Quantum dynamics: Applications in biological and materials systems

Quantum Dynamics: Applications in Biological and Materials Systems

Volumn , Issue , 2009, Pages 1-323

  Bittner, Eric R ^a  

^a UNIVERSITY OF HOUSTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MATERIALS; BIOLOGY; CURRICULA; DEGREES OF FREEDOM (MECHANICS); DYNAMICS; ELECTRON-PHONON INTERACTIONS; ELECTRONIC STRUCTURE; ENERGY TRANSFER; EXCITED STATES; QUANTUM COMPUTERS; REVIEWS; WAVE FUNCTIONS; WEBSITES;

CLASSICAL MECHANICS; DEVELOPMENT AND UTILIZATIONS; ELECTRON PHONON COUPLINGS; INTRODUCTORY COURSE; OPTICAL ELECTRONICS; PEDAGOGICAL APPROACH; SPECTROSCOPIC TECHNIQUE; THEORETICAL METHODS;

QUANTUM CHEMISTRY;

EID: 85055155191     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/b15835     Document Type: Book

References (130)

1. Louis de Broglie. Recherches sur la théorie des quanta. PhD thesis, Sorbonne, Paris, 1924.
2. Erwin Schrödinger. An undulatory theory of the mechanics of atoms and molecules. Phys. Rev., 28(6):1049–1070, December 1926.
3. Erwin Schrödinger. Über das verhältnis der Heisenberg-Born-Jordanschen quantenmechanik zu der meinen. Ann. Phys. (Leipzig), 1926.
4. E. Fermi. Nuclear Physics. University of Chicago Press, Chicago, 1950.
5. P. A. M. Dirac. The quantum theory of emission and absorption of radiation. Proc. R. Soc. London, Ser. A, 114:243–265, 1927.
6. Eric R. Bittner and Peter J. Rossky. Quantum decoherence in mixed quantum-classical systems: Nonadiabatic processes. J. Chem. Phys., 103(18):8130–8143, Nov 1995.
7. Eric R. Bittner and Peter J. Rossky. Decoherent histories and nonadiabatic quantum molecular dynamics simulations. J. Chem. Phys., 107(20):8611–8618, Nov 1997.
8. Robbie Grunwald and Raymond Kapral. Decoherence and quantum-classical master equation dynamics. J. Chem. Phys., 126(11):114109, 2007.
9. Klaus Hornberger. Master equation for a quantum particle in a gas. Phys. Rev. Lett., 97(6):060601, 2006.
10. Ahren W. Jasper and Donald G. Truhlar. Electronic decoherence time for non-Born-oOppenheimer trajectories. J. Chem. Phys., 123(6):064103, 2005.
11. Gunter Kab. Fewest switches adiabatic surface hopping as applied to vibrational energy relaxation. J. Phys. Chem. A, 110(9):3197–3215, 2006.
12. Gil Katz, Mark A Ratner, and Ronnie Kosloff. Decoherence control by tracking a Hamiltonian reference molecule. Phys. Rev. Lett., 98(20):203006, 2007.
13. M. Merkli, I. M. Sigal, and G. P. Berman. Decoherence and thermalization. Phys Rev Lett, 98(13):130401, 2007.
14. Maximilian A. Schlosshauer. Decoherence and the quantum-to-classical transition. Springer, Berlin, 2007.
15. L. D. Landau. Phy. Z. Sowjetunion, 1:89, 1932.
16. C. Zener. Proc. R. Soc. London, Ser. A, 137:696, 1933.
17. A. Nitzan. Chemical Dynamics in Condensed Phases. Oxford University Press, 2007.
18. R. A. Marcus. On the theory of electron-transfer reactions. Part VI. Unified treatment for homogeneous and electrode reactions. J. Chem. Phys., 43(2):679–701, Jul 1965.
19. Rudolph A. Marcus. Nobel lecture: Electron transfer reactions in chemistry. Theory and experiment. Rev. Mod. Phys., 65(3):599–610, 1993.
20. J. R. Miller, L Calcaterra, and G. L. Closs. “Intramolecular long-distance electron transfer in radical anions. The effects of free energy and solvent on the reaction rates.” J. Am. Chem. Soc., 106:3047, 1984.
