title: Single Molecule Spectroscopy of Monomeric LHCII: Experiment and Theory.
abstract: We derive approximate equations of motion for excited state dynamics of a multilevel open quantum system weakly interacting with light to describe fluorescence-detected single molecule spectra. Based on the Frenkel exciton theory, we construct a model for the chlorophyll part of the LHCII complex of higher plants and its interaction with previously proposed excitation quencher in the form of the lutein molecule Lut 1. The resulting description is valid over a broad range of timescales relevant for single molecule spectroscopy, i.e. from ps to minutes. Validity of these equations is demonstrated by comparing simulations of ensemble and single-molecule spectra of monomeric LHCII with experiments. Using a conformational change of the LHCII protein as a switching mechanism, the intensity and spectral time traces of individual LHCII complexes are simulated, and the experimental statistical distributions are reproduced. Based on our model, it is shown that with reasonable assumptions about its interaction with chlorophylls, Lut 1 can act as an efficient fluorescence quencher in LHCII.
authors.affiliation: Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.|Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic.
authors.forename: Pavel
authors.initials: P
authors.lastname: Malý
authors.affiliation: Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.
authors.forename: J Michael
authors.initials: JM
authors.lastname: Gruber
authors.affiliation: Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.
authors.forename: Rienk
authors.initials: R
authors.lastname: van Grondelle
authors.affiliation: Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.|Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic.
authors.forename: Tomáš
authors.initials: T
authors.lastname: Mančal