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Computer Simulation of Emission and Absorption Spectra for LH2 Ring

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Book cover Computational Problems in Science and Engineering

Part of the book series: Lecture Notes in Electrical Engineering ((LNEE,volume 343))

Abstract

Computer simulation of absorption and steady state fluorescence spectra for molecular system is presented. We focus on the B850 ring from peripheral cyclic antenna unit LH2 of the bacterial photosystem from purple bacteria. Uncorrelated static disorder in radial positions of molecules on the ring is taking into account in our simulations. We consider also influence of dynamic disorder, interaction with phonon bath, in Markovian approximation. Spectral responses are calculated by the cumulant-expansion method of Mukamel et al. Procedure in Fortran was created for calculation of single ring spectra within full Hamiltonian model. These new results are compared with our previous ones (within the nearest neighbour approximation model) that were obtained by software package Mathematica.

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References

  1. van Grondelle, R., Novoderezhkin, V.I.: Energy transfer in photosynthesis: experimental insights and quantitative models. Phys. Chem. Chem. Phys. 8, 793–807 (2003)

    Article  Google Scholar 

  2. McDermott, G., Prince, S.M., Freer, A.A., Hawthornthwaite-Lawiess, A.M., Papiz, M.Z., Cogdell, R.J., Isaacs, N.: Crystal structure of an integral membrane light harvesting complex from photosynthetic bacteria. Nature 374, 517–521 (1995)

    Article  Google Scholar 

  3. Papiz, M.Z., Prince, S.M., Howard, T., Cogdell, R.J., Isaacs, N.W.: The structure and thermal motion of the B800-850 LH2 complex from Rps. acidophila at 2.0 Ǻ over-circle resolution and 100 K: new structural features and functionally relevant motions. J. Mol. Biol. 326, 1523–1538 (2003)

    Article  Google Scholar 

  4. de Ruijter, W., Oellerich, S., Segura, J.-M., Lawless, A., Papiz, M., Aartsma, T.: Observation of the energy level structure of the low-light adapted B800 LH4 complex by single-molecule spectroscopy. Biophys. J. 87(5), 3413–3420 (2004)

    Article  Google Scholar 

  5. Kumble, R., Hochstrasser, R.: Disorder-induced exciton scattering in the light-harvesting systems of purple bacteria: influence on the anisotropy of emission and band → band transitions. J. Chem. Phys. 109, 855–865 (1998)

    Article  Google Scholar 

  6. Nagarajan, V., Alden, R., Williams, J., Parson, W.: Ultrafast exciton relaxation in the B850 antenna complex of Rhodobacter sphaeroides. Proc. Natl. Acad. Sci. U. S. A. 93(24), 13774–13779 (1996)

    Article  Google Scholar 

  7. Nagarajan, V., Johnson, E.T., Williams, J.C., Parson, W.W.: Femtosecond pump-probe spectroscopy of the B850 antenna complex of Rhodobacter sphaeroides at room temperature. J. Phys. Chem. B 103, 2297–2309 (1999)

    Article  Google Scholar 

  8. Nagarajan, V., Parson, W.W.: Femtosecond fluorescence depletion anisotropy: application to the B850 antenna complex of Rhodobacter sphaeroides. J. Phys. Chem. B 104, 4010–4013 (2000)

    Article  Google Scholar 

  9. Čápek, V., Barvík, I., Heřman, P.: Towards proper parametrization in the exciton transfer and relaxation problem: dimer. Chem. Phys. 270, 141–156 (2001)

    Article  Google Scholar 

  10. Heřman, P., Barvík, I.: Towards proper parametrization in the exciton transfer and relaxation problem II. Trimer. Chem. Phys. 274, 199–217 (2001)

    Article  Google Scholar 

  11. Heřman, P., Barvík, I., Urbanec, M.: Energy relaxation and transfer in excitonic trimer. J. Lumin. 108, 85–89 (2004)

    Article  Google Scholar 

  12. Heřman, P., Kleinekathöfer, U., Barvík, I., Schreiber, M.: Exciton scattering in light-harvesting systems of purple bacteria. J. Lumin. 94–95, 447–450 (2001)