21. Eyal Neria, Abraham Nitzan, R. N. Barnett, and Uzi Landman. Quantum dynamical simulations of nonadiabatic processes: Solvation dynamics of the hydrated electron. Phys. Rev. Lett., 67(8):1011–1014, Aug 1991.
22. Eyal Neria and Abraham Nitzan. Semiclassical evaluation of nonadiabatic rates in condensed phases. J. Chem. Phys., 99(2):1109–1123, 1993.
23. Louis de Broglie. Ondes et mouvements. Gauthiers-Villars, Paris, 1926.
24. Louis de Broglie. La mécanique ondulatoire. Gauthiers-Villars, Paris, 1928.
25. Peter Holland. The Quantum Theory of Motion: An Account of the de Broglie-Bohm Causal Interpretation of Quantum Mechanics. Cambridge, UK: Cambridge University Press, 1993.
26. P. A. M. Dirac. The Principles of Quantum Mechanics. Oxford University Press, Oxford, NY, 4th edition, 1958.
27. Julian Schwinger. Quantum Mechanics—Symbolism of Atomic Measurements. Physics and Astonomy. Springer, Berlin, 2001.
28. Philip Pechukas. Time-dependent semiclassical scattering theory. Part I potential scattering. Phys. Rev., 181(1):166–174, May 1969.
29. Philip Pechukas. Time-dependent semiclassical scattering theory. Part II atomic collisions. Phys. Rev., 181(1):174–185, May 1969.
30. John C. Tully. Molecular dynamics with electronic transitions. J. Chem. Phys., 93(2):1061–1071, 1990.
31. Frank J. Webster, Jurgen Schnitker, Mark S. Friedrichs, Richard A. Friesner, and Peter J. Rossky. Solvation dynamics of the hydrated electron: A nonadiabatic quantum simulation. Phys. Rev. Lett., 66(24):3172–3175, Jun 1991.
32. B. Space and D. F. Coker. Nonadiabatic dynamics of excited excess electrons in simple fluids. J. Chem. Phys., 94(3):1976–1984, 1991.
33. L. Allen and J. H. Eberly. Optical Resonance and Two-Level Atoms. Dover Publications, 1987.
34. E. L. Hahn. Spin echoes. Phys. Rev., 80(4):580–594, Nov 1950.
35. E. L. Hahn and D. E. Maxwell. Chemical shift and field independent frequency modulation of the spin echo envelope. Phys. Rev., 84(6):1246–1247, Dec 1951.
36. N. A. Kurnit, I. D. Abella, and S. R. Hartmann. Observation of a photon echo. Phys. Rev. Lett., 13(19):567–568, Nov 1964.
37. I. D. Abella, N. A. Kurnit, and S. R. Hartmann. Photon echoes. Phys. Rev., 141(1): 391–406, Jan 1966.
38. A.A. Ovchinnikov and N.S. Erikhman. Sov. Phys. JETP, 40:733, 1975.
39. A. Madhukar and W. Post. Phys. Rev. Lett., 39:1424, 1977.
40. A. M. Jayannavar and N. Kumar. Phys. Rev. Lett, 48:553, 1982.
41. S. M. Girvin and G. D. Mahan. Phys. Rev. B, 20:4896, 1979.
42. W. Fischer, H. Leschke, and P. Müller. Phys. Rev. Lett., 73:1578, 1994.
43. I. Burghardt and L. S. Cederbaum. Hydrodynamic equation for mixed quantum states. i. general formulation. J. Chem. Phys., 115(22):10303, December 2001.
44. I. Burghardt and L. S. Cederbaum. Hydrodynamic equations for mixed quantum states. ii. coupled electronic states. J. Chem. Phys., 115(22):10312, December 2001.
45. Yasuteru Shigeta, Hideaki Miyachi, and Kimihiko Hirao. Quantal cumulant dynamics: General theory. J. Chem. Phys., 125(24):244102, 2006.
46. Jeremy B. Maddox and Eric R. Bittner. Quantum relaxation dynamics using Bohmian trajectories. J. Chem. Phys., 115(14):6309–6316, 2001.
47. Jeremy B. Maddox and Eric R. Bittner. Quantum dissipation in unbounded systems. Phys. Rev. E, 65(2):026143, Jan 2002.
48. J. B. Maddox and E. R. Bittner. Quantum dissipation in the hydrodynamic moment hierarchy: A semiclassical truncation strategy. J. Phys. Chem. B, 106(33):7981–7990, 2002.
49. L. A. Khalfin. Sov. Phys. JETP, 6:1053, 1958.
