@article{738f1c783d1b4003bcb22d1a88c6fa86,
title = "Polymer reversal rate calculated via locally scaled diffusion map",
abstract = "A recent study on the dynamics of polymer reversal inside a nanopore by Huang and Makarov [J. Chem. Phys. 128, 114903 (2008)]10.1063/1.2890006 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.",
author = "Wenwei Zheng and Rohrdanz, {Mary A.} and Mauro Maggioni and Cecilia Clementi",
note = "Funding Information: We thank L. Huang and D. E. Makarov for sharing with us their computer program to simulate the polymer reversal dynamics and for insightful discussions. This work was supported by NSF (CDI-type I Grant No. 0835824 to C.C. and 0835712 to M.M., NSF CAREER award CHE-0349303 to C.C., and NSF CAREER award DMS-0650413 to M.M.), the Welch Foundation (C-1570 to C.C.), and the Sloan Foundation (to M.M.). Simulations and other computations were performed on the following shared resources at Rice University: the Rice Computational Research Clusters funded by NSF under Grant No. CNS-0421109 and in partnership between Rice University, AMD and Cray; the Cyberinfrastructure for Computational Research funded by NSF under Grant No. CNS-0821727; the Shared University Grid at Rice University funded by NSF under Grant No. EIA-0216467 and in partnership between Rice University, Sun Microsystems, and Sigma Solutions, Inc.; and a 2010 IBM Shared University Research (SUR) Award on IBM{\textquoteright}s Power7 high performance cluster (BlueBioU) to Rice University as part of IBM{\textquoteright}s Smarter Planet Initiatives in Life Science/Healthcare and in collaboration with the Texas Medical Center partners, with additional contributions from IBM, CISCO, Qlogic, and Adaptive Computing.",
year = "2011",
month = apr,
day = "14",
doi = "10.1063/1.3575245",
language = "English (US)",
volume = "134",
journal = "Journal of Chemical Physics",
issn = "0021-9606",
publisher = "American Institute of Physics Publising LLC",
number = "14",
}