Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments
arXiv:1105.0710 · doi:10.1103/PhysRevLett.107.098102
Abstract
To explain the observed dynamics in equilibrium single-molecule measurements of biomolecules, the experimental observable is often chosen as a putative reaction coordinate along which kinetic behavior is presumed to be governed by diffusive dynamics. Here, we invoke the splitting probability as a test of the suitability of such a proposed reaction coordinate. Comparison of the observed splitting probability with that computed from the kinetic model provides a simple test to reject poor reaction coordinates. We demonstrate this test for a force spectroscopy measurement of a DNA hairpin.
References in corpus (3)
- Optimized free energies from bidirectional single-molecule force spectroscopy
- Improving signal-to-noise resolution in single molecule experiments using molecular constructs with short handles
- Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments
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