50. Wayne M. Itano, D. J. Heinzen, J. J. Bollinger, and D. J. Wineland. Quantum zeno effect. Phys. Rev. A, 41(5):2295–2300, Mar 1990.
51. R. J. Cook. What are quantum jumps? Phys. Scr., T21:49, 1988.
52. E. P. Wigner. On the quantum correction for thermodynamic equilibrium. Phys. Rev., 40:749–759, 1932.
53. H. Weyl. The Theory of Groups and Quantum Mechanics. Dover, New York, 1931.
54. H. Weyl. Gruppentheorie und Quantenmechanik. Hirzel, Leipzig, 1928.
55. H. Weyl. Z. Phys., 46:1, 1927.
56. J. Ville. Théorie et applications de la notion de signal analytique. Cables et Transmission, 2A:61–74, 1948.
57. J. E. Moyal. Quantum mechanics as a statistical theory. Proc. Cambridge Philos. Soc., 45:737–740, 1949.
58. H. J. Groenewold. Physica, 12(405), 1946.
59. William Frensley. Boundary conditions for open quantum systems driven far from equilibrium. Rev. Mod. Phys., 62:745, 1990.
60. Jasper Koester and Shaul Mukamel. Transient gratings, four wave mixing, and polariton effects in non-linear optics. Phys. Rep., 205(1):1–58, 1991.
61. Roger F. Loring, Daniel S. Franchi, and Shaul Mukamel. Anderson localization in Liouville space: The effective dephasing approximation. Phys. Rev. B, 37(4):1874– 1883, Feb 1988.
62. Shaul Mukamel. Principles of Nonlinear Optics and Spectroscopy. Oxford University Press, 1995.
63. P. L. Bhatnagar, E. P. Gross, and M. Krook. A model for collision processes in gases. i. small amplitude processes in charged and neutral one-component systems. Phys. Rev., 94(3):511–525, May 1954.
64. T. Förster. Transfer mechanisms of electronic excitation. Discuss. Faraday Soc. Aberdeen, (7-18), 1960.
65. T. Förster. Zwischenmolekulare Energiewanderung und Fluoreszenz. Ann. Phys. (Leipzig), 2(55–75), 1948.
66. T. Förster. Energiewanderung und Fluoreszenz. Naturwissenschaften, 6(166–175), 1946.
67. T. Förster. Transfer mechanisms of electronic excitation. Discuss. Faraday Soc., 27:17, 1959.
68. E. Hass, E. Katchalski-Katzir, and I. Z. Steinberg. First demo of FRET in DNA loops. Biopolymers, 17(11–31), 1978.
69. Mark I. Wallace, Liming Ying, Shankar Balasubramanian, and David Klenerman. Non-arrhenius kinetics for the loop closure of a DNA hairpin. Proc. Nat. Acad. Sci., 98(10):5584–5589, 2001.
70. E. Zazopoulos, E. Lalli, D. M. Stocco, and P. Sassone-Corsi. Nature, 390:311–315, 1997.
71. X. Dai, M. B. Greizerstein, K. Nadas-Chinni, and L. B. Rothman-Denes. Proc. Nat. Acad. Sci., 94:2174, 1997.
72. S. Tyagi and F. R. Kramer. Molecular beacons. Nature Biotechnol., 14:303–308, 1996.
73. Wichard J. D. Beenken and Tõnu Pullerits. Excitonic coupling in polythiophenes: Comparison of different calculation methods. J. Chem. Phys., 120(5):2490–2495, 2004.
74. William Barford. Exciton transfer integrals between polymer chains. J. Chem. Phys., 126(13):134905, 2007.
75. B. P. Krueger, G. D. Scholes, and G. R. Fleming. Calculation of couplings and energy-transfer pathways between the pigments of lh2 by the ab initio transition density cube method. J. Phys. Chem. B, 102(27):5378–5386, Jul 1998.
76. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr. et al. Gaussian 03, Revision C.02. Gaussian, Inc., Wallingford, CT, 2004.
77. Frank Neese. ORCA—An ab initio Density Functional and Semiempirical Program Package, Version 2.4, Revision 45, Jan 2006. Max Planck Institute for Bioinorganic Chemistry, Muelheim, Germany.
