Publications in Preparation


1. D. Montemayor, P. Huo, and D.F. Coker, in preparation for submission to J. Chem. Phys. (2013)

Coherent Excitation Energy Transfer in the LH II Light Harvesting System: A Partial Linearized Density Matrix Dynamics Study of Energy Transfer Rates Between Different Sub-units

2. M. Bellucci and D.F. Coker, in preparation for submission to JACS. (2013)

Theoretical Study of Enantioselective Catalysis in Excited State 1,3 Dipolar Cycloaddition Reactions

4. P. Huo, J. Moix, J. Cao, and D.F. Coker, submitted to J. Phys. Chem. Letts. (2013)

Theoretical Exploration of Excitation Energy Transfer and Charge Separation Dynamics in Photosystem II

5. S. Sanyal, D. MacKernan, and D.F. Coker, submitted to Biophys J. (2014)

On the Design Rationale of FRET Based Uni-Molecular Probes

6. Y.P. Tambouret and D.F. Coker, in preparation for submission to J. Chem. Phys. (2013)

Theoretical Study of Back Proton Transfer in 3-hydroxyflavone



Year 2013


80. Y. Wang, D. MacKernan, D. Cubero, and D.F. Coker, submitted to J. Chem. Phys. (2013)

Single Electron States in Polyethylene

79. M. Masia, E. Rivera, D. Montemayor, D.A. Murray, and D.F. Coker, in preparation for submission to J. Chem. Phys. (2013)

Intramolecular Contributions to the Spectral Density of Light Harvesting Complexes

78. P. Huo and D.F. Coker Springer Book Chapter (March, 2013)

Excitation Energy Transfer in Biological Light Harvesting Systems

77. P. Huo, T.F. Miller III, and D.F. Coker, submitted to J. Chem. Phys. 139, 151103 (2013)

Communication: Predictive Partial Linearized Path Integral Simulation of Condensed Phase Electron Transfer Dynamics

76. E. Rivera, D. Montemayor, M. Masia, and D.F. Coker J.Phys.Chem. 117, 55105521 (2013)

Influence of Site Dependent Pigment-Protein Interactions on Excitation Energy Transfer in Photosynthetic Light Harvesting



Year 2012


75. P. Huo and D.F. Coker J. Chem. Phys. 137, 22A535 (2012)

74. M. Bellucci and D.F. Coker J. Chem. Phys. 136, 194505 (2012)

Molecular Dynamics of Excited State Intramolecular Proton Transfer: 3-hydroxyflavone in Solution

73. P. Huo and D.F. Coker Mol. Phys. 110, 1035 (2012)

Semi-Classical Path Integral Nonadiabatic Dynamics: A Partial Linearized Classical Mapping Hamiltonian Approach

72. P. Huo and D.F. Coker J. Chem. Phys. 136, 115102 (2012)

Influence of Environment Induced Correlation Fluctuations in Electronic Coupling on Coherent Excitation Energy Transfer Dynamics in Model Photosynthetic Systems



Year 2011


71. J. Moix, J. Wu, P. Huo, D.F. Coker, and J. Cao J. Phys. Chem. Letts. 2, 3045 (2011)

70. C.J. Margulis, H.V.R. Annapureddy, P. de Base, D.F. Coker, J. Kohanoff, M. del Popolo JACS 133, 20186 (2011)

Excess Electrons in Room-Temperature Ionic Liquids

69. P. Huo and D.F. Coker J. Chem. Phys. 135, 20101 (2011)

Partial Linearized Density Matrix Dynamics for Dissipative, Non-adiabatic Quantum Evolution

68. M.A. Bellucci and D.F. Coker J. Chem. Phys. 135, 044115 (2011)

Empirical Valence Bond Models for Reactive Potential Energy Surfaces: A Parallel Multilevel Genetic Program Approach

67. P. Huo and D.F. Coker J. Phys. Chem. Letts. 2, 825 (2011)

Theoretical Study of Coherent Excitation Energy Transfer in Cryptophyte Phycocyanin 645 at Physiological Temperature



