[CrossRef] [PubMed]

S. Schenkl, F. van Mourik, N. Friedman, M. Sheves, R. Schlesinger, S. Haacke, and M. Chergui, “Insights into excited-state and isomerization dynamics of bacteriorhodopsin from ultrafast transient UV absorption,” Proc. Natl. Acad. Sci. U.S.A.103(11), 4101–4106 (2006).
[CrossRef] [PubMed]

S. Roy and K. Kulshrestha, “All-optical switching in plant blue light photoreceptor phototropin,” IEEE Trans. Nanobioscience5(4), 281–287 (2006).
[CrossRef] [PubMed]

2005 (6)

P. Wu and D. V. G. L. N. Rao, “Controllable snail-paced light in biological bacteriorhodopsin thin film,” Phys. Rev. Lett.95(25), 253601 (2005).
[CrossRef] [PubMed]

P. Sharma, S. Roy, and C. P. Singh, “Low power spatial light modulator with pharaonis phoborhodopsin,” Thin Solid Films477(1-2), 227–232 (2005).
[CrossRef]

M. Iwamoto, Y. Sudo, K. Shimono, T. Araiso, and N. Kamo, “Correlation of the O-intermediate rate with the pKa of Asp-75 in the dark, the counterion of the Schiff base of pharaonis phoborhodopsin (sensory rhodopsin II),” Biophys. J.88(2), 1215–1223 (2005).
[CrossRef] [PubMed]

R. K. Banyal and B. R. Prasad, “High-contrast, all-optical switching in bacteriorhodopsin films,” Appl. Opt.44(26), 5497–5503 (2005).
[CrossRef] [PubMed]

P. Sharma, S. Roy, and C. P. Singh, “Dynamics of all-optical switching in polymethine dye molecules,” Thin Solid Films477(1-2), 42–47 (2005).
[CrossRef]

C. P. Singh, K. S. Bindra, B. Jain, and S. M. Oak, “All-optical switching characteristics of metalloporphyrins,” Opt. Commun.245(1-6), 407–414 (2005).
[CrossRef]

2004 (5)

V. R. Almeida, C. A. Barrios, R. R. Panepucci, and M. Lipson, “All-optical control of light on a silicon chip,” Nature431(7012), 1081–1084 (2004).
[CrossRef] [PubMed]

S. Roy, P. Sharma, A. K. Dharmadhikari, and D. Mathur, “All-optical switching with bacteriorhodopsin,” Opt. Commun.237(4-6), 251–256 (2004).
[CrossRef]

Y. Huang, S. T. Wu, and Y. Zhao, “All-optical switching characteristics in bacteriorhodopsin and its applications in integrated optics,” Opt. Express12(5), 895–906 (2004).
[CrossRef] [PubMed]

Z. Bálint, M. Lakatos, C. Ganea, J. K. Lanyi, and G. Váró, “The nitrate transporting photochemical reaction cycle of the pharaonis halorhodopsin,” Biophys. J.86(3), 1655–1663 (2004).
[CrossRef] [PubMed]

P. Sharma and S. Roy, “All-optical light modulation in pharaonis phoborhodopsin and its application to parallel logic gates,” J. Appl. Phys.96(3), 1687–1695 (2004).
[CrossRef]

2003 (3)

Y. Sudo, M. Yamabi, M. Iwamoto, K. Shimono, and N. Kamo, “Interaction of Natronobacterium pharaonis phoborhodopsin (sensory rhodopsin II) with its cognate transducer probed by increase in the thermal stability,” Photochem. Photobiol.78(5), 511–516 (2003).
[CrossRef] [PubMed]

C. P. Singh and S. Roy, “All-optical switching in bacteriorhodopsin based on M state dynamics and its application to photonic logic gates,” Opt. Commun.218(1-3), 55–66 (2003).
[CrossRef]

H. Abdeldayem, D. O. Frazier, and M. S. Paley, “An all-optical picosecond switch in polydiacetylene,” Appl. Phys. Lett.82(7), 1120–1122 (2003).
[CrossRef]

2002 (6)

J. L. Spudich and H. Luecke, “Sensory rhodopsin II: functional insights from structure,” Curr. Opin. Struct. Biol.12(4), 540–546 (2002).
[CrossRef] [PubMed]

K. J. Wise, N. B. Gillespie, J. A. Stuart, M. P. Krebs, and R. R. Birge, “Optimization of bacteriorhodopsin for bioelectronic devices,” Trends Biotechnol.20(9), 387–394 (2002).
[CrossRef] [PubMed]

P. Wu, D. V. G. L. N. Rao, B. R. Kimball, M. Nakashima, and B. S. DeCristofano, “Enhancement of photoinduced anisotropy and all-optical switching in bacteriorhodopsin films,” Appl. Phys. Lett.81(20), 3888–3890 (2002).
[CrossRef]

S. Roy, C. P. Singh, and K. P. J. Reddy, “Analysis of all optical switching in bacteriorhodopsin,” Curr. Sci.83, 623–627 (2002).