78. Arkadiusz Czader and Eric R. Bittner. Calculations of the exciton coupling elements between the DNA bases using the transition density cube method. J. Chem. Phys., 128(3):035101, 2008.
79. B. Bouvier, T. Gustavsson, D. Markovitsi, and P. Millie. Dipolar coupling between electronic transitions of the DNA bases and its relevance to exciton states in double helices. Chem. Phys., 275:75–92, 2002.
80. P. Claverie. Intermolecular Interactions—From Diatomic to Biopolymers., Chapter Elaboration of Approximate Formulas for the Interaction between Large Molecules: Application in Organic Chemistry, pages 69–306. Wiley, 1978.
81. J. C. Light, I. P. Hamilton, and J. V. Lill. Generalized discrete variable approximation in quantum mechanics. J. Chem. Phys., 82(3):1400–1409, 1985.
82. J. C. Light. Discrete variable representations in quantum dynamics. In Time-Dependent Quantum Molecular Dynamics. Plenum-Press, 1992.
83. E. Hückel. Zeitschrift für Physik, 76:628, 1932.
84. J. E. Lennard-Jones. Proc. R. Soc. London, 158:280, 1937.
85. C. A. Coulson and A. Streitwieser. Dictionary of π Electron Calculations. Pergammon, New York, 1965.
86. W. Kutzelnigg. Einführung in die Theoretische Cheme, Vol 2: Die Chemische Bindung. Wiley-VCH, 1978.
87. J. Barriol and J. J. Metzger. J. Chem. Phys., 47:433, 1950.
88. C. C. J. Roothaan. Self-consistent field theory for open shells of electronic systems. Rev. Mod. Phys., 32(2):179–185, 1960.
89. C. C. J. Roothaan. New developments in molecular orbital theory. Rev. Mod. Phys., 23(2):69–89, 1951.
90. Michael C. Zerner. Perspective on “New developments in molecular orbital theory.” Theor. Chim. Acta, 103(3):217–218, 2000.
91. G. G. Hall. Proc. R. Soc. London, Ser. A, 205:541, 1951.
92. G. C. Schatz and M. A. Ratner. Quantum Mechanics in Chemistry. Prentice Hall, 1993.
93. Karl F. Freed. Is there a bridge between ab initio and semiempirical theories of valence? Acc. Chem. Res., 16(4):137–144, 1983.
94. ν calculations. J. Chem. Phys., 100(10):7454–7470, 1994.
95. Charles. H. Martin, R. L. Graham, and Karl. F. Freed. Ab initio study of cyclobutadiene using the effective valence shell Hamiltonian method. J. Chem. Phys., 99(10):7833– 7844, 1993.
96. J. Hubbard. Electron correlations in narrow energy bands. Proc. R. Soc. London, Ser. A, 276(1365):238–257, Nov 1963.
97. Elliott H. Lieb and F. Y. Wu. Absence of Mott transition in an exact solution of the short-range, one-band model in one dimension. Phys. Rev. Lett., 20(25):1445–1448, Jun 1968.
98. Fabian H. L. Essler, Vladimir E. Korepin, and Kareljan Schoutens. Complete solution of the one-dimensional Hubbard model. Phys. Rev. Lett., 67(27):3848–3851, Dec 1991.
99. J. C. Slater. Atomic shielding constants. Phys. Rev., 36(1):57–64, Jul 1930.
100. S. F. Boys. Proc. R. Soc. London, Ser. A, 200:542, 1950.
101. Ira Levine. Quantum Chemistry. Prentice Hall, 4th edition, 1991.
102. W. P. Su, J. R. Schrieffer, and A. J. Heeger. Soliton excitations in polyacetylene. Phy. Rev. B, 22(4):2099–2111, Aug 1980.
103. W. P. Su, J. R. Schrieffer, and A. J. Heeger. Solitons in polyacetylene. Phys. Rev. Lett., 42(25):1698–1701, Jun 1979.
104. L. D. Landau. Phys. Z. Sowjetunion, 3:664, 1933.
105. E. I. Rashba and M. D. Sturge. Excitons. North-Holland, Amsterdam, Netherlands, 1982.
106. E. I. Rashba. Opt. Spektrosk., 2:568, 1957.
107. Mark N. Kobrak and Eric R. Bittner. A dynamic model for exciton self-trapping in conjugated polymers. Part I. Theory. J. Chem. Phys., 112(12):5399–5409, 2000.
