Published in Proc Natl Acad Sci U S A on July 19, 2010
Subcontinuum mass transport of condensed hydrocarbons in nanoporous media. Nat Commun (2015) 1.10
From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map. Proc Natl Acad Sci U S A (2011) 1.01
Using sketch-map coordinates to analyze and bias molecular dynamics simulations. Proc Natl Acad Sci U S A (2012) 0.98
Discovering conformational sub-states relevant to protein function. PLoS One (2011) 0.93
Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate:phosphate antiporter. Nat Commun (2015) 0.84
Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems. J Chem Theory Comput (2014) 0.84
Locating binding poses in protein-ligand systems using reconnaissance metadynamics. Proc Natl Acad Sci U S A (2012) 0.82
Evaluation of Dimensionality-reduction Methods from Peptide Folding-unfolding Simulations. J Chem Theory Comput (2013) 0.82
An experimental and computational investigation of spontaneous lasso formation in microcin J25. Biophys J (2010) 0.81
A Transport Model for Estimating the Time Course of ERK Activation in the C. elegans Germline. Biophys J (2015) 0.79
Rapid exploration of configuration space with diffusion-map-directed molecular dynamics. J Phys Chem B (2013) 0.79
Colloidal crystal grain boundary formation and motion. Sci Rep (2014) 0.77
Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions. J Chem Phys (2014) 0.75
Inherent structure versus geometric metric for state space discretization. J Comput Chem (2016) 0.75
A coarse-grained protein model in a water-like solvent. Sci Rep (2013) 0.75
Mapping and classifying molecules from a high-throughput structural database. J Cheminform (2017) 0.75
Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive Trajectories. ACS Cent Sci (2017) 0.75
VMD: visual molecular dynamics. J Mol Graph (1996) 117.02
GROMACS: fast, flexible, and free. J Comput Chem (2005) 27.22
Canonical dynamics: Equilibrium phase-space distributions. Phys Rev A Gen Phys (1985) 26.82
Some factors in the interpretation of protein denaturation. Adv Protein Chem (1959) 24.89
PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr (2004) 23.86
A global geometric framework for nonlinear dimensionality reduction. Science (2000) 23.62
Nonlinear dimensionality reduction by locally linear embedding. Science (2000) 19.41
Essential dynamics of proteins. Proteins (1993) 11.56
Interfaces and the driving force of hydrophobic assembly. Nature (2005) 8.54
Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem (2001) 7.13
Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps. Proc Natl Acad Sci U S A (2005) 6.24
Large-amplitude nonlinear motions in proteins. Phys Rev Lett (1992) 5.15
Reaction coordinates of biomolecular isomerization. Proc Natl Acad Sci U S A (2000) 3.71
Reaction coordinates and rates from transition paths. Proc Natl Acad Sci U S A (2005) 3.12
String method in collective variables: minimum free energy paths and isocommittor surfaces. J Chem Phys (2006) 2.53
Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics. Proteins (2002) 2.50
Hydrophobic free energy, micelle formation and the association of proteins with amphiphiles. J Mol Biol (1972) 2.40
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction. Proc Natl Acad Sci U S A (2006) 2.24
P versus Q: structural reaction coordinates capture protein folding on smooth landscapes. Proc Natl Acad Sci U S A (2006) 2.01
Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain. Proc Natl Acad Sci U S A (2007) 1.67
Graph Laplacian tomography from unknown random projections. IEEE Trans Image Process (2008) 1.54
Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water. Proc Natl Acad Sci U S A (2007) 1.49
Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution. J Am Chem Soc (2003) 1.44
Size-independent comparison of protein three-dimensional structures. Proteins (1995) 1.14
Learning the hidden structure of speech. J Acoust Soc Am (1988) 1.12
Detecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps. Proc Natl Acad Sci U S A (2009) 1.08
How complex is the dynamics of Peptide folding? Phys Rev Lett (2007) 0.97
Calculation of the free energy and cooperativity of protein folding. PLoS One (2007) 0.96
Deconstructing the native state: energy landscapes, function, and dynamics of globular proteins. J Phys Chem B (2009) 0.95
Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction. Proteins (2007) 0.91
Solubility and molecular conformations of n-alkane chains in water. J Phys Chem B (2009) 0.91
Conformation and solvation structure for an isolated n-octadecane chain in water, methanol, and their mixtures. J Phys Chem B (2006) 0.83
Coarse-graining the dynamics of a driven interface in the presence of mobile impurities: effective description via diffusion maps. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.79
Self-organization of n-alkane chains in water: length dependent crossover from helix and toroid to molten globule. J Phys Chem B (2009) 0.78
