Literature DB >> 33705118

Machine Learning Force Fields.

Oliver T Unke1,2, Stefan Chmiela1, Huziel E Sauceda1,3, Michael Gastegger1,2,3, Igor Poltavsky4, Kristof T Schütt1, Alexandre Tkatchenko4, Klaus-Robert Müller1,5,6,7,8.   

Abstract

In recent years, the use of machine learning (ML) in computational chemistry has enabled numerous advances previously out of reach due to the computational complexity of traditional electronic-structure methods. One of the most promising applications is the construction of ML-based force fields (FFs), with the aim to narrow the gap between the accuracy of ab initio methods and the efficiency of classical FFs. The key idea is to learn the statistical relation between chemical structure and potential energy without relying on a preconceived notion of fixed chemical bonds or knowledge about the relevant interactions. Such universal ML approximations are in principle only limited by the quality and quantity of the reference data used to train them. This review gives an overview of applications of ML-FFs and the chemical insights that can be obtained from them. The core concepts underlying ML-FFs are described in detail, and a step-by-step guide for constructing and testing them from scratch is given. The text concludes with a discussion of the challenges that remain to be overcome by the next generation of ML-FFs.

Entities:  

Year:  2021        PMID: 33705118      PMCID: PMC8391964          DOI: 10.1021/acs.chemrev.0c01111

Source DB:  PubMed          Journal:  Chem Rev        ISSN: 0009-2665            Impact factor:   60.622


  150 in total

1.  "Learn on the fly": a hybrid classical and quantum-mechanical molecular dynamics simulation.

Authors:  Gabor Csányi; T Albaret; M C Payne; A De Vita
Journal:  Phys Rev Lett       Date:  2004-10-19       Impact factor: 9.161

2.  The atomic simulation environment-a Python library for working with atoms.

Authors:  Ask Hjorth Larsen; Jens Jørgen Mortensen; Jakob Blomqvist; Ivano E Castelli; Rune Christensen; Marcin Dułak; Jesper Friis; Michael N Groves; Bjørk Hammer; Cory Hargus; Eric D Hermes; Paul C Jennings; Peter Bjerre Jensen; James Kermode; John R Kitchin; Esben Leonhard Kolsbjerg; Joseph Kubal; Kristen Kaasbjerg; Steen Lysgaard; Jón Bergmann Maronsson; Tristan Maxson; Thomas Olsen; Lars Pastewka; Andrew Peterson; Carsten Rostgaard; Jakob Schiøtz; Ole Schütt; Mikkel Strange; Kristian S Thygesen; Tejs Vegge; Lasse Vilhelmsen; Michael Walter; Zhenhua Zeng; Karsten W Jacobsen
Journal:  J Phys Condens Matter       Date:  2017-03-21       Impact factor: 2.333

Review 3.  First Principles Neural Network Potentials for Reactive Simulations of Large Molecular and Condensed Systems.

Authors:  Jörg Behler
Journal:  Angew Chem Int Ed Engl       Date:  2017-08-18       Impact factor: 15.336

4.  Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17.

Authors:  Lars Ruddigkeit; Ruud van Deursen; Lorenz C Blum; Jean-Louis Reymond
Journal:  J Chem Inf Model       Date:  2012-11-01       Impact factor: 4.956

5.  Quantum machine learning using atom-in-molecule-based fragments selected on the fly.

Authors:  Bing Huang; O Anatole von Lilienfeld
Journal:  Nat Chem       Date:  2020-09-14       Impact factor: 24.427

6.  Targeted Adversarial Learning Optimized Sampling.

Authors:  Jun Zhang; Yi Isaac Yang; Frank Noé
Journal:  J Phys Chem Lett       Date:  2019-09-18       Impact factor: 6.475

7.  Ensemble learning of coarse-grained molecular dynamics force fields with a kernel approach.

Authors:  Jiang Wang; Stefan Chmiela; Klaus-Robert Müller; Frank Noé; Cecilia Clementi
Journal:  J Chem Phys       Date:  2020-05-21       Impact factor: 3.488

Review 8.  Neural Network Potential Energy Surfaces for Small Molecules and Reactions.

Authors:  Sergei Manzhos; Tucker Carrington
Journal:  Chem Rev       Date:  2020-10-06       Impact factor: 60.622

9.  Efficient multi-objective molecular optimization in a continuous latent space.

Authors:  Robin Winter; Floriane Montanari; Andreas Steffen; Hans Briem; Frank Noé; Djork-Arné Clevert
Journal:  Chem Sci       Date:  2019-07-08       Impact factor: 9.825

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  31 in total

1.  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

2.  Scoring Functions for Protein-Ligand Binding Affinity Prediction using Structure-Based Deep Learning: A Review.

Authors:  Rocco Meli; Garrett M Morris; Philip C Biggin
Journal:  Front Bioinform       Date:  2022-06-17

Review 3.  Into the Unknown: How Computation Can Help Explore Uncharted Material Space.

Authors:  Austin M Mroz; Victor Posligua; Andrew Tarzia; Emma H Wolpert; Kim E Jelfs
Journal:  J Am Chem Soc       Date:  2022-10-07       Impact factor: 16.383

Review 4.  Protein Function Analysis through Machine Learning.

Authors:  Chris Avery; John Patterson; Tyler Grear; Theodore Frater; Donald J Jacobs
Journal:  Biomolecules       Date:  2022-09-06

Review 5.  Bottom-up Coarse-Graining: Principles and Perspectives.

Authors:  Jaehyeok Jin; Alexander J Pak; Aleksander E P Durumeric; Timothy D Loose; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2022-09-07       Impact factor: 6.578

6.  Predicting the failure of two-dimensional silica glasses.

Authors:  Francesc Font-Clos; Marco Zanchi; Stefan Hiemer; Silvia Bonfanti; Roberto Guerra; Michael Zaiser; Stefano Zapperi
Journal:  Nat Commun       Date:  2022-05-20       Impact factor: 17.694

7.  BIGDML-Towards accurate quantum machine learning force fields for materials.

Authors:  Huziel E Sauceda; Luis E Gálvez-González; Stefan Chmiela; Lauro Oliver Paz-Borbón; Klaus-Robert Müller; Alexandre Tkatchenko
Journal:  Nat Commun       Date:  2022-06-29       Impact factor: 17.694

Review 8.  Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective.

Authors:  Katya Ahmad; Andrea Rizzi; Riccardo Capelli; Davide Mandelli; Wenping Lyu; Paolo Carloni
Journal:  Front Mol Biosci       Date:  2022-06-08

9.  Theoretical studies on triplet-state driven dissociation of formaldehyde by quasi-classical molecular dynamics simulation on machine-learning potential energy surface.

Authors:  Shichen Lin; Daoling Peng; Weitao Yang; Feng Long Gu; Zhenggang Lan
Journal:  J Chem Phys       Date:  2021-12-07       Impact factor: 3.488

10.  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

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