相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap
Vojtech Spiwok et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Exploring the free energy surfaces of clusters using reconnaissance metadynamics
Gareth A. Tribello et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Determination of reaction coordinates via locally scaled diffusion map
Mary A. Rohrdanz et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Approaching a parameter-free metadynamics
Bradley M. Dickson
PHYSICAL REVIEW E (2011)
Simplifying the representation of complex free-energy landscapes using sketch-map
Michele Ceriotti et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Metadynamics
Alessandro Barducci et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2011)
Colored-Noise Thermostats a la Carte
Michele Ceriotti et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Free Energy Calculations: An Efficient Adaptive Biasing Potential Method
Bradley M. Dickson et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Systematic determination of order parameters for chain dynamics using diffusion maps
Andrew L. Ferguson et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
A self-learning algorithm for biased molecular dynamics
Gareth A. Tribello et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Atomic-Level Characterization of the Structural Dynamics of Proteins
David E. Shaw et al.
SCIENCE (2010)
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
Massimiliano Bonomi et al.
COMPUTER PHYSICS COMMUNICATIONS (2009)
Reconstructing the Equilibrium Boltzmann Distribution from Well-Tempered Metadynamics
M. Bonomi et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
Berk Hess et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Advillin Folding Takes Place on a Hypersurface of Small Dimensionality
Stefano Piana et al.
PHYSICAL REVIEW LETTERS (2008)
Well-tempered metadynamics: A smoothly converging and tunable free-energy method
Alessandro Barducci et al.
PHYSICAL REVIEW LETTERS (2008)
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
Alessandro Laio et al.
REPORTS ON PROGRESS IN PHYSICS (2008)
From A to B in free energy space
Davide Branduardi et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Complex network analysis of free-energy landscapes
D. Gfeller et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
How complex is the dynamics of peptide folding?
Rainer Hegger et al.
PHYSICAL REVIEW LETTERS (2007)
Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics
Giovanni Bussi et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Diffusion maps
Ronald R. Coifman et al.
APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS (2006)
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
Payel Das et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Geometric diffusions as a tool for harmonic analysis and structure definition of data: Multiscale methods
RR Coifman et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Laplacian eigenmaps for dimensionality reduction and data representation
M Belkin et al.
NEURAL COMPUTATION (2003)
Hessian eigenmaps: Locally linear embedding techniques for high-dimensional data
DL Donoho et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Free energy disconnectivity graphs: Application to peptide models
SV Krivov et al.
JOURNAL OF CHEMICAL PHYSICS (2002)
Escaping free-energy minima
A Laio et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Energy landscapes of model polyalanines
PN Mortenson et al.
JOURNAL OF CHEMICAL PHYSICS (2002)
A global geometric framework for nonlinear dimensionality reduction
JB Tenenbaum et al.
SCIENCE (2000)
分享论文