Inherent noise can facilitate coherence in collective swarm motion. Proc Natl Acad Sci U S A (2009) 2.19
Bistability and oscillations in the Huang-Ferrell model of MAPK signaling. PLoS Comput Biol (2007) 1.93
Hydrophobicity of protein surfaces: Separating geometry from chemistry. Proc Natl Acad Sci U S A (2008) 1.85
Anisotropic self-assembly of spherical polymer-grafted nanoparticles. Nat Mater (2009) 1.77
Optical imaging and control of genetically designated neurons in functioning circuits. Annu Rev Neurosci (2005) 1.68
Coarse master equation from Bayesian analysis of replica molecular dynamics simulations. J Phys Chem B (2005) 1.64
Oscillatory thermomechanical instability of an ultrathin catalyst. Science (2003) 1.51
Effect of surface polarity on water contact angle and interfacial hydration structure. J Phys Chem B (2007) 1.31
Effect of pressure on the phase behavior and structure of water confined between nanoscale hydrophobic and hydrophilic plates. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 1.30
The liquid-liquid transition in supercooled ST2 water: a comparison between umbrella sampling and well-tempered metadynamics. Faraday Discuss (2013) 1.30
Composite block copolymer stabilized nanoparticles: simultaneous encapsulation of organic actives and inorganic nanostructures. Langmuir (2007) 1.27
Enhanced surface hydrophobicity by coupling of surface polarity and topography. Proc Natl Acad Sci U S A (2009) 1.20
Preparation of poly(ethylene glycol) protected nanoparticles with variable bioconjugate ligand density. Biomacromolecules (2008) 1.19
Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation. J Chem Phys (2006) 1.18
Coarse-grained analysis of stochasticity-induced switching between collective motion states. Proc Natl Acad Sci U S A (2007) 1.15
Evaporation rate of water in hydrophobic confinement. Proc Natl Acad Sci U S A (2012) 1.13
A computational study of hydration, solution structure, and dynamics in dilute carbohydrate solutions. J Chem Phys (2005) 1.09
Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes. Phys Rev Lett (2005) 1.09
Detecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps. Proc Natl Acad Sci U S A (2009) 1.08
Liquid-liquid transition in ST2 water. J Chem Phys (2012) 1.03
Variable-free exploration of stochastic models: a gene regulatory network example. J Chem Phys (2007) 1.03
Effective potentials for 1:1 electrolyte solutions incorporating dielectric saturation and repulsive hydration. J Chem Phys (2007) 1.00
Water-like solvation thermodynamics in a spherically symmetric solvent model with two characteristic lengths. Proc Natl Acad Sci U S A (2007) 0.99
Generalization of the Wang-Landau method for off-lattice simulations. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 0.98
Apparent hysteresis in a driven system with self-organized drag. Phys Rev Lett (2004) 0.97
Universality of ionic criticality: size- and charge-asymmetric electrolytes. Phys Rev Lett (2005) 0.96
Integrating diffusion maps with umbrella sampling: application to alanine dipeptide. J Chem Phys (2011) 0.95
Properties of model atomic free-standing thin films. J Chem Phys (2011) 0.95
Phase transitions induced by nanoconfinement in liquid water. Phys Rev Lett (2009) 0.95
Chimeras in random non-complete networks of phase oscillators. Chaos (2012) 0.93
Managing heterogeneity in the study of neural oscillator dynamics. J Math Neurosci (2012) 0.93
Structure of the first- and second-neighbor shells of simulated water: quantitative relation to translational and orientational order. Phys Rev E Stat Nonlin Soft Matter Phys (2007) 0.92
Effect of interfacial water transport resistance on coupled proton and water transport across Nafion. J Phys Chem B (2011) 0.91
Solubility and molecular conformations of n-alkane chains in water. J Phys Chem B (2009) 0.91
Effect of temperature on the structure and phase behavior of water confined by hydrophobic, hydrophilic, and heterogeneous surfaces. J Phys Chem B (2009) 0.90
Model reduction for agent-based social simulation: coarse-graining a civil violence model. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.89
Fluid-phase behavior of binary mixtures in which one component can have two critical points. J Chem Phys (2006) 0.88
A computational investigation of thermodynamics, structure, dynamics and solvation behavior in modified water models. J Chem Phys (2008) 0.88
Family of tunable spherically symmetric potentials that span the range from hard spheres to waterlike behavior. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.87
Thermodynamic mechanism for solution phase chiral amplification via a lattice model. Proc Natl Acad Sci U S A (2009) 0.87
Coarse-grained computations for a micellar system. J Chem Phys (2005) 0.86
A constrained approach to multiscale stochastic simulation of chemically reacting systems. J Chem Phys (2011) 0.86
