Combining Theory and Experiment
Simulation and Interpretation of (Single Molecule) Experiments

Single molecule coherent diffractive imaging is a promising tool for structure determination of bio molecules. We develop methods allowing image reconstruction from spares scattering patterns and investigate from computer simulations how radiation damage limits the applicability of this method.
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The challenges of single molecule scattering experiments are the unknown random molecule orientation in each shot and the low signal to noise ratio due to the very low expected photon count. We developed a correlation-based approach to determine the molecular structure de novo from as few as three coherently scattered photons per image.
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Atomic force microscopy (AFM), biomembrane force probe experiments, and optical tweezer applications allow to measure the response of single molecules to mechanical stress with high precision. We developed a theory to reconstruct force profiles from AFM spectra at varying loading rates, without requiring increased resolution.
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The force required to rupture the streptavidin-biotin complex has been calculated by computer simulations which agrees well with the value obtained by single molecule atomic force microscope (AFM) experiments. Binding forces and their specificity are attributed to a hydrogen bond network and are studied in simulations of the rupture event.
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Single molecule fluorescence resonance energy transfer (smFRET) experiments exploit the distance dependency of the measurable transfer efficiency between two dyes to determine distances on the nm scale. In MD simulations, the mutual orientation of the dyes is accessible. Combining both methods results in more accurate distances.

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FRETsg is a tool for a fast qualitative analysis of multiple FRET (fluorescence resonance energy transfer) experiments. FRET experiments principally yield the distances between fluorescent dyes, which are commonly used for labelling proteins, DNA, RNA, etc. If multiple FRET experiments are done, it is possible to build a 3D model of the labelled positions.
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Single molecule Fluorescence Resonance Energy Transfer (FRET) experiments are a powerful and versatile tool for studying conformational motions of single biomolecules at a millisecond time scale. Typically, the small number of recorded photons limits the achieved time resolution.
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Activation of the titin kinase, the catalytic domain of the muscle protein titin, requires major conformational rearrangements resulting in the exposure of its phosphorylation site. Force probe MD simulations can give a detailed description of the activation mechanism and, hence, can test the hypothesis that it is the force sensor for the muscle cell.
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The mechanical properties of viral shells are crucial for viral assembly and infection. To study their distribution and heterogeneity on the viral surface, we have carried out atomistic force-probe molecular dynamics simulations of the complete shell of Southern Bean Mosaic Virus (SBMV), a prototypical T=3 virus, in explicit solvent.
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