@article{e27d25b7d387432088bd78a59af1b76e,
title = "Determination of reaction coordinates via locally scaled diffusion map",
abstract = "We present a multiscale method for the determination of collective reaction coordinates for macromolecular dynamics based on two recently developed mathematical techniques: diffusion map and the determination of local intrinsic dimensionality of large datasets. Our method accounts for the local variation of molecular configuration space, and the resulting global coordinates are correlated with the time scales of the molecular motion. To illustrate the approach, we present results for two model systems: all-atom alanine dipeptide and coarse-grained src homology 3 protein domain. We provide clear physical interpretation for the emerging coordinates and use them to calculate transition rates. The technique is general enough to be applied to any system for which a Boltzmann-sampled set of molecular configurations is available.",
author = "Rohrdanz, {Mary A.} and Wenwei Zheng and Mauro Maggioni and Cecilia Clementi",
note = "Funding Information: This work was supported by National Science Foundation (NSF) (CDI-type I Grant No. 0835824 to C.C. and Grant No. 0835712 to M.M., NSF CAREER Award No. CHE-0349303 to C.C., and NSF CAREER Award No. 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's Power7 high performance cluster (BlueBioU) to Rice University as part of IBM'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. We thank Paul Ledbetter for useful discussions.",
year = "2011",
month = mar,
day = "28",
doi = "10.1063/1.3569857",
language = "English (US)",
volume = "134",
journal = "Journal of Chemical Physics",
issn = "0021-9606",
publisher = "American Institute of Physics Publising LLC",
number = "12",
}