C. P. Singh and S. Roy, “Analysis of low power spatial light modulation characteristics of bacteriorhodopsin,” Optik (Stuttg.)113(9), 373–381 (2002).
[CrossRef]

Y. Sudo, M. Iwamoto, K. Shimono, and N. Kamo, “Association of pharaonis phoborhodopsin with its cognate transducer decreases the photo-dependent reactivity by water-soluble reagents of azide and hydroxylamine,” Biochim. Biophys. Acta1558(1), 63–69 (2002).
[CrossRef] [PubMed]

2001 (1)

N. Kamo, K. Shimono, M. Iwamoto, and Y. Sudo, “Photochemistry and photoinduced proton-transfer by pharaonis phoborhodopsin,” Biochemistry Mosc.66(11), 1277–1282 (2001).
[CrossRef] [PubMed]

2000 (1)

N. Hampp, “Bacteriorhodopsin as a photochromic retinal protein for optical memories,” Chem. Rev.100(5), 1755–1776 (2000).
[CrossRef] [PubMed]

1999 (1)

M. Iwamoto, K. Shimono, M. Sumi, and N. Kamo, “Positioning proton-donating residues to the Schiff-base accelerates the M-decay of pharaonis phoborhodopsin expressed in Escherichia coli,” Biophys. Chem.79(3), 187–192 (1999).
[CrossRef] [PubMed]

1998 (3)

K. Takao, T. Kikukawa, T. Araiso, and N. Kamo, “Azide accelerates the decay of M-intermediate of pharaonis phoborhodopsin,” Biophys. Chem.73(1-2), 145–153 (1998).
[CrossRef] [PubMed]

K. Shimono, M. Iwamoto, M. Sumi, and N. Kamo, “V108M mutant of pharaonis phoborhodopsin: substitution caused no absorption change but affected its M-state,” J. Biochem.124(2), 404–409 (1998).
[PubMed]

L. Ujj, S. Devanathan, T. E. Meyer, M. A. Cusanovich, G. Tollin, and G. H. Atkinson, “New photocycle intermediates in the photoactive yellow protein from Ectothiorhodospira halophila: picosecond transient absorption spectroscopy,” Biophys. J.75(1), 406–412 (1998).
[CrossRef] [PubMed]

1995 (2)

E. P. Lukashev and B. Robertson, “Bacteriorhodopsin retains its light-induced proton-pumping function after being heated to 140°C,” Bioelectrochem. Bioenerg.37(2), 157–160 (1995).
[CrossRef]

K. P. J. Reddy, “Analysis of light-induced processes in bacteriorhodopsin and its application for spatial light modulation,” J. Appl. Phys.77(12), 6108–6113 (1995).
[CrossRef]

1994 (2)

C. Li, L. Zhang, M. Yang, H. Wang, and Y. Wang, “Dynamic and steady-state behaviors of reverse saturable absorption in metallophthalocyanine,” Phys. Rev. A49(2), 1149–1157 (1994).
[CrossRef] [PubMed]

C. Li, L. Zhang, R. Wang, Y. Song, and Y. J. Wang, “Dynamics of reverse saturable absorption and all-optical switching in C60,” J. Opt. Soc. Am. B11(8), 1356–1360 (1994).
[CrossRef]

1993 (1)

Y. Shen, C. R. Safinya, K. S. Liang, A. F. Ruppert, and J. Rothschild, “Stabilization of the membrane protein bacteriorhodopsin to 140°C in two-dimensional films,” Nature366(6450), 48–50 (1993).
[CrossRef]

1992 (3)

M. Miyazaki, J. Hirayama, M. Hayakawa, and N. Kamo, “Flash photolysis study on pharaonis phoborhodopsin from a haloalkaliphilic bacterium (Natronobacterium pharaonis),” Biochim. Biophys. Acta1140(1), 22–29 (1992).
[CrossRef]

Y. Imamoto, Y. Shichida, J. Hirayama, H. Tomioka, N. Kamo, and T. Yoshizawa, “Nanosecond laser photolysis of phoborhodopsin: from natronobacterium pharaonis appearance of KL and L intermediates in the photocycle at room temperature,” Photochem. Photobiol.56(6), 1129–1134 (1992).
[CrossRef]

R. R. Birge, “Protein-based optical computing and memories,” IEEE Comput.25(11), 56–67 (1992).
[CrossRef]

1991 (1)

D. Oesterhelt, C. Bräuchle, and N. Hampp, “Bacteriorhodopsin: a biological material for information processing,” Q. Rev. Biophys.24(4), 425–478 (1991).
[CrossRef] [PubMed]

Abdeldayem, H.

H. Abdeldayem, D. O. Frazier, and M. S. Paley, “An all-optical picosecond switch in polydiacetylene,” Appl. Phys. Lett.82(7), 1120–1122 (2003).
[CrossRef]

Ågren, H.

G. S. He, J. Zhu, A. Baev, M. Samoć, D. L. Frattarelli, N. Watanabe, A. Facchetti, H. Ågren, T. J. Marks, and P. N. Prasad, “Twisted π-system chromophores for all-optical switching,” J. Am. Chem. Soc.133(17), 6675–6680 (2011).
[CrossRef] [PubMed]

Almeida, V. R.

