Publication
Exploring the energy landscapes of flexible molecular loops using higher-dimensional continuation
Journal Article (2013)
Journal
Journal of Computational Chemistry
Pages
234-244
Volume
34
Number
3
Doc link
http://dx.doi.org/10.1002/jcc.23128
File
Abstract
The conformational space of a flexible molecular loop includes the set of conformations fulfilling the geometric loop-closure constraints and its energy landscape can be seen as a scalar field defined on this implicit set. Higher-dimensional continuation tools, recently developed in dynamical systems and also applied to robotics, provide efficient algorithms to trace out implicitly defined sets. This article describes these tools and applies them to obtain full descriptions of the energy landscapes of short molecular loops that, otherwise, can only be partially explored, mainly via sampling. Moreover, to deal with larger loops, this article exploits the higher-dimensional continuation tools to find local minima and minimum energy transition paths between them, without deviating from the loop-closure constraints. The proposed techniques are applied to previously studied molecules revealing the intricate structure of their energy landscapes.
Categories
robots.
Author keywords
molecular loop modeling, energy landscapes, differential geometry, higher-dimensional continuation, manifolds, bifurcations
Scientific reference
J.M. Porta and L. Jaillet. Exploring the energy landscapes of flexible molecular loops using higher-dimensional continuation. Journal of Computational Chemistry, 34(3): 234-244, 2013.
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