Citation Impact

Citing Papers

Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation
2014 StandoutScienceNobel
Atomic-Level Characterization of the Structural Dynamics of Proteins
2010 StandoutScienceNobel
Coordinate-dependent diffusion in protein folding
2009
Reaction coordinates and rates from transition paths
2005
Full configuration interaction perspective on the homogeneous electron gas
2012
Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides
2009
GROMACS: Fast, flexible, and free
2005 Standout
Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water
2008
Atomic packing and short-to-medium-range order in metallic glasses
2006 StandoutNature
Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis 1 1Edited by A. R. Fersht
1999 StandoutNobel
The Amber biomolecular simulation programs
2005 Standout
Restoring the Density-Gradient Expansion for Exchange in Solids and Surfaces
2008 Standout
Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme
2009 Nature
Synthetic Par polarity induces cytoskeleton asymmetry in unpolarized mammalian cells
2023 StandoutNobel
Strongly Constrained and Appropriately Normed Semilocal Density Functional
2015 Standout
Scalable molecular dynamics with NAMD
2005 Standout
Uracil–DNA glycosylases SMUG1 and UNG2 coordinate the initial steps of base excision repair by distinct mechanisms
2007
Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA
1991 StandoutNobel
Uniquantal Release through a Dynamic Fusion Pore Is a Candidate Mechanism of Hair Cell Exocytosis
2014 StandoutNobel
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
2008 Standout
Relevance of the Slowly Varying Electron Gas to Atoms, Molecules, and Solids
2006
Microtubule Minus-End Stabilization by Polymerization-Driven CAMSAP Deposition
2014
Towards an exact description of electronic wavefunctions in real solids
2012 Nature
Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations
2003 StandoutNobel
Torsion angle dynamics for NMR structure calculation with the new program Dyana
1997 StandoutNobel
The crosstalk between microtubules, actin and membranes shapes cell division
2020
Pushing the frontiers of density functionals by solving the fractional electron problem
2021 StandoutScienceNobel
Heterogeneity of functional groups in a metal–organic framework displays magic number ratios
2015 StandoutNobel
The surface constraint all atom model provides size independent results in calculations of hydration free energies
1998 StandoutNobel
Machine learning for autonomous crystal structure identification
2017
Quantifying Transient 3D Dynamical Phenomena of Single mRNA Particles in Live Yeast Cell Measurements
2013 StandoutNobel
Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions
2013
From A to B in free energy space
2007
First-principles calculations for point defects in solids
2014 Standout
Transport in Proton Conductors for Fuel-Cell Applications:  Simulations, Elementary Reactions, and Phenomenology
2004 Standout
Computer Simulation of Liquids
2017 Standout
Femtosecond reaction dynamics in the gas-to-liquid transition region: Observation of a three-phase density dependence
1996 StandoutNobel
Calculating Structures and Free Energies of Complex Molecules:  Combining Molecular Mechanics and Continuum Models
2000 Standout
Tailored Porous Materials
1999 StandoutNobel
Keeping the shape but changing the charges: A simulation study of urea and its iso-steric analogs
1996 StandoutNobel
Lanthanide-Activated Phosphors Based on 4f-5d Optical Transitions: Theoretical and Experimental Aspects
2017 Standout
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
2007
Testing density functionals for structural phase transitions of solids under pressure: Si, SiO2, and Zr
2013
Accurate all-electron correlation energies for the closed-shell atoms from Ar to Rn and their relationship to the corresponding MP2 correlation energies
2011
Obtaining reaction coordinates by likelihood maximization
2006
Reversible multiple time scale molecular dynamics
1992 Standout
Constant pressure molecular dynamics simulation: The Langevin piston method
1995 Standout
How Hydrophobic Buckminsterfullerene Affects Surrounding Water Structure
2008 StandoutNobel
Detailed Hydration Maps of Benzene and Cyclohexane Reveal Distinct Water Structures
2004 StandoutNobel
Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach
2011
Evaluation and Optimization of Discrete State Models of Protein Folding
2012 StandoutNobel
Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide
2011
Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information
2009
Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method
2006
Constant pressure molecular dynamics algorithms
1994 Standout
Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein
2010
Further evidence for involvement of a noncanonical function of uracil DNA glycosylase in class switch recombination
2009 StandoutNobel
Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation
1997 Standout
Hydrogen-bond kinetics in liquid water
1996 StandoutNature
Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint
2009
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
2006
A meta-GGA Made Free of the Order of Limits Anomaly
2012
Canonical sampling through velocity rescaling
2007 Standout
Practical and conceptual path sampling issues
2015
Control of Chemical Dynamics by Lasers: Theoretical Considerations
2010
Detection of Subtle Dynamical Changes Induced by Unresolved “Conformational Coordinates” in Single-Molecule Trajectories via Goodness-of-Fit Tests
2010
Nonlinear machine learning in simulations of soft and biological materials
2017
Toward Accurate Microscopic Calculation of Solvation Entropies: Extending the Restraint Release Approach to Studies of Solvation Effects
2009 StandoutNobel
A reactive potential for hydrocarbons with intermolecular interactions
2000 Standout
The SIESTA method forab initioorder-Nmaterials simulation
2002 Standout
Photochromism of Diarylethene Molecules and Crystals: Memories, Switches, and Actuators
2014 Standout
Nonlinear Machine Learning of Patchy Colloid Self-Assembly Pathways and Mechanisms
2014
Quantum Mechanical Continuum Solvation Models
2005 Standout
Disentangling Rotational Dynamics and Ordering Transitions in a System of Self-Organizing Protein Nanorods via Rotationally Invariant Latent Representations
2021 StandoutNobel
String method in collective variables: Minimum free energy paths and isocommittor surfaces
2006
Determination of reaction coordinates via locally scaled diffusion map
2011
Isomerization of Bicyclo[1.1.0]butane by Means of the Diffusion Quantum Monte Carlo Method
2010
Fast Parallel Algorithms for Short-Range Molecular Dynamics
1995 Standout
Renormalizing SMD: The Renormalization Approach and Its Use in Long Time Simulations and Accelerated PMF Calculations of Macromolecules
2010 StandoutNobel
Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution
1997 StandoutNobel
Overcoming barriers in trajectory space: Mechanism and kinetics of rare events via Wang–Landau enhanced transition path sampling
2010
COMPASS:  An ab Initio Force-Field Optimized for Condensed-Phase ApplicationsOverview with Details on Alkane and Benzene Compounds
1998 Standout
Simulating the Effect of DNA Polymerase Mutations on Transition-State Energetics and Fidelity:  Evaluating Amino Acid Group Contribution and Allosteric Coupling for Ionized Residues in Human Pol β
2006 StandoutNobel
A smooth particle mesh Ewald method
1995 Standout
Competing nucleation pathways in a mixture of oppositely charged colloids: Out-of-equilibrium nucleation revisited
2009