Substrate-dependent control of ERK phosphorylation can lead to oscillations. Biophys J (2011) 0.86
An equation-free approach to analyzing heterogeneous cell population dynamics. J Math Biol (2007) 0.86
Free energy barriers to evaporation of water in hydrophobic confinement. J Phys Chem B (2012) 0.86
Nonlinear intrinsic variables and state reconstruction in multiscale simulations. J Chem Phys (2013) 0.85
Universality class of criticality in the restricted primitive model electrolyte. Phys Rev Lett (2002) 0.85
Molecular structural order and anomalies in liquid silica. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 0.85
Coarse graining the dynamics of heterogeneous oscillators in networks with spectral gaps. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.84
Protected peptide nanoparticles: experiments and brownian dynamics simulations of the energetics of assembly. Nano Lett (2009) 0.84
Reduced models for binocular rivalry. J Comput Neurosci (2010) 0.84
Dissecting the energetics of hydrophobic hydration of polypeptides. J Phys Chem B (2011) 0.83
Structural order in glassy water. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.83
Suppression of sub-surface freezing in free-standing thin films of a coarse-grained model of water. Phys Chem Chem Phys (2014) 0.83
Evolution from surface-influenced to bulk-like dynamics in nanoscopically confined water. J Phys Chem B (2009) 0.83
Lindemann measures for the solid-liquid phase transition. J Chem Phys (2007) 0.83
A comparison of implicit- and explicit-solvent simulations of self-assembly in block copolymer and solute systems. J Chem Phys (2011) 0.82
A compartmental model for the bicoid gradient. Dev Biol (2010) 0.82
Coarse-grained kinetic computations for rare events: application to micelle formation. J Chem Phys (2005) 0.82
A computational investigation of the phase behavior and capillary sublimation of water confined between nanoscale hydrophobic plates. J Chem Phys (2012) 0.82
Modeling the anisotropic self-assembly of spherical polymer-grafted nanoparticles. J Chem Phys (2009) 0.82
Effect of surface polarity on the structure and dynamics of water in nanoscale confinement. J Phys Chem B (2009) 0.82
Waterlike glass polyamorphism in a monoatomic isotropic Jagla model. J Chem Phys (2011) 0.82
Atomistic simulations of micellization of sodium hexyl, heptyl, octyl, and nonyl sulfates. J Phys Chem B (2012) 0.82
Coarse analysis of collective motion with different communication mechanisms. Math Biosci (2008) 0.81
Spatially distributed stochastic systems: Equation-free and equation-assisted preconditioned computations. J Chem Phys (2006) 0.81
Computational study of the stability of the miniprotein trp-cage, the GB1 β-hairpin, and the AK16 peptide, under negative pressure. J Phys Chem B (2014) 0.81
An experimental and computational investigation of spontaneous lasso formation in microcin J25. Biophys J (2010) 0.81
Temperature and length scale dependence of solvophobic solvation in a single-site water-like liquid. J Chem Phys (2013) 0.81
Micellization behavior of coarse grained surfactant models. J Chem Phys (2010) 0.81
Structure, dynamics, and thermodynamics of a family of potentials with tunable softness. J Chem Phys (2011) 0.81
Ergodic directional switching in mobile insect groups. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.80
The effect of sequence on the conformational stability of a model heteropolymer in explicit water. J Chem Phys (2008) 0.80
Equation-free implementation of statistical moment closures. Phys Rev E Stat Nonlin Soft Matter Phys (2008) 0.80
Coarse-grained simulations of rapid assembly kinetics for polystyrene-b-poly(ethylene oxide) copolymers in aqueous solutions. J Phys Chem B (2008) 0.80
Dynamic density functional theory of solid tumor growth: Preliminary models. AIP Adv (2012) 0.80
Role of hydrophobic hydration in protein stability: a 3D water-explicit protein model exhibiting cold and heat denaturation. J Phys Chem B (2012) 0.80
Monte carlo simulations of micellization in model ionic surfactants: application to sodium dodecyl sulfate. Langmuir (2006) 0.80
Computational probes of molecular motion in the Lewis-Wahnstrom model for ortho-terphenyl. J Chem Phys (2006) 0.79
Phase behavior of low-functionality, telechelic star block copolymers. Faraday Discuss (2010) 0.79
Log-rolling micelles in sheared amphiphilic thin films. Phys Rev Lett (2005) 0.79
Computational characterization of the sequence landscape in simple protein alphabets. Proteins (2006) 0.79
Dynamics of solvent-free grafted nanoparticles. J Chem Phys (2012) 0.79
Cooperative origin of low-density domains in liquid water. Phys Rev Lett (2002) 0.79
Coarse-graining the dynamics of a driven interface in the presence of mobile impurities: effective description via diffusion maps. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.79
Monte carlo study of coulombic criticality in polyelectrolytes. Phys Rev Lett (2003) 0.79