V. R. Almeida, C. A. Barrios, R. R. Panepucci, and M. Lipson, “All-optical control of light on a silicon chip,” Nature431(7012), 1081–1084 (2004).
[CrossRef] [PubMed]

Araiso, T.

M. Iwamoto, Y. Sudo, K. Shimono, T. Araiso, and N. Kamo, “Correlation of the O-intermediate rate with the pKa of Asp-75 in the dark, the counterion of the Schiff base of pharaonis phoborhodopsin (sensory rhodopsin II),” Biophys. J.88(2), 1215–1223 (2005).
[CrossRef] [PubMed]

K. Takao, T. Kikukawa, T. Araiso, and N. Kamo, “Azide accelerates the decay of M-intermediate of pharaonis phoborhodopsin,” Biophys. Chem.73(1-2), 145–153 (1998).
[CrossRef] [PubMed]

Atkinson, G. H.

L. Ujj, S. Devanathan, T. E. Meyer, M. A. Cusanovich, G. Tollin, and G. H. Atkinson, “New photocycle intermediates in the photoactive yellow protein from Ectothiorhodospira halophila: picosecond transient absorption spectroscopy,” Biophys. J.75(1), 406–412 (1998).
[CrossRef] [PubMed]

Baeken, C.

R. Moukhametzianov, J. P. Klare, R. Efremov, C. Baeken, A. Göppner, J. Labahn, M. Engelhard, G. Büldt, and V. I. Gordeliy, “Development of the signal in sensory rhodopsin and its transfer to the cognate transducer,” Nature440(7080), 115–119 (2006).
[CrossRef] [PubMed]

Baev, A.

G. S. He, J. Zhu, A. Baev, M. Samoć, D. L. Frattarelli, N. Watanabe, A. Facchetti, H. Ågren, T. J. Marks, and P. N. Prasad, “Twisted π-system chromophores for all-optical switching,” J. Am. Chem. Soc.133(17), 6675–6680 (2011).
[CrossRef] [PubMed]

Bálint, Z.

Z. Bálint, M. Lakatos, C. Ganea, J. K. Lanyi, and G. Váró, “The nitrate transporting photochemical reaction cycle of the pharaonis halorhodopsin,” Biophys. J.86(3), 1655–1663 (2004).
[CrossRef] [PubMed]

Banyal, R. K.

Barlow, S.

R. R. Dasari, M. M. Sartin, M. Cozzuol, S. Barlow, J. W. Perry, and S. R. Marder, “Synthesis and linear and nonlinear absorption properties of dendronised ruthenium(II) phthalocyanine and naphthalocyanine,” Chem. Commun. (Camb.)47(15), 4547–4549 (2011).
[CrossRef] [PubMed]

J. M. Hales, J. Matichak, S. Barlow, S. Ohira, K. Yesudas, J. L. Brédas, J. W. Perry, and S. R. Marder, “Design of polymethine dyes with large third-order optical nonlinearities and loss figures of merit,” Science327(5972), 1485–1488 (2010).
[CrossRef] [PubMed]

Barrios, C. A.

V. R. Almeida, C. A. Barrios, R. R. Panepucci, and M. Lipson, “All-optical control of light on a silicon chip,” Nature431(7012), 1081–1084 (2004).
[CrossRef] [PubMed]

Bazzana, L.

A. Charas, A. L. Mendonça, J. Clark, L. Bazzana, A. Nocivelli, G. Lanzani, and J. Morgado, “Stimulated emission and ultrafast optical switching in a ter(9,9′-spirobifluorene)-co-methylmethacrylate copolymer,” J. Polym. Sci., B, Polym. Phys.49(1), 52–61 (2011).
[CrossRef]

Bindra, K. S.

C. P. Singh, K. S. Bindra, B. Jain, and S. M. Oak, “All-optical switching characteristics of metalloporphyrins,” Opt. Commun.245(1-6), 407–414 (2005).
[CrossRef]

Birge, R. R.

K. J. Wise, N. B. Gillespie, J. A. Stuart, M. P. Krebs, and R. R. Birge, “Optimization of bacteriorhodopsin for bioelectronic devices,” Trends Biotechnol.20(9), 387–394 (2002).
[CrossRef] [PubMed]

R. R. Birge, “Protein-based optical computing and memories,” IEEE Comput.25(11), 56–67 (1992).
[CrossRef]

Bräuchle, C.

D. Oesterhelt, C. Bräuchle, and N. Hampp, “Bacteriorhodopsin: a biological material for information processing,” Q. Rev. Biophys.24(4), 425–478 (1991).
[CrossRef] [PubMed]

Brédas, J. L.

J. M. Hales, J. Matichak, S. Barlow, S. Ohira, K. Yesudas, J. L. Brédas, J. W. Perry, and S. R. Marder, “Design of polymethine dyes with large third-order optical nonlinearities and loss figures of merit,” Science327(5972), 1485–1488 (2010).
[CrossRef] [PubMed]

Büldt, G.

