Abstract
Ultrafast saturable and reverse saturable absorption has been theoretically analyzed in hemoprotein cytochrome-c (cyt-c). The effect of laser pulse intensity and pulse width, absorption cross-section, pulse frequency and lifetime of the excited states has been studied in detail to optimize saturable and reverse saturable absorption. The results have been used to design all-optical femtosecond AND, OR NOT and the universal NOR and NAND logic gates, at 530 and 460 nm respectively. Theoretical simulations are in good agreement with reported experimental results. The designs are the first application of cyt-c based all-optical logic gates with sub-picosecond switch off/on time. The advantages of simple design, ultrafast operation, high nonlinear optical coefficients and stability of cyt-c in a broad spectral range, make it prospective for photonic computing applications.
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References
Alwarappan, S., Joshi, R.K., Ram, M.K., Kumar, A.: Electron transfer mechanism of cytochrome c at graphene electrode. Appl. Phys. Lett. 96, 263702 (2010). doi:10.1063/1.3458698
Andrade, A.A., Misoguti, L., Neto, N.M.B., Zilio, S.C., Mendonca, C.R.: Excited state absorption properties in cytochrome c at pico and femtosecond regime. Ann. Opt. XXVI ENFMC 5, 1–4 (2003)
Andrade, A.A., Neto, N.M.B., Misoguti, L., De Boni, L., Zilio, S.C., Mendonca, C.R.: Two-photon absorption investigation in reduced and oxidized cyt c solutions. Chem. Phys. Lett. 390, 506–510 (2004)
Badran, H.A., AL-Ahmad, A.Y., AL-Mudhaffer, M.F., Emshary, C.A.: Nonlinear optical responses and limiting behavior of sulfadiazine-chromotropic acid azo dye. Opt. Quant. Electron. 47, 1859–1867 (2015)
Bhalla, V., Vij, V., Dhir, A., Kumar, M.: Hetero-oligophenylene-based AIEE material as a multiple probe for biomolecules and metal ions to construct logic circuits: application in bioelectronics and chemionics. Chem. Eur. J. 18, 3765–3772 (2012)
Caulfield, H.J., Dolev, S.: Why future supercomputing requires optics. Nat. Photon. 4, 261–263 (2010)
Choi, J.-W., Fujihira, M.: Molecular-scale biophotodiode consisting of green fluorescent protein/cytochrome c self-assembled heterolayer. Appl. Phys. Lett. 84, 2187–2189 (2004)
Choi, J.-W., Yoo, C.-J., Nam, Y.-S., Lee, W.H., Oh, S.-Y., Fujihira, M.: Optimal- fabrication conditions of cytochrome c LB Films. Mol. Cryst. Liq. Cryst. 370, 317–320 (2001a)
Choi, J.-W., Nam, Y.-S., Park, S.-J., Lee, W.-H., Kim, D., Fujihira, M.: Rectified photocurrent of molecular photodiode consisting of cytochrome c/GFP hetero thin films. Biosens. Bioelectron. 16, 819–825 (2001b)
Choi, J.-W., Nam, Y.-S., Kong, B.-S., Lee, W.-H., Park, K.M., Fujihira, M.: Bioelectronics device consisting of cytochrome c/poly-l-aspartic acid adsorbed hetero-Langmuir–Blodgett films. J. Biotech. 94, 225–233 (2002)
Clark, J., Lanzani, G.: Organic photonics for communications. Nat. Photon. 4, 438–446 (2010)
De Boni, L., Andrade, A.A., Misoguti, L., Zilio, S.C., Mendonca, C.R.: Excited-state absorption spectroscopy in oxidized cytochrome-c. Opt. Mater. 32, 526–529 (2010)
Deonarine, A.S., Clark, S.M., Konermann, L.: Implementation of multifunctional logic gate based on folding/unfolding transitions of a protein. Future Gener. Comput. Syst. 19, 87–97 (2003)
Fabian, L., Wolff, E.K., Oroszi, L., Ormos, P., Der, A.: Fast integrated optical switching by the protein bacteriorhodopsin. Appl. Phys. Lett. 97, 023305 (2010). doi:10.1063/1.3462940