Works of Ao Ma being referenced

Drosophila katanin is a microtubule depolymerase that regulates cortical-microtubule plus-end interactions and cell migration
2011
Monte Carlo simulations of biomolecules: The MC module in CHARMM
2005
Inhomogeneous backflow transformations in quantum Monte Carlo calculations
2006
All-electron quantum Monte Carlo calculations for the noble gas atoms He to Xe
2005
Isomerization and dissociation dynamics of HCN in a picosecond infrared laser field: A full-dimensional classical study
2005
Bias annealing: A method for obtaining transition paths de novo
2006
The actin-binding ERM protein Moesin binds to and stabilizes microtubules at the cell cortex
2013
Automatic Method for Identifying Reaction Coordinates in Complex Systems
2005
A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT
2008
Dynamic coupling between coordinates in a model for biomolecular isomerization
2006
Diamond toβ-tin phase transition in Si within diffusion quantum Monte Carlo
2010
Models of Single-Molecule Experiments with Periodic Perturbations Reveal Hidden Dynamics in RNA Folding
2009
Quantum Monte Carlo study of the Ne atom and the Ne+ ion
2006
Implications of Alternative Substrate Binding Modes for Catalysis by Uracil-DNA Glycosylase:  An Apparent Discrepancy Resolved
2006
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