R. Moukhametzianov, J. P. Klare, R. Efremov, C. Baeken, A. Göppner, J. Labahn, M. Engelhard, G. Büldt, and V. I. Gordeliy, “Development of the signal in sensory rhodopsin and its transfer to the cognate transducer,” Nature440(7080), 115–119 (2006).
[CrossRef] [PubMed]

Busch, K.

S. F. Mingaleev, A. E. Miroshnichenko, Y. S. Kivshar, and K. Busch, “All-optical switching, bistability, and slow-light transmission in photonic crystal waveguide-resonator structures,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys.74(4), 046603 (2006).
[CrossRef] [PubMed]

Cassidy, S.

F. Z. Henari and S. Cassidy, “Non-linear optical properties and all-optical switching of congo red in solution,” Optik (Stuttg.) (to be published).

Charas, A.

A. Charas, A. L. Mendonça, J. Clark, L. Bazzana, A. Nocivelli, G. Lanzani, and J. Morgado, “Stimulated emission and ultrafast optical switching in a ter(9,9′-spirobifluorene)-co-methylmethacrylate copolymer,” J. Polym. Sci., B, Polym. Phys.49(1), 52–61 (2011).
[CrossRef]

Chen, X.

X. Chen, J. Tao, G. Zou, W. Su, Q. Zhang, and P. Wang, “Thermosensitive silver/polydiacetylene nanocrystals with tunable nonlinear optical properties,” ChemPhysChem11(17), 3599–3603 (2010).
[CrossRef] [PubMed]

Chergui, M.

S. Schenkl, F. van Mourik, N. Friedman, M. Sheves, R. Schlesinger, S. Haacke, and M. Chergui, “Insights into excited-state and isomerization dynamics of bacteriorhodopsin from ultrafast transient UV absorption,” Proc. Natl. Acad. Sci. U.S.A.103(11), 4101–4106 (2006).
[CrossRef] [PubMed]

Christodoulides, D. N.

Clark, J.

A. Charas, A. L. Mendonça, J. Clark, L. Bazzana, A. Nocivelli, G. Lanzani, and J. Morgado, “Stimulated emission and ultrafast optical switching in a ter(9,9′-spirobifluorene)-co-methylmethacrylate copolymer,” J. Polym. Sci., B, Polym. Phys.49(1), 52–61 (2011).
[CrossRef]

Cozzuol, M.

R. R. Dasari, M. M. Sartin, M. Cozzuol, S. Barlow, J. W. Perry, and S. R. Marder, “Synthesis and linear and nonlinear absorption properties of dendronised ruthenium(II) phthalocyanine and naphthalocyanine,” Chem. Commun. (Camb.)47(15), 4547–4549 (2011).
[CrossRef] [PubMed]

Cusanovich, M. A.

L. Ujj, S. Devanathan, T. E. Meyer, M. A. Cusanovich, G. Tollin, and G. H. Atkinson, “New photocycle intermediates in the photoactive yellow protein from Ectothiorhodospira halophila: picosecond transient absorption spectroscopy,” Biophys. J.75(1), 406–412 (1998).
[CrossRef] [PubMed]

Dasari, R. R.

R. R. Dasari, M. M. Sartin, M. Cozzuol, S. Barlow, J. W. Perry, and S. R. Marder, “Synthesis and linear and nonlinear absorption properties of dendronised ruthenium(II) phthalocyanine and naphthalocyanine,” Chem. Commun. (Camb.)47(15), 4547–4549 (2011).
[CrossRef] [PubMed]

DeCristofano, B. S.

P. Wu, D. V. G. L. N. Rao, B. R. Kimball, M. Nakashima, and B. S. DeCristofano, “Enhancement of photoinduced anisotropy and all-optical switching in bacteriorhodopsin films,” Appl. Phys. Lett.81(20), 3888–3890 (2002).
[CrossRef]

Devanathan, S.

L. Ujj, S. Devanathan, T. E. Meyer, M. A. Cusanovich, G. Tollin, and G. H. Atkinson, “New photocycle intermediates in the photoactive yellow protein from Ectothiorhodospira halophila: picosecond transient absorption spectroscopy,” Biophys. J.75(1), 406–412 (1998).
[CrossRef] [PubMed]

Dharmadhikari, A. K.

S. Roy, P. Sharma, A. K. Dharmadhikari, and D. Mathur, “All-optical switching with bacteriorhodopsin,” Opt. Commun.237(4-6), 251–256 (2004).
[CrossRef]

Ding, C.

X. Hu, P. Jiang, C. Ding, H. Yang, and Q. Gong, “Picosecond and low-power all-optical switching based on an organic photonic bandgap microcavity,” Nat. Photonics2(3), 185–189 (2008).
[CrossRef]

Efremov, R.

R. Moukhametzianov, J. P. Klare, R. Efremov, C. Baeken, A. Göppner, J. Labahn, M. Engelhard, G. Büldt, and V. I. Gordeliy, “Development of the signal in sensory rhodopsin and its transfer to the cognate transducer,” Nature440(7080), 115–119 (2006).
[CrossRef] [PubMed]

Engelhard, M.

