Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables

Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

(2013) Mary A. Rohrdanz et al.   Annual Review of Physical Chemistry

Nonlinear manifold learning for model reduction in finite elastodynamics

(2013) Daniel Millán et al.   COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING

Demonstrating the Transferability and the Descriptive Power of Sketch-Map

(2013) Michele Ceriotti et al.   Journal of Chemical Theory and Computation

Simulations: The dark side

(2013) D. Frenkel   European Physical Journal Plus

Nonlinear manifold learning for meshfree finite deformation thin-shell analysis

(2012) Daniel Millán et al.   INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING

Reverse engineering the euglenoid movement

(2012) M. Arroyo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

(2012) G. A. Tribello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Essential dynamics: foundation and applications

(2012) Isabella Daidone et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

New advances in metadynamics

(2012) Ludovico Sutto et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide

(2011) Andrew L. Ferguson et al.   JOURNAL OF CHEMICAL PHYSICS

Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap

(2011) Vojtěch Spiwok et al.   JOURNAL OF CHEMICAL PHYSICS

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Weak Long-Range Correlated Motions in a Surface Patch of Ubiquitin Involved in Molecular Recognition

(2011) R. Bryn Fenwick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Simplifying the representation of complex free-energy landscapes using sketch-map

(2011) Michele Ceriotti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maps of protein structure space reveal a fundamental relationship between protein structure and function

(2011) M. Osadchy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations

(2010) Ron O. Dror et al.   JOURNAL OF GENERAL PHYSIOLOGY

Systematic determination of order parameters for chain dynamics using diffusion maps

(2010) A. L. Ferguson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A self-learning algorithm for biased molecular dynamics

(2010) Gareth A. Tribello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

On the optimum support size in meshfree methods: A variational adaptivity approach with maximum-entropy approximants

(2009) Adrian Rosolen et al.   INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING

Adaptive biasing force method for scalar and vector free energy calculations

(2008) Eric Darve et al.   JOURNAL OF CHEMICAL PHYSICS

Algorithmic dimensionality reduction for molecular structure analysis

(2008) W. Michael Brown et al.   JOURNAL OF CHEMICAL PHYSICS

Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes

(2008) Vojtěch Spiwok et al.   JOURNAL OF MOLECULAR MODELING

The Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 β-Hairpin

(2008) Massimiliano Bonomi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems

(2008) R. R. Coifman et al.   MULTISCALE MODELING & SIMULATION

A simple embedding method for solving partial differential equations on surfaces

(2007) Steven J. Ruuth et al.   JOURNAL OF COMPUTATIONAL PHYSICS