Literature DB >> 29021555

Bypassing the Kohn-Sham equations with machine learning.

Felix Brockherde1,2, Leslie Vogt3, Li Li4, Mark E Tuckerman5,6,7, Kieron Burke8,9, Klaus-Robert Müller10,11,12.   

Abstract

Last year, at least 30,000 scientific papers used the Kohn-Sham scheme of density functional theory to solve electronic structure problems in a wide variety of scientific fields. Machine learning holds the promise of learning the energy functional via examples, bypassing the need to solve the Kohn-Sham equations. This should yield substantial savings in computer time, allowing larger systems and/or longer time-scales to be tackled, but attempts to machine-learn this functional have been limited by the need to find its derivative. The present work overcomes this difficulty by directly learning the density-potential and energy-density maps for test systems and various molecules. We perform the first molecular dynamics simulation with a machine-learned density functional on malonaldehyde and are able to capture the intramolecular proton transfer process. Learning density models now allows the construction of accurate density functionals for realistic molecular systems.Machine learning allows electronic structure calculations to access larger system sizes and, in dynamical simulations, longer time scales. Here, the authors perform such a simulation using a machine-learned density functional that avoids direct solution of the Kohn-Sham equations.

Entities:  

Year:  2017        PMID: 29021555      PMCID: PMC5636838          DOI: 10.1038/s41467-017-00839-3

Source DB:  PubMed          Journal:  Nat Commun        ISSN: 2041-1723            Impact factor:   14.919


  32 in total

1.  Generalized Gradient Approximation Made Simple.

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Journal:  Phys Rev Lett       Date:  1996-10-28       Impact factor: 9.161

2.  Development and testing of a general amber force field.

Authors:  Junmei Wang; Romain M Wolf; James W Caldwell; Peter A Kollman; David A Case
Journal:  J Comput Chem       Date:  2004-07-15       Impact factor: 3.376

3.  Gaussian approximation potentials: the accuracy of quantum mechanics, without the electrons.

Authors:  Albert P Bartók; Mike C Payne; Risi Kondor; Gábor Csányi
Journal:  Phys Rev Lett       Date:  2010-04-01       Impact factor: 9.161

4.  Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases.

Authors:  Joost VandeVondele; Jürg Hutter
Journal:  J Chem Phys       Date:  2007-09-21       Impact factor: 3.488

5.  An introduction to kernel-based learning algorithms.

Authors:  K R Müller; S Mika; G Rätsch; K Tsuda; B Schölkopf
Journal:  IEEE Trans Neural Netw       Date:  2001

6.  Understanding and reducing errors in density functional calculations.

Authors:  Min-Cheol Kim; Eunji Sim; Kieron Burke
Journal:  Phys Rev Lett       Date:  2013-08-15       Impact factor: 9.161

7.  Projector augmented-wave method.

Authors: 
Journal:  Phys Rev B Condens Matter       Date:  1994-12-15

Review 8.  DFT: A Theory Full of Holes?

Authors:  Aurora Pribram-Jones; David A Gross; Kieron Burke
Journal:  Annu Rev Phys Chem       Date:  2015-04       Impact factor: 12.703

9.  Prediction of Intramolecular Polarization of Aromatic Amino Acids Using Kriging Machine Learning.

Authors:  Timothy L Fletcher; Stuart J Davie; Paul L A Popelier
Journal:  J Chem Theory Comput       Date:  2014-09-09       Impact factor: 6.006

10.  Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space.

Authors:  Katja Hansen; Franziska Biegler; Raghunathan Ramakrishnan; Wiktor Pronobis; O Anatole von Lilienfeld; Klaus-Robert Müller; Alexandre Tkatchenko
Journal:  J Phys Chem Lett       Date:  2015-06-18       Impact factor: 6.475

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  45 in total

1.  Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease.

Authors:  Troy W Whitfield; Debra A Ragland; Konstantin B Zeldovich; Celia A Schiffer
Journal:  J Chem Theory Comput       Date:  2020-01-16       Impact factor: 6.006

2.  A unified machine-learning protocol for asymmetric catalysis as a proof of concept demonstration using asymmetric hydrogenation.

Authors:  Sukriti Singh; Monika Pareek; Avtar Changotra; Sayan Banerjee; Bangaru Bhaskararao; P Balamurugan; Raghavan B Sunoj
Journal:  Proc Natl Acad Sci U S A       Date:  2020-01-08       Impact factor: 11.205

3.  Predicting Molecular Energy Using Force-Field Optimized Geometries and Atomic Vector Representations Learned from an Improved Deep Tensor Neural Network.

Authors:  Jianing Lu; Cheng Wang; Yingkai Zhang
Journal:  J Chem Theory Comput       Date:  2019-06-12       Impact factor: 6.006

4.  Machine Learning for Electronically Excited States of Molecules.

Authors:  Julia Westermayr; Philipp Marquetand
Journal:  Chem Rev       Date:  2020-11-19       Impact factor: 60.622

5.  Gaussian Process Regression for Materials and Molecules.

Authors:  Volker L Deringer; Albert P Bartók; Noam Bernstein; David M Wilkins; Michele Ceriotti; Gábor Csányi
Journal:  Chem Rev       Date:  2021-08-16       Impact factor: 60.622

Review 6.  Application of Computational Biology and Artificial Intelligence Technologies in Cancer Precision Drug Discovery.

Authors:  Nagasundaram Nagarajan; Edward K Y Yapp; Nguyen Quoc Khanh Le; Balu Kamaraj; Abeer Mohammed Al-Subaie; Hui-Yuan Yeh
Journal:  Biomed Res Int       Date:  2019-11-11       Impact factor: 3.411

7.  Artificial Neural Networks as Mappings between Proton Potentials, Wave Functions, Densities, and Energy Levels.

Authors:  Maxim Secor; Alexander V Soudackov; Sharon Hammes-Schiffer
Journal:  J Phys Chem Lett       Date:  2021-02-25       Impact factor: 6.475

Review 8.  Machine learning for molecular and materials science.

Authors:  Keith T Butler; Daniel W Davies; Hugh Cartwright; Olexandr Isayev; Aron Walsh
Journal:  Nature       Date:  2018-07-25       Impact factor: 49.962

9.  Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems.

Authors:  John A Keith; Valentin Vassilev-Galindo; Bingqing Cheng; Stefan Chmiela; Michael Gastegger; Klaus-Robert Müller; Alexandre Tkatchenko
Journal:  Chem Rev       Date:  2021-07-07       Impact factor: 60.622

10.  Dataset Construction to Explore Chemical Space with 3D Geometry and Deep Learning.

Authors:  Jianing Lu; Song Xia; Jieyu Lu; Yingkai Zhang
Journal:  J Chem Inf Model       Date:  2021-03-08       Impact factor: 4.956

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