Comparing normal modes across different models and scales: Hessian reductionversuscoarse-graining

Experimental and theoretical IR study of methanol and ethanol conversion over H-SAPO-34

(2011) Karen Hemelsoet et al.   CATALYSIS TODAY

Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian

(2011) An Ghysels et al.   Journal of Chemical Theory and Computation

MSCALE: A General Utility for Multiscale Modeling

(2011) H. Lee Woodcock et al.   Journal of Chemical Theory and Computation

Normal Mode Analysis in Zeolites: Toward an Efficient Calculation of Adsorption Entropies

(2011) Bart A. De Moor et al.   Journal of Chemical Theory and Computation

Theoretical Perspectives on Protein Folding

(2010) D. Thirumalai et al.   Annual Review of Biophysics

TAMkin: A Versatile Package for Vibrational Analysis and Chemical Kinetics

(2010) An Ghysels et al.   Journal of Chemical Information and Modeling

Efficient computation of compliance matrices in redundant internal coordinates from Cartesian Hessians for nonstationary points

(2010) Kai Brandhorst et al.   JOURNAL OF CHEMICAL PHYSICS

First Principle Kinetic Studies of Zeolite-Catalyzed Methylation Reactions

(2010) Veronique Van Speybroeck et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Application of Elastic Network Models to Proteins in the Crystalline State

(2009) Demian Riccardi et al.   BIOPHYSICAL JOURNAL

Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach

(2009) A. Ghysels et al.   JOURNAL OF CHEMICAL PHYSICS

Approximate normal mode analysis based on vibrational subsystem analysis with high accuracy and efficiency

(2009) Jeffrey Hafner et al.   JOURNAL OF CHEMICAL PHYSICS

Localizing normal modes in large molecules

(2009) Christoph R. Jacob et al.   JOURNAL OF CHEMICAL PHYSICS

Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules

(2009) A. Ghysels et al.   Journal of Chemical Theory and Computation

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Biomolecules under mechanical force

(2009) Sanjay Kumar et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Coordinate-dependent diffusion in protein folding

(2009) R. B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of Surface Water on Protein Dynamics Studied by a Novel Coarse-Grained Normal Mode Approach

(2008) Lei Zhou et al.   BIOPHYSICAL JOURNAL

A Unification of the Elastic Network Model and the Gaussian Network Model for Optimal Description of Protein Conformational Motions and Fluctuations

(2008) Wenjun Zheng   BIOPHYSICAL JOURNAL

CHARMMing: A New, Flexible Web Portal for CHARMM

(2008) Benjamin T. Miller et al.   Journal of Chemical Information and Modeling

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

(2008) H. Lee Woodcock et al.   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

Calculating Reaction Rates with Partial Hessians: Validation of the Mobile Block Hessian Approach

(2008) A. Ghysels et al.   Journal of Chemical Theory and Computation

Capture of hydroxymethylene and its fast disappearance through tunnelling

(2008) Peter R. Schreiner et al.   NATURE

Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model

(2008) E. P. O'Brien et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA