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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.
The syndecans represent an ongoing research field focused on their regulatory roles in normal and pathological conditions. Syndecans role in cancer progression becomes well-documented, implicating their importance in diagnosis and even proposing vari
The measured conductance distribution for single molecule benzenediamine-gold junctions, based on 59,000 individual conductance traces recorded while breaking a gold point contact in solution, has a clear peak at 0.0064 G$_{0}$ with a width of $pm$ 4
The coupling between molecular exciton and gap plasmons plays a key role in single molecular electroluminescence induced by a scanning tunneling microscope (STM). But it has been difficult to clarify the complex experimental phenomena. By employing t
The infrared spectroscopy and dynamics of -CO labels in wild type and mutant insulin monomer and dimer are characterized from molecular dynamics simulations using validated force fields. It is found that the spectroscopy of monomeric and dimeric form
Electronic transport properties for single-molecule junctions have been widely measured by several techniques, including mechanically controllable break junctions, electromigration break junctions or by means of scanning tunneling microscopes. In par