Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain
Abstract
With computer simulations of >100,000 atoms, the mechanism for the hydrophobic collapse of an idealized hydrated chain was obtained by tiling space with (0.2 nm)3 cubes and projecting the atomistic water molecule positions onto this grid. With the coarse-grained field thus defined, the string method in collective variables was used to compute a minimum free-energy pathway (MFEP) for the collapsing chain. These calculations provide a proof of principle for a coarse-grained description of water solvent. Furthermore, the calculated MFEP characterizes the mechanism for the collapse of the hydrated chain by providing a path of maximum likelihood for dynamical trajectories. The reliability of the calculated MFEP was confirmed with the use of conventional molecular dynamics trajectories. Analysis of the MFEP provides atomistic confirmation for the mechanism of hydrophobic collapse proposed by ten Wolde and Chandler. In particular, we show that length-scale-dependent hydrophobic dewetting is the rate-limiting step in the hydrophobic collapse of the considered chain.
Additional Information
© 2007 National Academy of Sciences. Freely available online through the PNAS open access option. Contributed by David Chandler, June 25, 2007 (received for review February 14, 2007) We thank Giovanni Ciccotti, Mauro Ferrario, Ray Kapral, and Luca Maragliano for useful discussions and the National Energy Research Scientific Computing Center for computing resources. T.F.M. was supported by Department of Energy Grants CHE-0345280 and DE-FG03–87ER13793. E.V.-E. was supported by the Miller Institute at University of California (Berkeley, CA), Office of Naval Research Grant N00014-04-1-0565, and National Science Foundation Grants DMS02-09959 and DMS02-39625. D.C. was supported by National Science Foundation Grant CHE-0543158. Author contributions: T.F.M., E.V.-E., and D.C. designed research, performed research, analyzed data, and wrote the paper. The authors declare no conflict of interest. This article contains supporting information online at www.pnas.org/cgi/content/full/0705830104/DC1.Attached Files
Published - MILpnas07.pdf
Supplemental Material - MILpnas07supfig10.pdf
Supplemental Material - MILpnas07supfig6.pdf
Supplemental Material - MILpnas07supfig7.pdf
Supplemental Material - MILpnas07supfig8.pdf
Supplemental Material - MILpnas07supfig9.pdf
Supplemental Material - MILpnas07suptxt.pdf
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Additional details
- PMCID
- PMC1955457
- Eprint ID
- 11034
- Resolver ID
- CaltechAUTHORS:MILpnas07
- Created
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2008-06-24Created from EPrint's datestamp field
- Updated
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2023-06-01Created from EPrint's last_modified field