Do Machine-Learning Atomic Descriptors and Order Parameters Tell the Same Story? The Case of Liquid Water

Ephemeral ice-like local environments in classical rigid models of liquid water

(2022) Riccardo Capelli et al.   JOURNAL OF CHEMICAL PHYSICS

High-Dimensional Fluctuations in Liquid Water: Combining Chemical Intuition with Unsupervised Learning

(2022) Adu Offei-Danso et al.   Journal of Chemical Theory and Computation

Multiscale machine-learning interatomic potentials for ferromagnetic and liquid iron

(2022) J Byggmästar et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Unsupervised Learning Methods for Molecular Simulation Data

(2021) Aldo Glielmo et al.   CHEMICAL REVIEWS

LAMMPS - A flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

(2021) Aidan P. Thompson et al.   COMPUTER PHYSICS COMMUNICATIONS

Charge transfer as a ubiquitous mechanism in determining the negative charge at hydrophobic interfaces

(2020) Emiliano Poli et al.   Nature Communications

The conformational space of a flexible amino acid at metallic surfaces

(2020) Dmitrii Maksimov et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Descriptors representing two- and three-body atomic distributions and their effects on the accuracy of machine-learned inter-atomic potentials

(2020) Ryosuke Jinnouchi et al.   JOURNAL OF CHEMICAL PHYSICS

A look inside the black box: Using graph-theoretical descriptors to interpret a Continuous-Filter Convolutional Neural Network (CF-CNN) trained on the global and local minimum energy structures of neutral water clusters

(2020) Jenna A. Bilbrey et al.   JOURNAL OF CHEMICAL PHYSICS

The effect of descriptor choice in machine learning models for ionic liquid melting point prediction

(2020) Kaycee Low et al.   JOURNAL OF CHEMICAL PHYSICS

Protein denaturation at the air-water interface and how to prevent it

(2019) Edoardo D'Imprima et al.   eLife

DScribe: Library of descriptors for machine learning in materials science

(2019) Lauri Himanen et al.   COMPUTER PHYSICS COMMUNICATIONS

The air-water interface stabilizes α-helical conformations of the insulin B-chain

(2019) David L. Cheung   JOURNAL OF CHEMICAL PHYSICS

Machine learning approaches to evaluate correlation patterns in allosteric signaling: A case study of the PDZ2 domain

(2018) Mohsen Botlani et al.   JOURNAL OF CHEMICAL PHYSICS

Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning

(2018) Yasuhiro Matsunaga et al.   eLife

Machine Learning a General-Purpose Interatomic Potential for Silicon

(2018) Albert P. Bartók et al.   Physical Review X

2D H-Bond Network as the Topmost Skin to the Air–Water Interface

(2017) Simone Pezzotti et al.   Journal of Physical Chemistry Letters

ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost

(2017) J. S. Smith et al.   Chemical Science

Water: A Tale of Two Liquids

(2016) Paola Gallo et al.   CHEMICAL REVIEWS

Markov state model of the two-state behaviour of water

(2016) Peter Hamm   JOURNAL OF CHEMICAL PHYSICS

Moment Tensor Potentials: A Class of Systematically Improvable Interatomic Potentials

(2016) Alexander V. Shapeev   MULTISCALE MODELING & SIMULATION

Comparing molecules and solids across structural and alchemical space

(2016) Sandip De et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Machine Learning Energies of 2 Million Elpasolite(ABC2D6)Crystals

(2016) Felix A. Faber et al.   PHYSICAL REVIEW LETTERS

Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab Initio Molecular Dynamics Simulations

(2015) Jan Kessler et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Aqueous Heterogeneity at the Air/Water Interface Revealed by 2D-HD-SFG Spectroscopy

(2014) Cho-Shuen Hsieh et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The structure of insulin at the air/water interface: monomers or dimers?

(2014) S. Mauri et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Water’s Structure around Hydrophobic Solutes and the Iceberg Model

(2013) N. Galamba   JOURNAL OF PHYSICAL CHEMISTRY B

Machine learning of molecular electronic properties in chemical compound space

(2013) Grégoire Montavon et al.   NEW JOURNAL OF PHYSICS

On representing chemical environments

(2013) Albert P. Bartók et al.   PHYSICAL REVIEW B

Atom-centered symmetry functions for constructing high-dimensional neural network potentials

(2011) Jörg Behler   JOURNAL OF CHEMICAL PHYSICS

Ultrafast vibrational energy transfer at the water/air interface revealed by two-dimensional surface vibrational spectroscopy

(2011) Zhen Zhang et al.   Nature Chemistry

Mixturelike Behavior Near a Liquid-Liquid Phase Transition in Simulations of Supercooled Water

(2011) Megan J. Cuthbertson et al.   PHYSICAL REVIEW LETTERS

Structural and dynamical aspects of water in contact with a hydrophobic surface

(2010) D. C. Malaspina et al.   EUROPEAN PHYSICAL JOURNAL E

Instantaneous Liquid Interfaces

(2010) Adam P. Willard et al.   JOURNAL OF PHYSICAL CHEMISTRY B

VORO++: A three-dimensional Voronoi cell library in C++

(2009) Chris H. Rycroft   CHAOS

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

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Evidence of a two-state picture for supercooled water and its connections with glassy dynamics

(2009) G. A. Appignanesi et al.   EUROPEAN PHYSICAL JOURNAL E

A computational investigation of thermodynamics, structure, dynamics and solvation behavior in modified water models

(2008) Swaroop Chatterjee et al.   JOURNAL OF CHEMICAL PHYSICS

Dual Function of the Hydration Layer around an Antifreeze Protein Revealed by Atomistic Molecular Dynamics Simulations

(2008) David R. Nutt et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY