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Systematic detection of hidden complexities in the unfolding mechanism of a cytosine-rich DNA strand

Author

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  • Smiatek, Jens
  • Janssen-Müller, Daniel
  • Friedrich, Rudolf
  • Heuer, Andreas

Abstract

We investigate the unfolding pathway of a cytosine-rich DNA structure via molecular dynamics simulations. By the study of the essential dynamics, we are able to identify a hidden complexity in the description of the dynamics in terms of the first two eigenvectors which are used as collective variables. This complexity can be mainly explained by non-Gaussian fluctuations due to contributions arising from the disregarded set of eigenvectors. We introduce the local non-Gaussian parameter as a tool for the detection of hidden complexities. The usage of this parameter allows a fast and reliable investigation for the determination of the important minimal number of eigenvectors which is needed for a sufficient description of molecular unfolding motion.

Suggested Citation

  • Smiatek, Jens & Janssen-Müller, Daniel & Friedrich, Rudolf & Heuer, Andreas, 2014. "Systematic detection of hidden complexities in the unfolding mechanism of a cytosine-rich DNA strand," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 394(C), pages 136-144.
    • Handle: RePEc:eee:phsmap:v:394:y:2014:i:c:p:136-144
    DOI: 10.1016/j.physa.2013.09.030
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