R. Moukhametzianov, J. P. Klare, R. Efremov, C. Baeken, A. Göppner, J. Labahn, M. Engelhard, G. Büldt, and V. I. Gordeliy, “Development of the signal in sensory rhodopsin and its transfer to the cognate transducer,” Nature440(7080), 115–119 (2006).
[CrossRef] [PubMed]

Facchetti, A.

G. S. He, J. Zhu, A. Baev, M. Samoć, D. L. Frattarelli, N. Watanabe, A. Facchetti, H. Ågren, T. J. Marks, and P. N. Prasad, “Twisted π-system chromophores for all-optical switching,” J. Am. Chem. Soc.133(17), 6675–6680 (2011).
[CrossRef] [PubMed]

Frattarelli, D. L.

G. S. He, J. Zhu, A. Baev, M. Samoć, D. L. Frattarelli, N. Watanabe, A. Facchetti, H. Ågren, T. J. Marks, and P. N. Prasad, “Twisted π-system chromophores for all-optical switching,” J. Am. Chem. Soc.133(17), 6675–6680 (2011).
[CrossRef] [PubMed]

Frazier, D. O.

H. Abdeldayem, D. O. Frazier, and M. S. Paley, “An all-optical picosecond switch in polydiacetylene,” Appl. Phys. Lett.82(7), 1120–1122 (2003).
[CrossRef]

Friedman, N.

S. Schenkl, F. van Mourik, N. Friedman, M. Sheves, R. Schlesinger, S. Haacke, and M. Chergui, “Insights into excited-state and isomerization dynamics of bacteriorhodopsin from ultrafast transient UV absorption,” Proc. Natl. Acad. Sci. U.S.A.103(11), 4101–4106 (2006).
[CrossRef] [PubMed]

Ganea, C.

Z. Bálint, M. Lakatos, C. Ganea, J. K. Lanyi, and G. Váró, “The nitrate transporting photochemical reaction cycle of the pharaonis halorhodopsin,” Biophys. J.86(3), 1655–1663 (2004).
[CrossRef] [PubMed]

Gillespie, N. B.

K. J. Wise, N. B. Gillespie, J. A. Stuart, M. P. Krebs, and R. R. Birge, “Optimization of bacteriorhodopsin for bioelectronic devices,” Trends Biotechnol.20(9), 387–394 (2002).
[CrossRef] [PubMed]

Gong, Q.

X. Hu, P. Jiang, C. Ding, H. Yang, and Q. Gong, “Picosecond and low-power all-optical switching based on an organic photonic bandgap microcavity,” Nat. Photonics2(3), 185–189 (2008).
[CrossRef]

Göppner, A.

R. Moukhametzianov, J. P. Klare, R. Efremov, C. Baeken, A. Göppner, J. Labahn, M. Engelhard, G. Büldt, and V. I. Gordeliy, “Development of the signal in sensory rhodopsin and its transfer to the cognate transducer,” Nature440(7080), 115–119 (2006).
[CrossRef] [PubMed]

Gordeliy, V. I.

R. Moukhametzianov, J. P. Klare, R. Efremov, C. Baeken, A. Göppner, J. Labahn, M. Engelhard, G. Büldt, and V. I. Gordeliy, “Development of the signal in sensory rhodopsin and its transfer to the cognate transducer,” Nature440(7080), 115–119 (2006).
[CrossRef] [PubMed]

Gosztola, D. J.

G. A. Wurtz, R. Pollard, W. Hendren, G. P. Wiederrecht, D. J. Gosztola, V. A. Podolskiy, and A. V. Zayats, “Designed ultrafast optical nonlinearity in a plasmonic nanorod metamaterial enhanced by nonlocality,” Nat. Nanotechnol.6(2), 107–111 (2011).
[CrossRef] [PubMed]

Haacke, S.

S. Schenkl, F. van Mourik, N. Friedman, M. Sheves, R. Schlesinger, S. Haacke, and M. Chergui, “Insights into excited-state and isomerization dynamics of bacteriorhodopsin from ultrafast transient UV absorption,” Proc. Natl. Acad. Sci. U.S.A.103(11), 4101–4106 (2006).
[CrossRef] [PubMed]

Hales, J. M.

J. M. Hales, J. Matichak, S. Barlow, S. Ohira, K. Yesudas, J. L. Brédas, J. W. Perry, and S. R. Marder, “Design of polymethine dyes with large third-order optical nonlinearities and loss figures of merit,” Science327(5972), 1485–1488 (2010).
[CrossRef] [PubMed]

Hampp, N.

N. Hampp, “Bacteriorhodopsin as a photochromic retinal protein for optical memories,” Chem. Rev.100(5), 1755–1776 (2000).
[CrossRef] [PubMed]

D. Oesterhelt, C. Bräuchle, and N. Hampp, “Bacteriorhodopsin: a biological material for information processing,” Q. Rev. Biophys.24(4), 425–478 (1991).
[CrossRef] [PubMed]

Haque, S. A.