Year 2010


66. P. Huo and D.F. Coker J. Chem. Phys. 133, 184108 (2010)

Iterative Linearized Density Matrix Propagation for Modeling Coherent Excitation Energy Transfer in Photosynthetic Light Harvesting Systems

65. P. Huo, S. Bonella, L. Chen, and D.F. Coker Chem. Phys. 370, 87 (2010)

Linearized Approximations for Condensed Phase Non-Adiabatic Dynamics: Multi-layered Baths and Browninan Dynamics Implementation



Year 2009


64. J. Peng, T.C. Castonguay, D.F. Coker, and L.D. Ziegler J. Chem. Phys 131, 054501 (2009)

Ultrafast H2 and D2 Rotational Raman Responses in Near Critical CO2: An Experimental and Theoretical Study of Anistropic Solvation Dynamics

63. S. Bonella, D.F. Coker, D. MacKernan, R. Kapral, and G. Ciccotti in 'Energy Transfer Dynamics in Biomaterial Systems', Eds. I. Burghardt, V. May, D.A. Micha, and E.R. Bittner, Springer Series in Chemical Physics, Vol. 93, Springer Verlag, Heidelberg/Berlin (2009), ISBN 978-3-642-02307-1 (Print) 978-3-642-02306-4 (Online)

Trajectory Based Simulations of Quantum-Classical Systems



Year 2008


62. D.F. Coker, L. Chen, P. Huo, and S. Bonella in 'Multidmensional Quantum Mechanics with Trajectories', ed. by D.V. Shalashilin and M.P. de Miranda, p. 22-30 (CCP6, Daresbury Laboratory, 2008) ISBN: 978-0-9545289-8-0

Exploring the Linearized Approximation for Condensed Phase Non-adiabatic Dynamics: Multi-layered Baths

61.E. Dunkel, S. Bonella, and D.F. Coker, J. Chem. Phys. 129, 114106 (2008)

Iterative Linearized Approach to Non-adiabatic Dynamics

60. Z. Ma and D.F. Coker J. Chem. Phys. 128, 244108 (2008)

Quantum Initial Condition Sampling for Linearized Density Matrix Dynamics: Vibrational Pure Dephasing of Iodine in Krypton Matrices



Year 2006


59. D.F. Coker and S. Bonella in 'Computer Simulations in Condensed Matter: From Materials to Chemical Biology', Volume 1, Editors:M. Ferrario, G. Ciccotti, and K. Binder. Lecture Notes in Physics 703, 553 (Springer, Berlin, 2006)

Linearized Path Integral Methods for Quantum Time Correlation functions

58. D. F. Coker and S. Bonella in 'Quantum Dynamicsof Complex Molecular Systems', Editors: David Micha and Irene Burghardt, Chemical Physics 83, 275-294, (Springer, Berlin, 2006)

Linearized Non-adiabatic Dynamics in the Adiabatic Representation

57. G. Ciccott, D.F. Coker, and R. Krapral in 'Quantum Dynamics of Complex Molecular Systems' Editors: David Micha and Irene Burghardt, Chemical Physics 83, 275-294, (Springer, Berlin, 2006)

Quantum Statistical Dynamics with Trajectories



Year 2005


56. Z. Li, R. Sansom, S. Bonella, D.F. Coker, and A.S. Mullin J. Phys. Chem A. 109, 7657 (2005)

Trajectory Study of Supercollison Relaxation in Highly Vibrational Excited Pyrazine and CO2

55. S. Bonella and D.F. Coker J. Chem. Phys. 122, 194102 (2005)

Land-map, Linearized Approach to Non-adiabatic Dynamics Using the Mapping Formalism

54. S. Bonella, D. Montemayor, and D.F. Coker Proc. Natl. Acad. Sci. 102, 6715 (2005)

Linearized Path Integral Mapping Hamiltonian Approach for Calculating Nonadiabatic Time Correlation Functions

