Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics

At What Chain Length Do Unbranched Alkanes Prefer Folded Conformations?

(2014) Jason N. Byrd et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Nonlinear Machine Learning of Patchy Colloid Self-Assembly Pathways and Mechanisms

(2014) Andrew W. Long et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Systematic screening of the cellular uptake of designed alpha-helix peptides

(2013) Kenji Usui et al.   BIOORGANIC & MEDICINAL CHEMISTRY

The new view of hydrophobic free energy

(2013) Robert L. Baldwin   FEBS LETTERS

Inhibition of α-helix-mediated protein–protein interactions using designed molecules

(2013) Valeria Azzarito et al.   Nature Chemistry

Time-Scale Separation from Diffusion-Mapped Delay Coordinates

(2013) T. Berry et al.   SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS

Helical poly(arginine) mimics with superior cell-penetrating and molecular transporting properties

(2013) Haoyu Tang et al.   Chemical Science

The Last Globally Stable Extended Alkane

(2012) Nils O. B. Lüttschwager et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

Metal–Organic-Framework-Based Tandem Molecular Sieves as a Dual Platform for Selective Microextraction and High-Resolution Gas Chromatographic Separation ofn-Alkanes in Complex Matrixes

(2011) Na Chang et al.   ANALYTICAL CHEMISTRY

Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach

(2011) Andrew L. Ferguson et al.   CHEMICAL PHYSICS LETTERS

Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide

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

Polymer reversal rate calculated via locally scaled diffusion map

(2011) Wenwei Zheng 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

Anomalous Behavior of Linear Hydrocarbon Chains in Water–DMSO Binary Mixture at Low DMSO Concentration

(2011) Rikhia Ghosh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis

(2011) G. Bhabha et al.   SCIENCE

Ionic polypeptides with unusual helical stability

(2011) Hua Lu et al.   Nature Communications

An Experimental and Computational Investigation of Spontaneous Lasso Formation in Microcin J25

(2010) Andrew L. Ferguson et al.   BIOPHYSICAL JOURNAL

Temperature dependent free energy surface of polymer folding from equilibrium and quench studies

(2010) Suman Chakrabarty et al.   JOURNAL OF CHEMICAL PHYSICS

Are Long-Chain Alkanes Hydrophilic?

(2010) Robin Underwood et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

DichroCalc--circular and linear dichroism online

(2009) B. M. Bulheller et al.   BIOINFORMATICS

Self-Organization ofn-Alkane Chains in Water: Length Dependent Crossover from Helix and Toroid to Molten Globule

(2009) Suman Chakrabarty et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Solubility and Molecular Conformations ofn-Alkane Chains in Water

(2009) Andrew L. Ferguson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-graining the dynamics of a driven interface in the presence of mobile impurities: Effective description via diffusion maps

(2009) Benjamin E. Sonday et al.   PHYSICAL REVIEW E

Detecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps

(2009) A. Singer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Cofactor binding and enzymatic activity in an unevolved superfamily ofde novodesigned 4-helix bundle proteins

(2009) Shona C. Patel et al.   PROTEIN SCIENCE

Graph Laplacian Tomography From Unknown Random Projections

(2008) R.R. Coifman et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

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

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

Proteins with weakly funneled energy landscapes challenge the classical structure-function paradigm

(2008) G. A. Papoian   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA