Literature DB >> 35654918

A new active learning approach for adsorbate-substrate structural elucidation in silico.

Maicon Pierre Lourenço1, Lizandra Barrios Herrera2, Jiří Hostaš2, Patrizia Calaminici3, Andreas M Köster3, Alain Tchagang4, Dennis R Salahub2.   

Abstract

Adsorbate interactions with substrates (e.g. surfaces and nanoparticles) are fundamental for several technologies, such as functional materials, supramolecular chemistry, and solvent interactions. However, modeling these kinds of systems in silico, such as finding the optimum adsorption geometry and energy, is challenging, due to the huge number of possibilities of assembling the adsorbate on the surface. In the current work, we have developed an artificial intelligence (AI) approach based on an active learning (AL) method for adsorption optimization on the surface of materials. AL uses machine learning (ML) regression algorithms and their uncertainties to make a decision (based on a policy) for the next unexplored structures to be computed, increasing, though, the probability of finding the global minimum with a small number of calculations. The methodology allows an accurate and automated structural elucidation of the adsorbate on the surface, based on the minimization of the total electronic energy. The new AL method for adsorption optimization was developed and implemented in the quantum machine learning software/agent for material design and discovery (QMLMaterial) program and was applied for C60@TiO2 anatase (101). It marks another software extension with a new feature in addition to the automatic structural elucidation of defects in materials and of nanoparticles as well. SCC-DFTB calculations were used to build the complex search surfaces with a reasonably low computational cost. An artificial neural network (NN) was employed in the AL framework evaluated together with two uncertainty quantification methods: K-fold cross-validation and non-parametric bootstrap (BS) resampling. Also, two different acquisition functions for decision-making were used: expected improvement (EI) and the lower confidence bound (LCB).
© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

Entities:  

Keywords:  Active learning; Adsorption; Functional materials; Machine learning; SCC-DFTB

Mesh:

Year:  2022        PMID: 35654918     DOI: 10.1007/s00894-022-05173-0

Source DB:  PubMed          Journal:  J Mol Model        ISSN: 0948-5023            Impact factor:   1.810


  11 in total

1.  An evolutionary algorithm for the global optimization of molecular clusters: application to water, benzene, and benzene cation.

Authors:  J L Llanio-Trujillo; J M C Marques; F B Pereira
Journal:  J Phys Chem A       Date:  2011-03-03       Impact factor: 2.781

2.  Imaging three-dimensional surface objects with submolecular resolution by atomic force microscopy.

Authors:  César Moreno; Oleksandr Stetsovych; Tomoko K Shimizu; Oscar Custance
Journal:  Nano Lett       Date:  2015-03-18       Impact factor: 11.189

3.  DFTB-Assisted Global Structure Optimization of 13- and 55-Atom Late Transition Metal Clusters.

Authors:  Maxime Van den Bossche
Journal:  J Phys Chem A       Date:  2019-03-15       Impact factor: 2.781

4.  An adaptive design approach for defects distribution modeling in materials from first-principle calculations.

Authors:  Maicon Pierre Lourenço; Alexandre Dos Santos Anastácio; Andreia L Rosa; Thomas Frauenheim; Maurício Chagas da Silva
Journal:  J Mol Model       Date:  2020-07-01       Impact factor: 1.810

5.  Accurate SCC-DFTB Parametrization for Bulk Water.

Authors:  Maicon Pierre Lourenço; Egon Campos Dos Santos; Lars G M Pettersson; Hélio Anderson Duarte
Journal:  J Chem Theory Comput       Date:  2020-02-21       Impact factor: 6.006

6.  Molybdenum carbide nanocatalysts at work in the in situ environment: a density functional tight-binding and quantum mechanical/molecular mechanical study.

Authors:  Xingchen Liu; Dennis R Salahub
Journal:  J Am Chem Soc       Date:  2015-03-20       Impact factor: 15.419

7.  DFTB+, a software package for efficient approximate density functional theory based atomistic simulations.

Authors:  B Hourahine; B Aradi; V Blum; F Bonafé; A Buccheri; C Camacho; C Cevallos; M Y Deshaye; T Dumitrică; A Dominguez; S Ehlert; M Elstner; T van der Heide; J Hermann; S Irle; J J Kranz; C Köhler; T Kowalczyk; T Kubař; I S Lee; V Lutsker; R J Maurer; S K Min; I Mitchell; C Negre; T A Niehaus; A M N Niklasson; A J Page; A Pecchia; G Penazzi; M P Persson; J Řezáč; C G Sánchez; M Sternberg; M Stöhr; F Stuckenberg; A Tkatchenko; V W-Z Yu; T Frauenheim
Journal:  J Chem Phys       Date:  2020-03-31       Impact factor: 3.488

Review 8.  Array programming with NumPy.

Authors:  Charles R Harris; K Jarrod Millman; Stéfan J van der Walt; Ralf Gommers; Pauli Virtanen; David Cournapeau; Eric Wieser; Julian Taylor; Sebastian Berg; Nathaniel J Smith; Robert Kern; Matti Picus; Stephan Hoyer; Marten H van Kerkwijk; Matthew Brett; Allan Haldane; Jaime Fernández Del Río; Mark Wiebe; Pearu Peterson; Pierre Gérard-Marchant; Kevin Sheppard; Tyler Reddy; Warren Weckesser; Hameer Abbasi; Christoph Gohlke; Travis E Oliphant
Journal:  Nature       Date:  2020-09-16       Impact factor: 49.962

Review 9.  SciPy 1.0: fundamental algorithms for scientific computing in Python.

Authors:  Pauli Virtanen; Ralf Gommers; Travis E Oliphant; Matt Haberland; Tyler Reddy; David Cournapeau; Evgeni Burovski; Pearu Peterson; Warren Weckesser; Jonathan Bright; Stéfan J van der Walt; Matthew Brett; Joshua Wilson; K Jarrod Millman; Nikolay Mayorov; Andrew R J Nelson; Eric Jones; Robert Kern; Eric Larson; C J Carey; İlhan Polat; Yu Feng; Eric W Moore; Jake VanderPlas; Denis Laxalde; Josef Perktold; Robert Cimrman; Ian Henriksen; E A Quintero; Charles R Harris; Anne M Archibald; Antônio H Ribeiro; Fabian Pedregosa; Paul van Mulbregt
Journal:  Nat Methods       Date:  2020-02-03       Impact factor: 28.547

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