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. 2011 May 24;6(5):e19791. doi: 10.1371/journal.pone.0019791

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Hoefling et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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Comparison of different photon accumulation methods for a full polyproline-20 ensemble at with the experiment (black). Three different accumulation methods (colors) were considered. First, efficiencies were calculated from the full ensemble (blue), for which each photon burst has been combined from photons of all cis and trans simulations, and which therefore average over all motions and heterogeneities covered by the simulations. Second, each efficiency value was calculated from photons of all simulations of a randomly chosen isomer (green), thereby averaging over all dye motions but not over different isomers. Third, each efficiency value is derived from photons of one single trajectory, and weighted by the appropriate ensemble probability (red). The impact of the cis-isomers is demonstrated by comparison to the all-trans only efficiency histogram (magenta). The bootstrapping standard error (Fig. 8) of the all-trans isomers is drawn as light red area. Efficiency histograms were normalized to their maxima.

Inline graphic — Comparison of different photon accumulation methods for a full polyproline-20 ensemble at with the experiment (black). Three different accumulation methods (colors) were considered. First, efficiencies were calculated from the full ensemble (blue), for which each photon burst has been combined from photons of all cis and trans simulations, and which therefore average over all motions and heterogeneities covered by the simulations. Second, each efficiency value was calculated from photons of all simulations of a randomly chosen isomer (green), thereby averaging over all dye motions but not over different isomers. Third, each efficiency value is derived from photons of one single trajectory, and weighted by the appropriate ensemble probability (red). The impact of the cis-isomers is demonstrated by comparison to the all-trans only efficiency histogram (magenta). The bootstrapping standard error (Fig. 8) of the all-trans isomers is drawn as light red area. Efficiency histograms were normalized to their maxima.