Think globally, move locally: Coarse graining of effective free energy surfaces

Payel Das, Thomas A. Frewen, Yannis Kevrekidis, Cecilia Clementi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

Abstract

We present a multi-scale simulation methodology, based on data-mining tools for the extraction of low-dimensional reduction coordinates, to explore dynamically a protein model on its underlying effective folding free energy landscape. In practice, the averaged coarse-grained description of the local protein dynamics is extracted in terms of a few reduction coordinates from multiple, relatively short molecular dynamics trajectories. By exploiting the information collected from the fast relaxation dynamics of the system, the reduction coordinates are extrapolated "backward-in-time" to map globally the underlying low-dimensional free energy landscape. We demonstrate that the proposed method correctly identifies the transition state region on the reconstructed two-dimensional free energy surface of a model protein folding transition.

Original languageEnglish (US)
Title of host publicationCoping with Complexity
Subtitle of host publicationModel Reduction and Data Analysis
Pages113-131
Number of pages19
DOIs
StatePublished - Jan 1 2011
EventInternational Research Workshop: Coping with Complexity: Model Reduction and Data Analysis - Ambleside, United Kingdom
Duration: Aug 31 2009Sep 4 2009

Publication series

NameLecture Notes in Computational Science and Engineering
Volume75 LNCSE
ISSN (Print)1439-7358

Other

OtherInternational Research Workshop: Coping with Complexity: Model Reduction and Data Analysis
CountryUnited Kingdom
CityAmbleside
Period8/31/099/4/09

All Science Journal Classification (ASJC) codes

  • Modeling and Simulation
  • Engineering(all)
  • Discrete Mathematics and Combinatorics
  • Control and Optimization
  • Computational Mathematics

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    Das, P., Frewen, T. A., Kevrekidis, Y., & Clementi, C. (2011). Think globally, move locally: Coarse graining of effective free energy surfaces. In Coping with Complexity: Model Reduction and Data Analysis (pp. 113-131). (Lecture Notes in Computational Science and Engineering; Vol. 75 LNCSE). https://doi.org/10.1007/978-3-642-14941-2_6