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201
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Subramanian V, Evans DG. Excitation Energy Transfer in Model Light-Harvesting Antennae. J Phys Chem B 2003. [DOI: 10.1021/jp034196b] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vijaya Subramanian
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87113
| | - Deborah G. Evans
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87113
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202
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Mukamel S, Berman O. Self-consistent density matrix algorithm for electronic structure and excitations of molecules and aggregates. J Chem Phys 2003. [DOI: 10.1063/1.1625365] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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203
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Kleinekathöfer U, Barvík I, Heřman P, Kondov I, Schreiber M. Memory Effects in the Fluorescence Depolarization Dynamics Studied within the B850 Ring of Purple Bacteria. J Phys Chem B 2003. [DOI: 10.1021/jp035801d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Ulrich Kleinekathöfer
- International University Bremen, P.O. Box 750 561, 28725 Bremen, Germany, Institute of Physics, Charles University, Ke Karlovu 5, CZ-12116 Prague, Czech Republic, Department of Physics, University of Hradec Králové, V. Nejedlého 573, CZ-50003 Hradec Králové, Czech Republic, and Institut für Physik, Technische Universität, 09107 Chemnitz, Germany
| | - Ivan Barvík
- International University Bremen, P.O. Box 750 561, 28725 Bremen, Germany, Institute of Physics, Charles University, Ke Karlovu 5, CZ-12116 Prague, Czech Republic, Department of Physics, University of Hradec Králové, V. Nejedlého 573, CZ-50003 Hradec Králové, Czech Republic, and Institut für Physik, Technische Universität, 09107 Chemnitz, Germany
| | - Pavel Heřman
- International University Bremen, P.O. Box 750 561, 28725 Bremen, Germany, Institute of Physics, Charles University, Ke Karlovu 5, CZ-12116 Prague, Czech Republic, Department of Physics, University of Hradec Králové, V. Nejedlého 573, CZ-50003 Hradec Králové, Czech Republic, and Institut für Physik, Technische Universität, 09107 Chemnitz, Germany
| | - Ivan Kondov
- International University Bremen, P.O. Box 750 561, 28725 Bremen, Germany, Institute of Physics, Charles University, Ke Karlovu 5, CZ-12116 Prague, Czech Republic, Department of Physics, University of Hradec Králové, V. Nejedlého 573, CZ-50003 Hradec Králové, Czech Republic, and Institut für Physik, Technische Universität, 09107 Chemnitz, Germany
| | - Michael Schreiber
- International University Bremen, P.O. Box 750 561, 28725 Bremen, Germany, Institute of Physics, Charles University, Ke Karlovu 5, CZ-12116 Prague, Czech Republic, Department of Physics, University of Hradec Králové, V. Nejedlého 573, CZ-50003 Hradec Králové, Czech Republic, and Institut für Physik, Technische Universität, 09107 Chemnitz, Germany
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204
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Novoderezhkin V, Wendling M, van Grondelle R. Intra- and Interband Transfers in the B800−B850 Antenna of Rhodospirillum molischianum: Redfield Theory Modeling of Polarized Pump−Probe Kinetics. J Phys Chem B 2003. [DOI: 10.1021/jp035432l] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir Novoderezhkin
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory, 119992, Moscow, Russia, and Department of Biophysics and Physics of Complex Systems, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Markus Wendling
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory, 119992, Moscow, Russia, and Department of Biophysics and Physics of Complex Systems, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Rienk van Grondelle
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory, 119992, Moscow, Russia, and Department of Biophysics and Physics of Complex Systems, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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205
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Freiberg A, Rätsep M, Timpmann K, Trinkunas G, Woodbury NW. Self-Trapped Excitons in LH2 Antenna Complexes between 5 K and Ambient Temperature. J Phys Chem B 2003. [DOI: 10.1021/jp0344848] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Arvi Freiberg
- Institute of Physics, University of Tartu, Riia 142, Tartu 51014, Estonia, Department of Chemistry and Biochemistry and Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287, and Institute of Physics, Savanoriu pr. 231, LT-2053 Vilnius, Lithuania
| | - Margus Rätsep
- Institute of Physics, University of Tartu, Riia 142, Tartu 51014, Estonia, Department of Chemistry and Biochemistry and Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287, and Institute of Physics, Savanoriu pr. 231, LT-2053 Vilnius, Lithuania
| | - Kõu Timpmann
- Institute of Physics, University of Tartu, Riia 142, Tartu 51014, Estonia, Department of Chemistry and Biochemistry and Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287, and Institute of Physics, Savanoriu pr. 231, LT-2053 Vilnius, Lithuania
| | - Gediminas Trinkunas
- Institute of Physics, University of Tartu, Riia 142, Tartu 51014, Estonia, Department of Chemistry and Biochemistry and Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287, and Institute of Physics, Savanoriu pr. 231, LT-2053 Vilnius, Lithuania
| | - Neal W. Woodbury
- Institute of Physics, University of Tartu, Riia 142, Tartu 51014, Estonia, Department of Chemistry and Biochemistry and Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287, and Institute of Physics, Savanoriu pr. 231, LT-2053 Vilnius, Lithuania
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206
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207
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Spezia R, Aschi M, Nola AD, Valentin MD, Carbonera D, Amadei A. The effect of protein conformational flexibility on the electronic properties of a chromophore. Biophys J 2003; 84:2805-13. [PMID: 12719215 PMCID: PMC1302846 DOI: 10.1016/s0006-3495(03)70010-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
In this paper we address the question of how a protein environment can modulate the absorption spectrum of a chromophore during a molecular dynamics simulation. The effect of the protein is modeled as an external field acting on the unperturbed eigenstates of the chromophore. Using a first-principles method recently developed in our group, we calculated the perturbed electronic energies for each frame and the corresponding wavelength absorption during the simulation. We apply this method to a nanosencond timescale molecular dynamics simulation of the light-harvesting peridinin-chlorophyll-protein complex from Amphidinium carterae, where chlorophyll was selected among the chromophores of the complex for the calculation. The combination of this quantum-classical calculation with the analysis of the large amplitude motions of the protein makes it possible to point out the relationship between the conformational flexibility of the environment and the excitation wavelength of the chromophore. Results support the idea of the existence of a correlation between protein conformational flexibility and chlorophyll electronic transitions induced by light.
