Correlated fluctuations in the exciton dynamics and spectroscopy of DNA

The absorption of ultraviolet light creates excitations in DNA, which subsequently start moving in the helix. Their fate is important for an understanding of photodamage, and is determined by the interplay of electronic couplings between bases and the structure of the DNA environment. We model the effect of dynamical fluctuations in the environment and study correlation, which is present when multiple base pairs interact with the same mode in the environment. We find that the correlations strongly affect the exciton dynamics, and show how they are observed in the decay of the anisotropy as a function of coherence and population time in a nonlinear optical experiment.

[1]  A. Ishizaki,et al.  Quantum Dynamics of System Strongly Coupled to Low-Temperature Colored Noise Bath: Reduced Hierarchy Equations Approach , 2005 .

[2]  A. Ishizaki,et al.  Nonperturbative non-Markovian quantum master equation: Validity and limitation to calculate nonlinear response functions , 2008 .

[3]  S. Marguet,et al.  UVB/UVC induced processes in model DNA helices studied by time-resolved spectroscopy: Pitfalls and tricks , 2006 .

[4]  R. Kubo,et al.  Time Evolution of a Quantum System in Contact with a Nearly Gaussian-Markoffian Noise Bath , 1989 .

[5]  C. Crespo-Hernández,et al.  UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases , 2008, Proceedings of the National Academy of Sciences.

[6]  B. Bouvier,et al.  Dipolar coupling between electronic transitions of the DNA bases and its relevance to exciton states in double helices , 2002 .

[7]  S. Mukamel.  Principles of Nonlinear Optical Spectroscopy , 1995 .

[8]  S. Roche.  Sequence dependent DNA-mediated conduction. , 2003, Physical review letters.

[9]  Qiang Shi,et al.  Efficient hierarchical Liouville space propagator to quantum dissipative dynamics. , 2009, The Journal of chemical physics.

[10]  A. V. Malyshev,et al.  Effects of the environment on the electric conductivity of double-stranded DNA molecules , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.

[11]  G. Fleming,et al.  Theoretical examination of quantum coherence in a photosynthetic system at physiological temperature , 2009, Proceedings of the National Academy of Sciences.

[12]  G. Cuniberti,et al.  Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories. , 2009, The Journal of chemical physics.

[13]  J. Knoester,et al.  Localization and coherent dynamics of excitons in the two-dimensional optical spectrum of molecular J-aggregates. , 2008, The Journal of chemical physics.

[14]  A. Leggett,et al.  Dynamics of the dissipative two-state system , 1987 .

[15]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[16]  Chandler,et al.  Coherent-incoherent transition and relaxation in condensed-phase tunneling systems. , 1991, Physical review. A, Atomic, molecular, and optical physics.

[17]  Midori Tanaka,et al.  Quantum Dissipative Dynamics of Electron Transfer Reaction System: Nonperturbative Hierarchy Equations Approach , 2009 .

[18]  T. Mančal,et al.  Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems , 2007, Nature.

[19]  Qiang Shi,et al.  Optical line shapes of molecular aggregates: hierarchical equations of motion method. , 2009, The Journal of chemical physics.

[20]  D. Markovitsi,et al.  Fluorescence of the DNA double helices (dAdT)n.(dAdT)n studied by femtosecond spectroscopy. , 2007, Physical chemistry chemical physics : PCCP.

[21]  S. Mukamel,et al.  Multidimensional femtosecond correlation spectroscopies of electronic and vibrational excitations. , 2000, Annual review of physical chemistry.

[22]  G. Cuniberti,et al.  Charge transport through biomolecular wires in a solvent: bridging molecular dynamics and model Hamiltonian approaches. , 2009, Physical review letters.

[23]  Minhaeng Cho,et al.  Coherent two-dimensional optical spectroscopy. , 2008, Chemical reviews.

[24]  E. Bittner,et al.  Calculations of the exciton coupling elements between the DNA bases using the transition density cube method. , 2007, The Journal of chemical physics.

[25]  E. Conwell,et al.  Charge-transfer excitons in DNA. , 2008, The journal of physical chemistry. B.

[26]  T. Jansen,et al.  Nonadiabatic effects in the two-dimensional infrared spectra of peptides: application to alanine dipeptide. , 2006, The journal of physical chemistry. B.