53. S. Bonella and D.F. Coker Comp. Phys. Commun. 169, 267 (2005)

Lienarized, Time-dependent, Non-adiabatic Quantum Correlation Functions

52. S. Causo, G. Ciccotti, S. Bonella, D. Montemayor, and D.F. Coker J. Phys. Chem. B. 109 6855 (2005)

An Adiabatic Linearized Path Integral Approach for Quantum Time Correlation Functions: Electronic Transport in Metal-Molten Salt Solutions



Year 2004


51. N. Yu and D.F. Coker Mol. Phys. 102, 1031 (2004)

Ion Pair state Emission of I2 in Rare Gas Matrices: Effects of Solvent Induced Symmetry Breaking

50. N. Yu, C.J. Margulis, and D.F. Coker J. Chem. Phys. 120, 3657 (2004)

Ultrafast Non-adiabatic Dynamics: Quasiclassical Calculation of the Transient Photoelectron Spectrum of I2-(CO2)8 Clusters



Year 2003


49. D. Cubero, N. Quirke, and D.F. Coker J. Chem. Phys. 119 2669 (2006)

Electronic Transport in Disordered N-alkanes: From Fluid Methane to Amorphous Polyethylene

48. D. Cubero, N. Quirke, and D.F. Coker Chem. Phys. Letts. 370, 21 (2003)

Electronic States for Excess Electrons in Polyethylene Compared to Long Chain Alkanes

47. S. Bonella and D.F. Coker J. Chem. Phys. 118, 4370 (2003)

Semi-classical Implementation of the Mapping Hamiltonian Approach for Non-adiabatic Dynamics: Focused Initial Distribution Sampling



Year 2001


46. N. Yu, C.J. Margulis, and D.F. Coker J. Phys. Chem. B. 105, 6728 (2001)

Influence of Solvation Environment on Excited State Avoided Crossings and Photo-dissociation Dynamics

45. C.J. Margulis, D.F. Coker, and R.M. Lynden-Bell Chem. Phys. Lett. 341, 557 (2001)

Symmetry Breaking of the Triiodide Ion in Acetonitrile Solution

44. S. Bonella and D.F. Coker J. Chem. Phys. 114, 7778 (2001)

A Semi-classical Limit for the Mapping Hamiltonian Approach to Electronically Non-adiabatic Dynamics

43. S. Bonella and D.F. Coker Chem. Phys. 268, 323 (2001)

Semiclassical Implementation of Mapping Hamiltonian Methods for General Nonadabatic Problems

42. J.A. MacKinnon, J. Eckert, D.F. Coker, and A.L.R. Bug J. Chem. Phys. 114, 10137 (2001)

Computational Study of Molecular Hydrogen in Zeolite Na-N Part II: Density of Rotational States and Inelastic Neutron Scattering Spectra

41. C.J. Margulis and D.F. Coker J. Chem. Phys. 114, 6744 (2001)

Modeling Solvation of Excited Electronic States of Flexible Polyatomic Molecules: DIM for I3 in Argon Clusters

40. C.J. Margulis, D.F. Coker, and R.M. Lynden-Bell J. Chem. Phys. 114, 367 (2001)

A Monte Carlo Study of the Symmetry Breaking of I3- in Aqeous Solution Using Multistate Diabatic Hamiltonian



Year 2000


39. C.J. Margulis and D.F. Coker J. Chem. Phys. 113, 6113 (2000)

Applying DIM for Flexible Polyatomic Electronic Excited States



Year 1999


38. C.J. Margulis, D.A. Horner, S. Bonella, and D.F. Coker J. Phys. Chem. A. 103, 9552 (1999)

Vibrational Dynamics of the I3 radical

37. C.R. Anderson, D.F. Coker, J. Eckert, and A.L.R. Bug J. Chem Phys. 111, 7599 (1999)

Computational Study of Molecular Hydrogen in Zeolite Na-A Part I: Potential Energy Surfaces and Thermodynamic Separation Factors for Ortho and Para Hydrogen