S. A. Haque and J. Nelson, “Physics. Toward organic all-optical switching,” Science327(5972), 1466–1467 (2010).
[CrossRef] [PubMed]

Hari, M.

M. Hari, S. Mathew, B. Nithyaja, S. A. Joseph, V. P. N. Nampoori, and P. Radhakrishnan, “Saturable and reverse saturable absorption in aqueous silver nanoparticles at off-resonant wavelngth,” Opt. Quantum Electron.43(1-5), 49–58 (2012).
[CrossRef]

Hayakawa, M.

M. Miyazaki, J. Hirayama, M. Hayakawa, and N. Kamo, “Flash photolysis study on pharaonis phoborhodopsin from a haloalkaliphilic bacterium (Natronobacterium pharaonis),” Biochim. Biophys. Acta1140(1), 22–29 (1992).
[CrossRef]

He, G. S.

G. S. He, J. Zhu, A. Baev, M. Samoć, D. L. Frattarelli, N. Watanabe, A. Facchetti, H. Ågren, T. J. Marks, and P. N. Prasad, “Twisted π-system chromophores for all-optical switching,” J. Am. Chem. Soc.133(17), 6675–6680 (2011).
[CrossRef] [PubMed]

Henari, F. Z.

F. Z. Henari and S. Cassidy, “Non-linear optical properties and all-optical switching of congo red in solution,” Optik (Stuttg.) (to be published).

Hendren, W.

G. A. Wurtz, R. Pollard, W. Hendren, G. P. Wiederrecht, D. J. Gosztola, V. A. Podolskiy, and A. V. Zayats, “Designed ultrafast optical nonlinearity in a plasmonic nanorod metamaterial enhanced by nonlocality,” Nat. Nanotechnol.6(2), 107–111 (2011).
[CrossRef] [PubMed]

Hirayama, J.

Y. Imamoto, Y. Shichida, J. Hirayama, H. Tomioka, N. Kamo, and T. Yoshizawa, “Nanosecond laser photolysis of phoborhodopsin: from natronobacterium pharaonis appearance of KL and L intermediates in the photocycle at room temperature,” Photochem. Photobiol.56(6), 1129–1134 (1992).
[CrossRef]

M. Miyazaki, J. Hirayama, M. Hayakawa, and N. Kamo, “Flash photolysis study on pharaonis phoborhodopsin from a haloalkaliphilic bacterium (Natronobacterium pharaonis),” Biochim. Biophys. Acta1140(1), 22–29 (1992).
[CrossRef]

Hu, X.

X. Hu, P. Jiang, C. Ding, H. Yang, and Q. Gong, “Picosecond and low-power all-optical switching based on an organic photonic bandgap microcavity,” Nat. Photonics2(3), 185–189 (2008).
[CrossRef]

Huang, Y.

Imamoto, Y.

Y. Imamoto, Y. Shichida, J. Hirayama, H. Tomioka, N. Kamo, and T. Yoshizawa, “Nanosecond laser photolysis of phoborhodopsin: from natronobacterium pharaonis appearance of KL and L intermediates in the photocycle at room temperature,” Photochem. Photobiol.56(6), 1129–1134 (1992).
[CrossRef]

Iwamoto, M.

M. Iwamoto, Y. Sudo, K. Shimono, T. Araiso, and N. Kamo, “Correlation of the O-intermediate rate with the pKa of Asp-75 in the dark, the counterion of the Schiff base of pharaonis phoborhodopsin (sensory rhodopsin II),” Biophys. J.88(2), 1215–1223 (2005).
[CrossRef] [PubMed]

Y. Sudo, M. Yamabi, M. Iwamoto, K. Shimono, and N. Kamo, “Interaction of Natronobacterium pharaonis phoborhodopsin (sensory rhodopsin II) with its cognate transducer probed by increase in the thermal stability,” Photochem. Photobiol.78(5), 511–516 (2003).
[CrossRef] [PubMed]

Y. Sudo, M. Iwamoto, K. Shimono, and N. Kamo, “Association of pharaonis phoborhodopsin with its cognate transducer decreases the photo-dependent reactivity by water-soluble reagents of azide and hydroxylamine,” Biochim. Biophys. Acta1558(1), 63–69 (2002).
[CrossRef] [PubMed]

N. Kamo, K. Shimono, M. Iwamoto, and Y. Sudo, “Photochemistry and photoinduced proton-transfer by pharaonis phoborhodopsin,” Biochemistry Mosc.66(11), 1277–1282 (2001).
[CrossRef] [PubMed]

M. Iwamoto, K. Shimono, M. Sumi, and N. Kamo, “Positioning proton-donating residues to the Schiff-base accelerates the M-decay of pharaonis phoborhodopsin expressed in Escherichia coli,” Biophys. Chem.79(3), 187–192 (1999).
[CrossRef] [PubMed]

K. Shimono, M. Iwamoto, M. Sumi, and N. Kamo, “V108M mutant of pharaonis phoborhodopsin: substitution caused no absorption change but affected its M-state,” J. Biochem.124(2), 404–409 (1998).
[PubMed]

Jain, B.