[27]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[28]  Milen Raytchev,et al.  Electronic energy delocalization and dissipation in single- and double-stranded DNA , 2007, Proceedings of the National Academy of Sciences.

[29]  Frenkel exciton model of ultrafast excited state dynamics in at DNA double helices , 2006, cond-mat/0610784.

[30]  T. Jansen,et al.  Simulation of vibrational energy transfer in two-dimensional infrared spectroscopy of amide I and amide II modes in solution. , 2008, The Journal of chemical physics.

[31]  G. Fleming,et al.  Unified treatment of quantum coherent and incoherent hopping dynamics in electronic energy transfer: reduced hierarchy equation approach. , 2009, The Journal of chemical physics.

[32]  G. Scholes,et al.  Coherent Intrachain Energy Migration in a Conjugated Polymer at Room Temperature , 2009, Science.

[33]  E. Díaz,et al.  THz oscillating currents enhanced by long-range correlations in DNA , 2009 .

[34]  G. Schatz,et al.  Electronic excitations and spectra in single-stranded DNA. , 2008, Journal of the American Chemical Society.

[35]  E. Bittner.  Lattice theory of ultrafast excitonic and charge-transfer dynamics in DNA. , 2006, The Journal of chemical physics.

[36]  W. Olson,et al.  3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. , 2003, Nucleic acids research.

[37]  Y. Tanimura.  Stochastic Liouville, Langevin, Fokker–Planck, and Master Equation Approaches to Quantum Dissipative Systems , 2006 .

[38]  C. Dekker,et al.  Direct measurement of electrical transport through DNA molecules , 2000, Nature.

[39]  R. Silbey,et al.  Optimization of exciton trapping in energy transfer processes. , 2009, The journal of physical chemistry. A.

[40]  H. Eugene Stanley,et al.  Metal–insulator transition in chains with correlated disorder , 2002, Nature.

[41]  V. Malyshev.  Localization length of one-dimensional exciton and low-temperature behaviour of radiative lifetime of J-aggregated dye solutions , 1993 .

[42]  K. Schulten,et al.  Light harvesting complex II B850 excitation dynamics. , 2009, The Journal of chemical physics.

[43]  R. Lavery,et al.  Influence of conformational dynamics on the exciton states of DNA oligomers , 2003 .

[44]  M. Cho,et al.  Ultrafast exciton transfers in DNA and its nonlinear optical spectroscopy. , 2008, The Journal of chemical physics.

[45]  Akihito Ishizaki,et al.  Dynamics of a multimode system coupled to multiple heat baths probed by two-dimensional infrared spectroscopy. , 2007, The journal of physical chemistry. A.

[46]  N. Makri.  Quantum Dissipative Dynamics: A Numerically Exact Methodology , 1998 .

[47]  R. Hochstrasser.  Two-dimensional IR-spectroscopy: polarization anisotropy effects , 2001 .

[48]  H. Torii.  Effects of intermolecular vibrational coupling and liquid dynamics on the polarized Raman and two-dimensional infrared spectral profiles of liquid N,N-dimethylformamide analyzed with a time-domain computational method. , 2006, The journal of physical chemistry. A.

[49]  N. Makri,et al.  Path Integral Calculation of Quantum Nonadiabatic Rates in Model Condensed Phase Reactions , 1996 .

[50]  S. Lloyd,et al.  Environment-assisted quantum walks in photosynthetic energy transfer. , 2008, The Journal of chemical physics.

[51]  Shaul Mukamel,et al.  Optical Stark Spectroscopy of a Brownian Oscillator in Intense Fields , 1994 .

[52]  David Beljonne,et al.  Beyond Förster resonance energy transfer in biological and nanoscale systems. , 2009, The journal of physical chemistry. B.

[53]  Animesh Datta,et al.  Highly efficient energy excitation transfer in light-harvesting complexes: The fundamental role of n , 2009, 0901.4454.

[54]  T. Jansen,et al.  Waiting time dynamics in two-dimensional infrared spectroscopy. , 2009, Accounts of chemical research.

[55]  Gil C. Claudio,et al.  Conformational disorder and ultrafast exciton relaxation in PPV-family conjugated polymers. , 2009, The journal of physical chemistry. B.