Fabian, L., Heiner, Z., Mero, M., Kiss, M., Wolff, E.K., Ormos, P., Osvay, K., Der, A.: Protein-based ultrafast photonic switching. Opt. Express 19, 18861–18870 (2011)
Fujita, K., MacFarlane, D.R., Forsyth, M., Fujita, M.Y., Murata, K., Nakamura, N., Ohno, H.: Solubility and stability of cytochrome c in hydrated ionic liquids: effect of oxo acid residues and kosmotropicity. Biomacromolecules 8, 2080–2086 (2007)
Hales, J.M., Matichak, J., Barlow, S., Ohira, S., Yesudas, K., Bredas, J.-L., Perry, J.W., Marder, S.R.: Design of polymethine dyes with large third-order optical nonlinearities and loss figures of merit. Science 327, 1485–1488 (2010)
Hampp, N.: Bacteriorhodopsin as a photochromic retinal protein for optical memories. Chem. Rev. 100, 1755–1776 (2000)
Han, J., Yao, B., Gao, P., Chen, L., Huang, M.: All-optical logic gates based on photoinduced anisotropy of bacteriorhodopsin film. J. Mod. Opt. 59, 636–642 (2012)
Haque, S.A., Nelson, J.: Toward organic all-optical switching. Science 327, 1466–1467 (2010)
Kim, S.T., Lee, Y.-J., Hwang, Y.-S., Lee, S.: Study on aggregation behavior of cytochrome c-conjugated silver nanoparticles using asymmetrical flow field-flow fractionation. Talanta 132, 939–944 (2015)
Lee, B.T., Kim, S.-U., Min, J., Choi, J.-W.: Multilevel biomemory device consisting of recombinant azurin/cytochrome c. Adv. Mater. 22, 510–514 (2010a)
Lee, T., Kim, S.-U., Min, J., Choi, J.-W.: Biomolecular memory device composed of cytochrome c on a self-assembled 11-mercaptoundecanoic acid layer. Jpn. J. Appl. Phys. 49, 01AG01 (2010b)
Lee, T., Chung, Y.-H., Chen, Q., Min, J., Choi, J.-W.: Fatigue test of cytochrome c self-assembled on a 11-MUA layer based on electrochemical analysis for bioelectronic device. J. Nanosci. Nanotechnol. 15, 5537–5542 (2015)
Li, D.-W., Qin, L.-X., Li, Y., Nia, R.P., Long, Y.-T., Chen, H.-Y.: CdSe/ZnS quantum dot-cytochrome c bioconjugates for selective intracellular O2 sensing. Chem. Commun. 47, 8539–8541 (2011)
Loh, K.P., Bao, Q., Eda, G., Chhowalla, M.: Graphene oxide as a chemically tunable platform for optical applications. Nat. Chem. 2, 1015–1024 (2010)
Lowenich, D., Kleinermanns, K., Karunakaran, V., Kovalenko, S.A.: Transient and Stationary spectroscopic of cytochrome c: ultrafast internal conversion controls photoreduction. Photochem. Photobiol. 84, 193–201 (2008)
Mathesz, A., Fabian, L., Valkai, S., Alexandre, D., Marques, P.V.S., Ormos, P., Wolff, E.K., Der, A.: High-speed integrated optical logic based on the protein bacteriorhodopsin. Biosens. Bioelectron. 46, 48–52 (2013)
Nam, S., Kim, H., Degenaar, P., Ha, C.-S., Kim, Y.: Extremely slow photocurrent response from hemoprotein films in planar diode geometry. Appl. Phys. Lett. 101, 223701 (2012). doi:10.1063/1.4764948
Ogawa, J., Sulistyaningdyah, W.T., Li, Q.-S., Tanaka, H., Xie, S.-X., Kano, K., Ikeda, T., Shimizu, S.: Two extracellular proteins with alkaline for oxidase activity, a novel cytochrome c and a catalase-peroxidase, from Bacillus sp. No. 13. BioChim. Biophys. Acta Proteins Proteom. 1699, 65–75 (2004)
Patila, M., Pavlidis, I.V., Kouloumpis, A., Dimos, K., Spyrou, K., Katapodis, P., Stamatis, H.: Graphene oxide derivatives with variable alkyl chain length and terminal functional groups as supports for stabilization of cytochrome c. Intl. J. Biol. Macromol. 84, 227–235 (2016)
Roy, S., Kulshrestha, K.: All-optical switching in plant blue light photoreceptor phototropin. IEEE Trans. Nanobiosci. 5, 281–287 (2006)
