Linked Life Data

21495744

Source:http://linkedlifedata.com/resource/pubmed/id/21495744

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
14
pubmed:dateCreated
2011-4-18
pubmed:abstractText
A recent study on the dynamics of polymer reversal inside a nanopore by Huang and Makarov [J. Chem. Phys. 128, 114903 (2008)] demonstrated that the reaction rate cannot be reproduced by projecting the dynamics onto a single empirical reaction coordinate, a result suggesting the dynamics of this system cannot be correctly described by using a single collective coordinate. To further investigate this possibility we have applied our recently developed multiscale framework, locally scaled diffusion map (LSDMap), to obtain collective reaction coordinates for this system. Using a single diffusion coordinate, we obtain a reversal rate via Kramers expression that is in good agreement with the exact rate obtained from the simulations. Our mathematically rigorous approach accounts for the local heterogeneity of molecular configuration space in constructing a diffusion map, from which collective coordinates emerge. We believe this approach can be applied in general to characterize complex macromolecular dynamics by providing an accurate definition of the collective coordinates associated with processes at different time scales.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Apr
pubmed:issn
1089-7690
pubmed:author
pubmed:issnType
Electronic
pubmed:day
14
pubmed:volume
134
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
144109
pubmed:meshHeading
pubmed:year
2011
pubmed:articleTitle
Polymer reversal rate calculated via locally scaled diffusion map.
pubmed:affiliation
Department of Chemistry, Rice University, Houston, Texas 77005, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, Non-P.H.S., Research Support, Non-U.S. Gov't