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note
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In the dynamic hole burning experiment, the ca. 1 ps pump pulse is asymmetric in time (see Materials and Methods), so delay zero is not well-defined. It was chosen 600 fs after the initial fast rise of the pump pulse.
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One principal difference between refs 8 and 9 and our model should be mentioned: refs 8 and 9 follow the idea of a normal mode calculation, and consequently the coupling matrix contains forces while in our model the coupling Hamiltonian has the units of an energy.
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note
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The terminal carboxyl groups and carboxyl groups of amino acid side chains can be neglected since their frequency is somewhat lower or higher than the typical amide I frequency, depending on protonation, i.e., pH.
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The fact that the location of the individual dipoles with respect to the peptide groups matters arises because the dipole approximation is used for V.
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6 Diagonalizing of one sample matrix of one conformer of scyllatoxin takes ca. 1 min on a silicon graphics 2000 workstation and would take 45 h for BPTI.
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