C. P. Singh, K. S. Bindra, B. Jain, and S. M. Oak, “All-optical switching characteristics of metalloporphyrins,” Opt. Commun.245(1-6), 407–414 (2005).
[CrossRef]

Jiang, P.

X. Hu, P. Jiang, C. Ding, H. Yang, and Q. Gong, “Picosecond and low-power all-optical switching based on an organic photonic bandgap microcavity,” Nat. Photonics2(3), 185–189 (2008).
[CrossRef]

Joseph, S. A.

M. Hari, S. Mathew, B. Nithyaja, S. A. Joseph, V. P. N. Nampoori, and P. Radhakrishnan, “Saturable and reverse saturable absorption in aqueous silver nanoparticles at off-resonant wavelngth,” Opt. Quantum Electron.43(1-5), 49–58 (2012).
[CrossRef]

Kamo, N.

S. Roy, T. Kikukawa, P. Sharma, and N. Kamo, “All-optical switching in Pharaonis phoborhodopsin protein molecules,” IEEE Trans. Nanobioscience5(3), 178–187 (2006).
[CrossRef] [PubMed]

M. Iwamoto, Y. Sudo, K. Shimono, T. Araiso, and N. Kamo, “Correlation of the O-intermediate rate with the pKa of Asp-75 in the dark, the counterion of the Schiff base of pharaonis phoborhodopsin (sensory rhodopsin II),” Biophys. J.88(2), 1215–1223 (2005).
[CrossRef] [PubMed]

Y. Sudo, M. Yamabi, M. Iwamoto, K. Shimono, and N. Kamo, “Interaction of Natronobacterium pharaonis phoborhodopsin (sensory rhodopsin II) with its cognate transducer probed by increase in the thermal stability,” Photochem. Photobiol.78(5), 511–516 (2003).
[CrossRef] [PubMed]

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Y. Sudo, M. Iwamoto, K. Shimono, and N. Kamo, “Association of pharaonis phoborhodopsin with its cognate transducer decreases the photo-dependent reactivity by water-soluble reagents of azide and hydroxylamine,” Biochim. Biophys. Acta1558(1), 63–69 (2002).
[CrossRef] [PubMed]

N. Kamo, K. Shimono, M. Iwamoto, and Y. Sudo, “Photochemistry and photoinduced proton-transfer by pharaonis phoborhodopsin,” Biochemistry Mosc.66(11), 1277–1282 (2001).
[CrossRef] [PubMed]

M. Iwamoto, K. Shimono, M. Sumi, and N. Kamo, “Positioning proton-donating residues to the Schiff-base accelerates the M-decay of pharaonis phoborhodopsin expressed in Escherichia coli,” Biophys. Chem.79(3), 187–192 (1999).
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K. Shimono, M. Iwamoto, M. Sumi, and N. Kamo, “V108M mutant of pharaonis phoborhodopsin: substitution caused no absorption change but affected its M-state,” J. Biochem.124(2), 404–409 (1998).
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K. J. Wise, N. B. Gillespie, J. A. Stuart, M. P. Krebs, and R. R. Birge, “Optimization of bacteriorhodopsin for bioelectronic devices,” Trends Biotechnol.20(9), 387–394 (2002).
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M. Iwamoto, Y. Sudo, K. Shimono, T. Araiso, and N. Kamo, “Correlation of the O-intermediate rate with the pKa of Asp-75 in the dark, the counterion of the Schiff base of pharaonis phoborhodopsin (sensory rhodopsin II),” Biophys. J.88(2), 1215–1223 (2005).
[CrossRef] [PubMed]

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[CrossRef] [PubMed]

Y. Sudo, M. Iwamoto, K. Shimono, and N. Kamo, “Association of pharaonis phoborhodopsin with its cognate transducer decreases the photo-dependent reactivity by water-soluble reagents of azide and hydroxylamine,” Biochim. Biophys. Acta1558(1), 63–69 (2002).
[CrossRef] [PubMed]

N. Kamo, K. Shimono, M. Iwamoto, and Y. Sudo, “Photochemistry and photoinduced proton-transfer by pharaonis phoborhodopsin,” Biochemistry Mosc.66(11), 1277–1282 (2001).
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M. Hari, S. Mathew, B. Nithyaja, S. A. Joseph, V. P. N. Nampoori, and P. Radhakrishnan, “Saturable and reverse saturable absorption in aqueous silver nanoparticles at off-resonant wavelngth,” Opt. Quantum Electron.43(1-5), 49–58 (2012).
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Figures (12)

Fig. 1
Fig. 1

Schematic of the typical photocycle of ppR molecule. The maximum absorption wavelengths of the intermediates are shown in brackets. Solid and dashed arrows represent thermal and photo-induced transitions respectively.

Fig. 2
Fig. 2

(a) Variation of NTPI at 390 nm for normalized input pulse at 498 nm (dashed line) with time for different Ip′ values in WT-ppR, and variation of the normalized population density of ppR, M and O states for normalized input pulse at 498 nm (dashed line) with time for (b) Weak probe intensity, (c) Ip′ = 10 mW/cm2 and (d) Ip′ = 50 mW/cm2, with Δt = 1 s, Im0′ = 50 mW/cm2 for C = 47.02 μM.