36. M.F. Herman and D.F. Coker J. Chem. Phys. 111, 1801 (1999)

Classical Mechanics and the Spreading of the Localized Wavepackets in Condensed Phase Molecular Systems

35. V.S. Batista and D.F. Coker J. Chem. Phys. 110, 6583 (1999)

Erratum: On Nonadiabatic Molecular Dynamics Simulations of the Photofragmentation and Geminate Recombination Dynamics in Size-Selected I2-Arn Cluster Ions

34. C. Margulis and D.F. coker J. Chem. Phys. 110, 5677 (1999)

Nonadiabatic Molecular Dynamics Simulations of the Photofragmentation and Geminate Recombination Dynamics in Size-Selected I2-(CO2)n Cluster Ions



Year 1998


33. Classical and Quantum Dynamics in Condensed Matter Simulations, Eds., B.J. Berne, G. Ciccotti, and D.F. Coker World Scentific, 1998

32. D.F. Coker, H.S. Mei, and J.P. Ryckaert, pp 539 - 582 in 'Classical and Quantum Dynamics in Condensed Matter Simulations', Eds. B.J. Berne, G. Ciccotti, and D.F. Coker World Scientific, 1998

Thermal Average Time Correlation Functions from Nonadabatic MD: Application to Rate Constants for Condensed Phase Non-adiabatic Reactions

31. D. Laria, G. Ciccotti, D.F. Coker, R. Kapral, and M. Ferrario, pp 697 - 720 in 'Cassical and Quantum Dynamics in Condensed Matter Simulations', Eds B.J. Berne, G. Ciccotti, and D.F. Coker World Scientific, 1998

Nonadiabatic Molecular Dynamics Method for Diffusion



Year 1997


30. V.S. Batista and D.F. Coker J. Chem. Phys. 106, 6923 (1997)

Nonadiabatic Molecular Dynamics Simulation of Ultrafast Pump-Probe Experiments on I2 in Solid Rare Gases

29. V.S. Batista and D.F. Coker J. Chem. Phys. 106, 7102 (1997)

Nonadiabatic Molecular Dynamics Simulation of the Photofragmentation and Geminate Recomination Dynamics in Size-Selected I2-Arn Cluster Ions



Year 1996


28. S. Bonella, G. Ciccotti, and D.F. Coker Molec. Phys. 89, 1203 (1996)

Research Note on the Semiclassical Limit of the Intermediate Scattering Function

27. V.S. Batista and D.F. Coker J.Chem.Phys. 105, 4033 (1996)

Nonadiabatic Molecular Dynamics Simulation of Photodissociation of I2 in Liquid Xenon

26. H.S. Mei, L. Xiao, and D.F. Coker J. Chem. Phys. 105, 3938 (1996)

Calculation of the Rotational Raman Spectrum of H2 in Ice

25. H.S. Mei and D.F. Coker J. Chem. Phys. 104, 4755 (1996)

Quantum Molecular Dynamics Studies of H2 Transport in Water



Year 1995


24. L. Xiao and D.F. Coker J. Chem. Phys. 102, 1107 (1995)

Nonadiabatic Dynamical Studies of the Rotational Raman Spectrum of H2 in Water

23. D.F. Coker and L. Xiao J. Chem. Phys. 102, 496 (1995)

Methods for Molecular Dynamics with Nonadiabatic Transitions



Year 1994


22. W. Wang, K.A. Nelson, L. Xiao, and D.F. Coker J. Chem. Phys. 101 9663 (1994)

Molecular Dynamics Simulation Studies of Solvent Cage Effects on Photodissociation in Condensed Phases

21. W. Wang, L. Dhar, J. Fourkas, K.A. Nelson, L. Xiao, and D.F. Coker in Femtosecond Reation Dynamics, Editor D.A. Weisma, (North-Holland, Amsterdam, 1994)