108. Mark N. Kobrak and Eric R. Bittner. A dynamic model for exciton self-trapping in conjugated polymers. ii. implementation. J. Chem. Phys., 112(12):5410–5419, 2000.
109. Mark N. Kobrak and Eric R. Bittner. A quantum molecular dynamics study of exciton self-trapping in conjugated polymers: Temperature dependence and spectroscopy. J. Chem. Phys., 112(17):7684–7692, 2000.
110. Hitoshi Sumi and Atsuko Sumi. Dimensionality dependence in self-trapping of excitons. J. Phys. Soc. Jp. 63(2):637–657, 1994.
111. I. Franco and S. Tretiak. Electron-vibrational dynamics of photoexcited polyfluorenes. J. Am. Chem. Soc., 126(38):12130–12140, Sep 2004.
112. Kirill I. Igumenshchev, Sergei Tretiak, and Vladimir Y. Chernyak. Excitonic effects in a time-dependent density functional theory. J. Chem. Phys., 127(11):114902, 2007.
113. S. Tretiak, A. Saxena, R. L. Martin, and A. R. Bishop. Photoexcited breathers in conjugated polyenes: An excited-state molecular dynamics study. Proc. Nat. Acad. Sci., 100(5):2185–2190, Mar 2003.
114. S. Tretiak, A. Saxena, R. L. Martin, and A. R. Bishop. Conformational dynamics of photoexcited conjugated molecules. Phys. Rev. Lett., 89(9):097402, 2002.
115. Sergei Tretiak, Kirill Igumenshchev, and Vladimir Chernyak. Exciton sizes of conducting polymers predicted by time-dependent density functional theory. Phys. Rev. B, 71(3):033201–4, 2005.
116. Stoyan Karabunarliev, Martin Baumgarten, Eric R. Bittner, and Klaus Müllen. Rigorous Franck–Condon absorption and emission spectra of conjugated oligomers from quantum chemistry. J. Chem. Phys., 113(24):11372–11381, 2000.
117. Stoyan Karabunarliev and Eric R. Bittner. Polaron–excitons and electron–vibrational band shapes in conjugated polymers. J. Chem. Phys., 118(9):4291–4296, Mar 2003.
118. A. S. Davydov. Excitons and solitons in molecular systems. Int. Rev. Cytology, 106:183, 1987.
119. A. S. Davydov. Solitons and energy transfer along protein molecules. J. Theor. Biol., 66(2):379–387, 1977.
120. A. S. Davydov. The theory of contraction of proteins under their excitation. J. Theor. Biol., 38:559–569, 1973.
121. Alwyn Scott. Davydov’s soliton. Phys. Rep., 217(1):1–67, 1992.
122. V. E. Zakharov and A. B. Shabat. Exact theory of two dimensional self-focusing and one-dmensional modulations of waves in nonlinear media. Sov. Phys. JETP, 34:62–69, 1972.
123. P. S. Lomdahl and W. C. Kerr. Do Davydov solitons exist at 300 K? Phys. Rev. Lett., 55(11):1235–1238, Sep 1985.
124. J. W. Schweitzer. Lifetime of the Davydov soliton. Phys. Rev. A, 45(12):8914–8923, Jun 1992.
125. W. Förner. Davydov solitons in proteins. Int. J. Quantum Chem., 64(3):351, 1997.
126. Konrad Knoll and Richard R. Schrock. Preparation of tert-butyl-capped polyenes containing up to 15 double bonds. J. Am. Chem. Soc., 111(20):7989–8004, 1989.
127. Stoyan Karabunarliev, Eric R. Bittner, and Martin Baumgarten. Franck–Condon spectra and electron-libration coupling in para-polyphenyls. J. Chem. Phys., 114(13):5863– 5870, 2001.
128. W. M. Gelbart, K. G. Speers, K. F. Freed, J. Jortner, and S. A. Rice. Boltzmann statistics and radiationless decay large molecules: optical selection rules. Chem. Phys. Lett., 6(4):354, 1970.
129. Walter Harrison. Applied Quantum Mechanics. World Scientific Publishing Company, Singapore, 2000.
130. Donald A. McQuarrie. Statistical Mechanics. Harper and Row, New York, 1976.