Fig. 3
Fig. 3

Variation of NTPI at (a) 498 nm and (b) 390 nm, for input pulse at 390 nm with time for different Ip′ values in WT-ppR, with Δt = 1 s, Im0′ = 50 mW/cm2 for C = 47.02 μM.

Fig. 4
Fig. 4

(a) Variation of NTPI at 560 nm for normalized input pulse at 498 nm (dashed line) with time for different Ip′ values in WT-ppR, and variation of the normalized population density of ppR, M and O states for normalized input pulse at 498 nm (dashed line) with time for (b) Ip′ = 6 mW/cm2, (c) Ip′ = 15 mW/cm2 and (d) Ip′ = 95 mW/cm2, for Δt = 1 s, Im0′ = 50 mW/cm2, C = 120 μM.

Fig. 5
Fig. 5

Variation of NTPI at (a) 498 nm and (b) 560 nm, for input pulse at 560 nm with time for different Ip′ values in WT-ppR, with Δt = 1 s, Im0′ = 50 mW/cm2 for C = 120 μM.

Fig. 6
Fig. 6

(a) Variation of NTPI at 390 nm with time for different Ip′ values in F86D/L40T-ppR at pH = 5, and variation of the normalized population density of ppR, M and O states for normalized input pulse at 498 nm (dashed line) with time for (b) Weak probe intensity, (c) Ip′ = 15 mW/cm2 and (d) Ip′ = 95 mW/cm2, with Δt = 1 s, Im0′ = 50 mW/cm2 for C = 44.8 μM.

Fig. 7
Fig. 7

Variation of NTPI at 498 nm for input pulse at 390 nm with time for different Ip′ values in F86D/L40T-ppR, with Δt = 1 s, Im0′ = 50 mW/cm2 for C = 47.02 μM.

Fig. 8
Fig. 8

Variation of NTPI at (a) 498 nm and (b) 560 nm, for input pulse at 560 nm with time for different Ip′ values in F86D/L40T-ppR, with Δt = 1 s, Im0′ = 50 mW/cm2 for C = 120 μM.

Fig. 9
Fig. 9

(a) Variation of NTPI at 390 nm with time for different Ip′ values in F86D-ppR at pH = 5, and variation of the normalized population density of ppR, M and O states for normalized input pulse at 498 nm (dashed line) with time for (b) Weak probe intensity, (c) Ip′ = 15 mW/cm2 and (d) Ip′ = 95 mW/cm2, with Δt = 1 s, Im0′ = 50 mW/cm2 for C = 44.8 μM.

Fig. 10
Fig. 10

Variation of NTPI at 498 nm and for input pulse at 390 nm with time for different Ip′ values in F86D-ppR, with Δt = 1 s, Im0′ = 50 mW/cm2 for C = 47.02 μM.

Fig. 11
Fig. 11

Variation of NTPI at 498 nm for input pulse at 560 nm with time for different Ip′ values in F86D-ppR, with Δt = 1 s, Im0′ = 50 mW/cm2 for C = 120 μM.

Fig. 12
Fig. 12

(a) Simplified level diagram having three states; G: Ground State, E1 and E2: Intermediate States. (b) The arbitrary absorption spectra of all the three states.

Tables (2)

Tables Icon

Table 1 Absorption Cross-sections and Rate Constants of Different Intermediates of WT-ppR [3944]

Tables Icon

Table 2 Relative Effect of Probe Intensity on Switching Characteristics at Different Spectral and Kinetic Conditions of Molecular System Represented in Fig. 12

Equations (4)

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d N R ( t ) dt =( I m σ R ψ R + I p σ Rp ) N R ( t )+( I m σ K + I p σ Kp ) N K ( t )+( I m σ KL + I p σ KLp ) N KL ( t ) +( I m σ L + I p σ Lp ) N L ( t )+( I m σ M + I p σ Mp ) N M ( t )+( k O + I m σ O + I p σ Op ) N O ( t ) d N K ( t ) dt =( I m σ R ψ R + I p σ Rp ) N R ( t )( k K + I m σ K + I p σ Kp ) N K ( t ) d N KL ( t ) dt = k K N K ( t )( k KL + I m σ KL + I p σ KLp ) N KL ( t ) d N L ( t ) dt = k KL N KL ( t )( k L + I m σ L + I p σ Lp ) N L ( t ) d N M ( t ) dt = k L N L ( t )( k M + I m σ M + I p σ Mp ) N M ( t ) d N O ( t ) dt = k M N M ( t )( k O + I m σ O + I p σ Op ) N O ( t )
I m = I m0 ( c ( t t m Δt ) 2 )
α p ( I m , I p )= N R ( I m , I p ) σ Rp + N K ( I m , I p ) σ Kp + N KL ( I m , I p ) σ KLp + N L ( I m , I p ) σ Lp + N M ( I m , I p ) σ Mp + N O ( I m , I p ) σ Op
I pout I pin =exp{ α p ( I m , I p )L}

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