Femtosecond Spectroscopy of Reaction Dynamics in Condensed Phases

20. L. Xiao and D.F. Coker J. Chem. Phys. 100 8646 (1994)

The Influence of Nonadiabatic Rotational Transitions on the Lineshapes of the Rotational Raman Spectrum of H2 in Liquid Argon



Year 1993


19. D.F. Coker, 315-377 in Computer Simulation in Chemica Physics, Eds. M. Allen and D. Tildesley, NATO ASI series, (Kluwer, Dodrecht, 1993)

Computer Simulation Methods for Nonadiabatic Dynamics in Condensed Systems



Year 1992


18. D. Hsu and D.F. Coker J. Chem. Phys. 97, 5931 (1992)

Comment on: Quantum Dynamics via Mobile Basis Sets: The Diract Variational Principle

17. B. Space, H. Liu, B.J. Berne, and G. Martyna J. Chem. Phys. 97, 2002 (1992)

Density Dependence of Excess Electronic Ground State Energies in Simple Atomic Fluids

16. D. Hsu and D.F. Cooker J. Chem. PHys. 96 4266 (1992)

Quantum Dynamics via Mobile Basis Sets: The Dirac Virational Principle

15. B. Space and D.F. Coker J. Chem. Phys. 96, 652 (1992)

Dynamics of Trapping and Localization of Excess Electrons in Simple Fluids



Year 1991


14. J. Alper, H. Dothe, and D.F. Coker Chem. Phys. 153, 51 (1991)

Vibrational Structure of the Solvated Glycine Zwitterion

13. D.F. Coker and B.J. Berne 'Excess Electrons in Dielectric Media' Ed. Jean-Paul Jay Gerin and C. Ferradini (CRC Press, Boca Raton, Florida) 211-257 (1991)

Quantum Calculations on Excess Electrons in Disordered Media

12. B. Space and D.F. Coker J. Chem. Phys. 94, 1976 (1991)

Nonadiabatic Dynamics of Excited Excess Electrons in Simple Fluids M



Before 1990


11. D.F. Coker and B.J. Berne J. Chem. Phys. 89, 2128 (1988)

Excess Electronic States in Fluid Helium

10. D.F. Coker and R.O. Watts J. Phys. Chem. 91, 4866 (1987)

The Diffusion Monte Carlo Method for Quantum Systems at Non-Zero Temperatures

9. D.F. Coker and R.O. Watts J. Chem. Phys. 86, 5703 (1987)

Diffusion Monte Carlo Simulation of Condensed Systems

8. D.F. Coker, D. Thirumalai, and B.J. Berne J. Chem. Phys. 86, 5689 (1987)

Path Integral Monte Carlo Studies of the Behavior of Excess Electrons in simple Fluids

7. D.F. Coker and R.O. Watts, J. Phys. Chem. 91, 2513 (1987)

Structure and Vibrational Spectroscopy of the Water Dimer Using Quantum Simulation

6. D.F. Coker and R.O. Watts Molec. Phys. 58, 1113 (1986)

Quantum Simulations of Systems with Nodal Surfaces

5. D.F. Coker, R.E. Miller, and R.O. Watts J. Chem. Phys. 82, 3554 (1985)

The Infrared Predissociation Spectra of Water Clusters

4. L.A. Westling, M.G. Raymer, M.G. Sceats, and D.F. Coker Opt. Comm. 47, 212 (1983)

Observation of Intensity Fluctuations and Mode Correlations in a Broadband CW Dye Laser

3. D.F. Coker, J.R. Reimers, and R.O. Watts Aust. J. Phys. 35, 623 (1982)

Infrared Absorption Spectrum of Water

2. D.F. Coker and R.O. Watts, Molec. Phys. 44, 1303 (1981)

Chemical Equilibria in Mixtures of Bromine and Chlorine

1. D.F. Coker and R.O. Watts, Chem. Phys. Letts. 78, 333 (1981)

Computer Simulation of Reactive Liquids in Chemical Equilibrium



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