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Affiliation(s)
- Riccardo Spezia
- Dipartimento di Chimica, Università di Roma La Sapienza, Italy
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208
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Excitonic optical line shapes of cyclic and elliptically deformed molecular aggregates with 18 units: influence of quasi-static and dynamic disorder. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00003-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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209
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Novoderezhkin V, Salverda JM, van Amerongen H, van Grondelle R. Exciton Modeling of Energy-Transfer Dynamics in the LHCII Complex of Higher Plants: A Redfield Theory Approach. J Phys Chem B 2003. [DOI: 10.1021/jp027003d] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir Novoderezhkin
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory, 119992, Moscow, Russia, and Department of Biophysics, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Jante M. Salverda
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory, 119992, Moscow, Russia, and Department of Biophysics, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Herbert van Amerongen
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory, 119992, Moscow, Russia, and Department of Biophysics, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Rienk van Grondelle
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory, 119992, Moscow, Russia, and Department of Biophysics, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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210
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Tajkhorshid E, Aksimentiev A, Balabin I, Gao M, Isralewitz B, Phillips JC, Zhu F, Schulten K. Large Scale Simulation of Protein Mechanics and Function. PROTEIN SIMULATIONS 2003; 66:195-247. [PMID: 14631820 DOI: 10.1016/s0065-3233(03)66006-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois, USA
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211
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212
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Dahlbom M, Beenken W, Sundström V, Pullerits T. Collective excitation dynamics and polaron formation in molecular aggregates. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)01372-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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213
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Beenken WJD, Dahlbom M, Kjellberg P, Pullerits T. Potential surfaces and delocalization of excitons in dimers. J Chem Phys 2002. [DOI: 10.1063/1.1502647] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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214
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Damjanović A, Vaswani HM, Fromme P, Fleming GR. Chlorophyll Excitations in Photosystem I of Synechococcus elongatus. J Phys Chem B 2002. [DOI: 10.1021/jp020963f] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana Damjanović
- Department of Chemistry, University of California, Berkeley, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Max-Volmer-Laboratorium für Biophysikalische Chemie and Biochemie, Technische Universität Berlin, Berlin, Germany, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604
| | - Harsha M. Vaswani
- Department of Chemistry, University of California, Berkeley, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Max-Volmer-Laboratorium für Biophysikalische Chemie and Biochemie, Technische Universität Berlin, Berlin, Germany, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604
| | - Petra Fromme
- Department of Chemistry, University of California, Berkeley, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Max-Volmer-Laboratorium für Biophysikalische Chemie and Biochemie, Technische Universität Berlin, Berlin, Germany, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604
| | - Graham R. Fleming
- Department of Chemistry, University of California, Berkeley, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Max-Volmer-Laboratorium für Biophysikalische Chemie and Biochemie, Technische Universität Berlin, Berlin, Germany, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604
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215
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Sener MK, Lu D, Ritz T, Park S, Fromme P, Schulten K. Robustness and Optimality of Light Harvesting in Cyanobacterial Photosystem I. J Phys Chem B 2002. [DOI: 10.1021/jp020708v] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Melih K. Sener
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, Max-Volmer Laboratorium für Biophysikalische Chemie, Institut für Chemie, Fakultät 2, Technische Universität Berlin, D-10623 Berlin, Germany, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Deyu Lu
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, Max-Volmer Laboratorium für Biophysikalische Chemie, Institut für Chemie, Fakultät 2, Technische Universität Berlin, D-10623 Berlin, Germany, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Thorsten Ritz
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, Max-Volmer Laboratorium für Biophysikalische Chemie, Institut für Chemie, Fakultät 2, Technische Universität Berlin, D-10623 Berlin, Germany, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Sanghyun Park
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, Max-Volmer Laboratorium für Biophysikalische Chemie, Institut für Chemie, Fakultät 2, Technische Universität Berlin, D-10623 Berlin, Germany, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Petra Fromme
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, Max-Volmer Laboratorium für Biophysikalische Chemie, Institut für Chemie, Fakultät 2, Technische Universität Berlin, D-10623 Berlin, Germany, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Klaus Schulten
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, Max-Volmer Laboratorium für Biophysikalische Chemie, Institut für Chemie, Fakultät 2, Technische Universität Berlin, D-10623 Berlin, Germany, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
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216
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Zazubovich V, Jankowiak R, Small GJ. A High-Pressure Spectral Hole Burning Study of Correlation between Energy Disorder and Excitonic Couplings in the LH 2 Complex from Rhodopseudomonas Acidophila. J Phys Chem B 2002. [DOI: 10.1021/jp020540d] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- V. Zazubovich
- Ames Laboratory, U.S. Department of Energy and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - R. Jankowiak
- Ames Laboratory, U.S. Department of Energy and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - G. J. Small
- Ames Laboratory, U.S. Department of Energy and Department of Chemistry, Iowa State University, Ames, Iowa 50011
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