Roy, S., Kulshrestha, K.: Controlling light with light in blue light plant photoreceptor phototropin. Curr. Sci. 92, 1275–1280 (2007)
Roy, S., Sharma, P.: Analysis of all-optical light modulation in proteorhodopsin protein molecules. Optik 119, 192–202 (2008)
Roy, S., Yadav, C.: All-optical ultrafast logic gates based on saturable to reverse saturable absorption transition in CuPc-doped PMMA thin films. Opt. Commun. 284, 4435–4440 (2011)
Roy, S., Yadav, C.: Femtosecond all-optical parallel logic gates based on tunable saturable to reverse saturable absorption in graphene-oxide thin films. Appl. Phys. Lett. 103, 241113 (2013). doi:10.1063/1.4846535
Roy, S., Yadav, C.: All-optical sub-ps switching and parallel logic gates with bacteriorhodopsin (BR) protein and BR-gold nanoparticles. Laser Phys. Lett. 11, 125901 (2014). doi:10.1088/1612-2011/11/12/125901
Roy, S., Kikukawa, T., Sharma, P., Kamo, N.: All-optical switching in pharaonis phoborhodopsin protein molecules. IEEE Trans. Nanobiosci. 5, 178–187 (2006)
Roy, S., Prasad, M., Topolancik, J., Vollmer, F.: All-optical switching with bacteriorhodopsin protein coated microcavities and its application to low-power computing circuits. J. Appl. Phys. 107, 053115 (2010). doi:10.1063/1.3310385
Sahoo, D., Bhattacharya, P., Patra, H.K., Mandal, P., Chakravorti, S.: Gold nanoparticle induced conformational changes in heme protein. J. Nanopart. Res. 13, 6755–6760 (2011)
Sharma, P., Roy, S., Singh, C.P.: Low power spatial light modulator with pharaonis phoborhodopsin. Thin Solid Films 477, 227–232 (2005)
Simsikova, M., Antalik, M., Kanuchova, M., Skvarla, J.: Cytochrome c conjugated to ZnO–MAA nanoparticles: the study of interaction and influence on protein structure. Int. J. Biol. Macromol. 59, 235–241 (2013)
Singh, C.P., Bindra, K.S.: Saturation and reverse saturable absorption in semiconductor doped glass and its application to parallel logic gates. Opt. Quant. Electron. 47, 3313–3321 (2015)
Wada, O.: Femtosecond all-optical devices for ultrafast communication and signal processing. New J. Phys. 6, 183 (2004)
Wu, P., Zhao, T., Zhang, J., Wu, L., Hou, X.: Analyte-activable probe for protease based on cytochrome c-capped MN: ZnS quantum dots. Anal. Chem. 86, 10078–10083 (2014)
Yadav, C., Roy, S.: Ultrafast all-optical universal logic gates with graphene and graphene-oxide metal porphyrin composites. J. Comput. Electron. 14, 209–213 (2015)
Zaidi, S., Hassan, M.I., Islam, A., Ahmad, F.: The role of key residues in structure, function and stability of cytochrome-c. Cell. Mol. Life Sci. 71, 229–255 (2014)
Zhu, A., Luo, Y., Tian, Y.: Switching the direction of plasmon induced photocurrents by cytochrome c at Au–TiO2 nanocomposites. Chem. Commun. 42, 6448–6450 (2009)
Acknowledgments
The authors are grateful to the Department of Science and Technology and the University Grants Commission (UGC), Government of India, for partial support of this work. SR is grateful to ICTP, Trieste, Italy for the award of the Research Associateship. CY thanks UGC for the award of a research fellowship.
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Yadav, C., Roy, S. Ultrafast nonlinear absorption in hemoprotein cytochrome-c and its application to computing. Opt Quant Electron 48, 377 (2016). https://doi.org/10.1007/s11082-016-0643-6
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DOI: https://doi.org/10.1007/s11082-016-0643-6