    Google Scholar 

  13. He Heřman, P., Kleinekathöfer, U., Barvík, I., Schreiber, M.: Influence of static and dynamic disorder on the anisotropy of emission in the ring antenna subunits of purple bacteria photosynthetic systems. Chem. Phys. 275, 1–13 (2002)

    Article  Google Scholar 

  14. Heřman, P., Barvík, I.: Non-Markovian effects in the anisotropy of emission in the ring antenna subunits of purple bacteria photosynthetic systems. Czech. J. Phys. 53, 579–605 (2003)

    Article  Google Scholar 

  15. Heřman, P., Barvík, I.: Temperature dependence of the anisotropy of fluorescence in ring molecular systems. J. Lumin. 122–123, 558–561 (2007)

    Google Scholar 

  16. Heřman, P., Zapletal, D., Barvík, I.: Lost of coherence due to disorder in molecular rings. Phys. Stat. Sol. C 6, 89–92 (2009)

    Article  Google Scholar 

  17. Heřman, P., Barvík, I.: Coherence effects in ring molecular systems. Phys. Stat. Sol. C 3, 3408–3413 (2006)

    Article  Google Scholar 

  18. Heřman, P., Barvík, I., Zapletal, D.: Energetic disorder and exciton states of individual molecular rings. J. Lumin. 119–120, 496–503 (2006)

    Google Scholar 

  19. Heřman, P., Zapletal, D., Barvík, I.: The anisotropy of fluorescence in ring units III: tangential versus radial dipole arrangement. J. Lumin. 128, 768–770 (2008)

    Article  Google Scholar 

  20. Heřman, P., Barvík, I., Zapletal, D.: Computer simulation of the anisotropy of fluorescence in ring molecular systems: tangential vs. radial dipole arrangement. In: Bubak, M., van Albada, G.D., Dongarra, J., Sloot, P.M.A. (eds.) Computational science—ICCS 2008. LNCS, vol. 5101, pp. 661–670. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  21. Heřman, P., Zapletal, D., Barvík, I.: Computer simulation of the anisotropy of fluorescence in ring molecular systems: influence of disorder and ellipticity. In: Proceedings of IEEE 12th International Conference on Computational Science and Engineering, pp. 437–442. IEEE Computer Society (2009)

    Google Scholar 

  22. Heřman, P., Zapletal, D., Šlégr, J.: Comparison of emission spectra of single LH2 complex for different types of disorder. Phys. Procedia 13, 14–17 (2011)

    Article  Google Scholar 

  23. Heřman, P., Zapletal, D., Horák, M.: Computer simulation of steady state emission and absorption spectra for molecular ring. In: ADVCOMP2011—The Fifth International Conference on Advanced Engineering Computing and Applications in Sciences, pp. 759–762. IARIA (2011)

    Google Scholar 

  24. Zapletal, D., Heřman, P.: Simulation of molecular ring emission spectra: localization of exciton states and dynamics. Int. J. Math. Comp. Sim. 6, 144–152 (2012)

    Google Scholar 

  25. Horák, M., Heřman, P., Zapletal, D.: Simulation of molecular ring emission spectra-LH4 complex: localization of exciton states and dynamics. Int. J. Math. Comp. Sim. 7(1), 85–93 (2013)

    Google Scholar 

  26. Heřman, P., Zapletal, D.: Intermolecular coupling fluctuation effect on absorption and emission spectra for LH4 ring. Int. J. Math. Comp. Sim. 7(3), 249–257 (2013)

    Google Scholar 

  27. Horák, M., Heřman, P., Zapletal, D.: Modeling of emission spectra for molecular rings—LH2 and LH4 complexes. Phys. Procedia 44, 10–18 (2013)

    Article  Google Scholar 

  28. Heřman, P., Zapletal, D., Horák, M.: Emission spectra of LH2 complex: full hamiltonian model. Eur. Phys. J. B 86, Art. number 215 (2013)

    Google Scholar 

  29. Heřman, P., Zapletal, D.: Emission spectra of LH4 complex: full Hamiltonian model. Int. J. Math. Comp. Sim. 7(6), 249–257 (2013)

    Google Scholar 

  30. Heřman, P., Zapletal, D.: Simulation of emission spectra for LH4 ring: intermolecular coupling fluctuation effect. Int. J. Math. Comp. Sim. 8, 73–81 (2014)

    Google Scholar 

  31. Mukamel, S.: Principles of nonlinear optical spectroscopy. Oxford University Press, New York (1995)

    Google Scholar 

  32. Zhang, W., Chernyak, V., Mukamel, S.: Exciton-migration and three-pulse femtosecond optical spectroscopies of photosynthetic antenna complexes. J. Chem. Phys. 108(18), 7763–7774 (1998)

    Article  Google Scholar 

  33. Novoderezhkin, V.I., Rutkauskas, D., van Grondelle, R.: Dynamics of the emission spectrum of a single LH2 complex: interplay of slow and fast nuclear motions. Biophys. J. 90, 2890–2902 (2006)

    Article  Google Scholar 

  34. Redfield, A.G.: The theory of relaxation processes. Adv. Magn. Reson. 1, 1–32 (1965)

    Article  Google Scholar 

  35. Rutkauskas, D., Novoderezhkin, V., Cogdel, R., van Grondelle, R.: Fluorescence spectral fluctuations of single LH2 complexes from Rhodopseudomonas acidophila strain 10050. Biochemistry 43(15), 4431–4438 (2004)

    Article  Google Scholar 

  36. Rutkauskas, D., Novoderezhkin, V., Cogdel, R., van Grondelle, R.: Fluorescence spectroscopy of conformational changes of single LH2 complexes. Biophys. J. 88(1), 422–435 (2005)

    Article  Google Scholar 

  37. May, V., Kűhn, O.: Charge and energy transfer in molecular systems. Wiley, Berlin (2000)

    Google Scholar 

  38. Zerlauskiene, O., Trinkunas, G., Gall, A., Robert, B., Urboniene, V., Valkunas, L.: Static and dynamic protein impact on electronic properties of light-harvesting complex LH2. J. Phys. Chem. B 112, 15883–15892 (2008)

    Article  Google Scholar 

  39. Wolfram, S.: The Mathematica Book, 5th edn. Wolfram Media, Champaign (2003)

    Google Scholar 

  40. Zapletal, D., Heřman, P.: Photosynthetic complex LH2—absorption and steady state fluorescence spectra. Energy 77, 212–219 (2014)

    Article  Google Scholar 

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Acknowledgments

This work was supported in part by the Faculty of Science, University of Hradec Králové—specific research project no. 2106/2014.

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Authors and Affiliations

  1. Faculty of Science, Department of Physics, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic

    Pavel Heřman

  2. Faculty of Economics and Administration, Institute of Mathematics and Quantitative Methods, University of Pardubice, Studentská 95, Pardubice, 532 10, Czech Republic

    David Zapletal

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  1. Pavel Heřman
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Correspondence to Pavel Heřman .

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Editors and Affiliations

  1. Technical University of Sofia, Sofia, Bulgaria

    Nikos Mastorakis

  2. Departamentul de Inginerie Electrica, University of Craiova, Craiova, Romania

    Aida Bulucea

  3. Naval Academy, Piraeus, Greece

    George Tsekouras

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Heřman, P., Zapletal, D. (2015). Computer Simulation of Emission and Absorption Spectra for LH2 Ring. In: Mastorakis, N., Bulucea, A., Tsekouras, G. (eds) Computational Problems in Science and Engineering. Lecture Notes in Electrical Engineering, vol 343. Springer, Cham. https://doi.org/10.1007/978-3-319-15765-8_11

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  • DOI: https://doi.org/10.1007/978-3-319-15765-8_11

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-15764-1

  • Online ISBN: 978-3-319-15765-8

  • eBook Packages: EngineeringEngineering (R0)

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