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Title: A generalized deep learning approach for local structure identification in molecular simulations

Journal Article · · Chemical Science
DOI: https://doi.org/10.1039/C9SC02097G · OSTI ID:1542673

Identifying local structure in molecular simulations is of utmost importance. The most common existing approach to identify local structure is to calculate some geometrical quantity referred to as an order parameter. In simple cases order parameters are physically intuitive and trivial to develop (e.g., ion-pair distance), however in most cases, order parameter development becomes a much more difficult endeavor (e.g., crystal structure identification). Using ideas from computer vision, we adapt a specific type of neural network called a PointNet to identify local structural environments in molecular simulations. A primary challenge in applying machine learning techniques to simulation is selecting the appropriate input features. This challenge is system-specific and requires significant human input and intuition. In contrast, our approach is a generic framework that requires no system-specific feature engineering and operates on the raw output of the simulations, i.e., atomic positions. We demonstrate the method on crystal structure identification in Lennard-Jones (four different phases), water (eight different phases), and mesophase (six different phases) systems. The method achieves as high as 99.5% accuracy in crystal structure identification. The method is applicable to heterogeneous nucleation and it can even predict the crystal phases of atoms near external interfaces. We demonstrate the versatility of our approach by using our method to identify surface hydrophobicity based solely upon positions and orientations of surrounding water molecules. Our results suggest the approach will be broadly applicable to many types of local structure in simulations.

Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
Grant/Contract Number:
SC0015448
OSTI ID:
1542673
Alternate ID(s):
OSTI ID: 1612289
Journal Information:
Chemical Science, Journal Name: Chemical Science Journal Issue: 32 Vol. 10; ISSN 2041-6520; ISSN CSHCBM
Publisher:
Royal Society of ChemistryCopyright Statement
Country of Publication:
United Kingdom
Language:
English

References (61)

Developing Local Order Parameters for Order–Disorder Transitions From Particles to Block Copolymers: Application to Macromolecular Systems journal November 2018
Identifying Structural Flow Defects in Disordered Solids Using Machine-Learning Methods journal March 2015
Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water journal November 2012
Neural networks for local structure detection in polymorphic systems journal October 2013
Efficient Method To Characterize the Context-Dependent Hydrophobicity of Proteins journal January 2014
Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps journal May 2005
Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design journal August 2018
Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations journal May 2016
Heterogeneous Ice Nucleation: Interplay of Surface Properties and Their Impact on Water Orientations journal October 2017
Automatic Method for Identifying Reaction Coordinates in Complex Systems journal April 2005
Direct calculation of ice homogeneous nucleation rate for a molecular model of water journal August 2015
Nucleation mechanism of clathrate hydrates of water-soluble guest molecules journal November 2017
Ice Nucleation Efficiency of Hydroxylated Organic Surfaces Is Controlled by Their Structural Fluctuations and Mismatch to Ice journal February 2017
Self-Assembly of Mesophases from Nanoparticles journal September 2017
Bond-orientational order in liquids and glasses journal July 1983
Identification of Clathrate Hydrates, Hexagonal Ice, Cubic Ice, and Liquid Water in Simulations: the CHILL+ Algorithm journal November 2014
Molecular Dynamics Study of Carbon Dioxide Hydrate Dissociation journal June 2011
NaCl nucleation from brine in seeded simulations: Sources of uncertainty in rate estimates journal June 2018
Machine learning for autonomous crystal structure identification journal January 2017
Two-component order parameter for quantifying clathrate hydrate nucleation and growth journal April 2014
Robust structural identification via polyhedral template matching journal May 2016
Machine learning coarse grained models for water journal January 2019
Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach journal June 2011
A simple method for displaying the hydropathic character of a protein journal May 1982
Developing Local Order Parameters for Order–Disorder Transitions From Particles to Block Copolymers: Methodological Framework journal November 2018
Mapping hydrophobicity at the nanoscale: Applications to heterogeneous surfaces and proteins journal January 2010
Machine learning for crystal identification and discovery journal March 2018
Deformation-mechanism map for nanocrystalline metals by molecular-dynamics simulation journal December 2003
Seeding approach to crystal nucleation journal January 2016
Self-Assembly of Colloidal Nanocrystals: From Intricate Structures to Functional Materials journal August 2016
Molecular dynamics study of melting and freezing of small Lennard-Jones clusters journal September 1987
Molecular dynamics simulations of ice growth from supercooled water journal November 2005
Deep learning journal May 2015
Role of stacking disorder in ice nucleation journal November 2017
The surface charge distribution affects the ice nucleating efficiency of silver iodide journal December 2016
Self-assembly and applications of anisotropic nanomaterials: A review journal February 2015
Characterizing Solvent Density Fluctuations in Dynamical Observation Volumes journal January 2019
A Simple Atomic-Level Hydrophobicity Scale Reveals Protein Interfacial Structure journal January 2014
Neural network potential-energy surfaces in chemistry: a tool for large-scale simulations journal January 2011
Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context journal November 2017
Reweighted autoencoded variational Bayes for enhanced sampling (RAVE) journal August 2018
Order parameters for the multistep crystallization of clathrate hydrates journal August 2011
Structure and Dynamics of the Quasi-Liquid Layer at the Surface of Ice from Molecular Simulations journal September 2018
Adsorption of amino acids on graphene: assessment of current force fields journal January 2019
Machine learning of accurate energy-conserving molecular force fields journal May 2017
Automated crystal characterization with a fast neighborhood graph analysis method journal January 2018
Machine learning determination of atomic dynamics at grain boundaries journal October 2018
Kinetic Pathways of Ion Pair Dissociation in Water journal May 1999
Ice nucleation on carbon surface supports the classical theory for heterogeneous nucleation journal May 2015
DeepIce: A Deep Neural Network Approach To Identify Ice and Water Molecules journal March 2019
Predicting polymorphism in molecular crystals using orientational entropy journal September 2018
Pre-critical fluctuations and what they disclose about heterogeneous crystal nucleation journal December 2017
Quantifying Density Fluctuations in Volumes of All Shapes and Sizes Using Indirect Umbrella Sampling journal August 2011
Premelting, fluctuations, and coarse-graining of water-ice interfaces journal November 2014
Machine-learning approach for local classification of crystalline structures in multiphase systems journal July 2017
Why Is Gyroid More Difficult to Nucleate from Disordered Liquids than Lamellar and Hexagonal Mesophases? journal April 2018
Applications of local crystal structure measures in experiment and simulation journal February 2006
Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces journal April 2007
Accurate determination of crystal structures based on averaged local bond order parameters journal September 2008
Reaction coordinates for the crystal nucleation of colloidal suspensions extracted from the reweighted path ensemble journal October 2011
Characterizing Hydration Properties Based on the Orientational Structure of Interfacial Water Molecules journal January 2018