Simulation of molecular ring emission spectra: Localization of exciton states and dynamics

International Journal of Mathematics and Computers in Simulation

Volumn 6, Issue 1, 2012, Pages 144-152

  Zapletal, David ^a   Heřman, Pavel ^b  

^a UNIVERSITY OF PARDUBICE   (Czech Republic)

^b UNIVERSITY OF HRADEC KRALOVE   (Czech Republic)

Author keywords

Dynamic disorder; Exciton states; Fluorescence spectrum; LH2; Mathematica; Static disorder

Indexed keywords

EID: 84857304406     PISSN: 19980159     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (35)

1. G. McDermott et al., Crystal-structure of an integral membrane lightharvesting complex from photosynthetic bacteria, Nature 374, 1995, pp. 517-521.
2. M. Z. Papiz et al., The structure and thermal motion of the B800-850 LH2 complex from Rps. acidophila at 2.0 Å over-circle resolution and 100 K: New structural features and functionally relevant motions, J. Mol. Biol. 326, 2003, pp. 1523-1538.
3. R. Kumble, R. Hochstrasser, 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, 1998, pp. 855-865.
4. V. Nagarajan et al., Ultrafast exciton relaxation in the B850 antenna complex of Rhodobacter sphaeroides, Proc. Natl. Acad. Sci. USA 93, 1996, pp. 13774-13779.
5. V. Nagarajan et al., Femtosecond pump-probe spectroscopy of the B850 antenna complex of Rhodobacter sphaeroides at room temperature, J. Phys. Chem. B 103, 1999, pp. 2297-2309.
6. V. Nagarajan, W. W. Parson, Femtosecond fluorescence depletion anisotropy: Application to the B850 antenna complex of Rhodobacter sphaeroides, J. Phys. Chem. B 104, 2000, pp. 4010-4013.
7. V. ̌C ápek, I. Barvík, P. Heřman, Towards proper parametrization in the exciton transfer and relaxation problem: dimer, Chem. Phys. 270, 2001, pp. 141-156.
8. P. Heřman, I. Barvík, Towards proper parametrization in the exciton transfer and relaxation problem. II. Trimer, Chem. Phys. 274, 2001, pp. 199-217.
9. P. Heřman, I. Barvík, M. Urbanec, Energy relaxation and transfer in excitonic trimer, J. Lumin. 108, 2004, pp. 85-89.
10. P. Heřman et al., Exciton scattering in light-harvesting systems of purple bacteria, J. Lumin. 94-95, 2001, pp. 447-450.
11. P. Heřman, I. Barvík, Non-Markovian effects in the anisotropy of emission in the ring antenna subunits of purple bacteria photosynthetic systems, Czech. J. Phys. 53, 2003, pp. 579-605.
12. P. Heřman et al., Influence of static and dynamic disorder on the anisotropy of emission in the ring antenna subunits of purple bacteria photosynthetic systems, Chem. Phys. 275, 2002, pp. 1-13.
13. P. Heřman, I. Barvík, Temperature dependence of the anisotropy of fluorescence in ring molecular systems, J. Lumin. 122-123, 2007, pp. 558-561.
14. P. Heřman, I. Barvík, Coherence effects in ring molecular systems, Phys. Stat. Sol. C 3, 2006, 3408-3413.
15. P. Heřman, D. Zapletal, I. Barvík, The anisotropy of fluorescence in ring units III: Tangential versus radial dipole arrangement, J. Lumin. 128, 2008, pp. 768-770.
16. P. Heřman, I. Barvík, D. Zaplet-aletal/et-al, Computer simulation of the anisotropy of fluorescence in ring molecular systems: Tangential vs. radial dipole arrangement, Lecture Notes in Computer Science 5101, 2008, pp. 661-670.
17. P. Heřman, D. Zaplet-aletal/et-al, J. Šlégr, Comparison of emission spectra of single LH2 complex for different types of disorder, Physics Procedia 13, 2011, pp. 14-17.
18. D. Zapletal, P. Heřman, Computer simulation of fluorexcence spectra for molecular ring: exciton dynamics, in Proceedings of the 13th WSEAS International Conference on Mathematical and Computational Methods in Science and Engineering (MACMESE'11) WSEAS Press, 2011, pp. 182-187.
19. V. I. Novoderezhkin, D. Rutkauskas, R. van Grondelle, Dynamics of the emission spectrum of a single LH2 complex: Interplay of slow and fast nuclear motions, Biophys. J. 90, 2006, pp. 2890-2902.
20. W. M. Zhang et al., Exciton-migration and three-pulse femtosecond optical spectroscopies of photosynthetic antenna complexes, J. Chem. Phys. 108, 1998, pp. 7763-7774.
21. S. Mukamel, Principles of nonlinear optical spectroscopy. New York: Oxford University Press, 1995.
22. A. G. Redfield, The Theory of Relaxation Processes, Adv. Magn. Reson. 1, 1965, pp. 1-32.
23. D. Rutkauskas et al., Fluorescence spectroscopy of conformational changes of single LH2 complexes, Biophys. J. 88, 2005, pp. 422-435.
24. D. Rutkauskas et al., Fluorescence spectral fluctuations of single LH2 complexes from Rhodopseudomonas acidophila strain 10050, Biochemistry 43, 2004, pp. 4431-4438.
25. V. May, O. Kühn, Charge and Energy Transfer in Molecular Systems. Berlin: Wiley-WCH, 2000.
26. O. Zerlauskiene et al., Static and Dynamic Protein Impact on Electronic Properties of Light-Harvesting Complex LH2, J. Phys. Chem. B 112, 2008, pp. 15883-15892.
27. S. Wolfram, The Mathematica Book, 5th ed., Wolfram Media, 2003.
28. A. A. Keller, Genetic Search Algorithms to Fuzzy Multiobjective Games: A Mathematica Implementation, in 10th WSEAS International Conference on Applied Computer Science, Athens, 2010, pp. 351-359.
29. D. Ustundag, M. Cevri, Bayesian Parameter Estimation of Sinusoids with Simulated Annealing, in 8th WSEAS International Conference on Signal Processing, Conputational Geometry and Artificial Vision, Athens, 2008, pp. 106-112.
30. M. C. Voicu, Computational Methods and Analytical Study for Detecting the Attractors of a Particular Type of k-Order, Nonlinear, Exchange Rate Models, in 13th WSEAS International Conference on Computers, Athens, 2009, pp. 289-302.
31. M. Trott, The Mathematica GuideBook for Symbolics. New York: Springer Science+Business Media, Inc., 2006.
32. M. Trott, The Mathematica GuideBook for Numerics. New York: Springer Science+Business Media, Inc., 2006.
33. P. Heřman, D. Zaplet-aletal/et-al, I. Barvík, Computer simulation of the anisotropy of fluorescence in ring molecular systems: Influence of disorder and ellipticity, in Proc. IEEE 12th International Conference on Computational Science and Engineering (CSE'09), Vancouver, 2009, pp. 437-442.
34. P. Heřman, I. Barvík, D. Zaplet-aletal/et-al, Energetic disorder and exciton states of individual molecular rings, J. Lumin. 119-120, 2006, pp. 496-503.
35. P. Heřman, D. Zaplet-aletal/et-al, M. Horák, Computer simulation of steady state emission and absorption spectra for molecular ring, in Proc. 5th International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP2011), Lisbon, 2011, accepted.