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

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

Physica A: Statistical Mechanics and its Applications, 2014, vol. 394, issue C, 136-144

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.

Keywords: Hidden complexities; Collective variables; Non-Gaussian parameter; Cytosine-rich DNA (search for similar items in EconPapers)
Date: 2014
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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:394:y:2014:i:c:p:136-144

DOI: 10.1016/j.physa.2013.09.030

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