1
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Macdonald RL. State-to-state study of non-equilibrium recombination of oxygen and nitrogen molecules. J Chem Phys 2024; 160:134307. [PMID: 38568944 DOI: 10.1063/5.0195238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Rapidly cooled mixtures are of interest for several applications, including hypersonic flows due to the presence of strong cooling temperature gradients in regions such as hypersonic boundary layers and expanding nozzles. There have been very few studies of rapidly cooled mixtures using the high-fidelity rovibrational databases afforded by ab initio potential energy surfaces. This work makes use of existing rovibrational state-specific databases to study rapidly cooled mixtures. In particular, we seek to understand the importance of thermal non-equilibrium in recombining mixtures using both rovibrational and vibrational state-to-state methods for oxygen and nitrogen molecules. We find that although there is significant non-equilibrium during recombination, it is well captured by the vibrational state-specific approach. Finally, we compare the global recombination rate computed based on the state-specific recombination rate coefficients and the global recombination rate computed based on the time local dissociation rate coefficient, which is reversed using the principle of detailed balance. The local dissociation rate coefficient is computed by weighting the state-specific dissociation rate coefficients with the state-specific distribution of energy states. We find a large difference between these rates, highlighting a potential source of errors in hypersonic flow predictions.
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Affiliation(s)
- Robyn L Macdonald
- Aerospace Engineering Sciences, University of Colorado Boulder, Boulder, Colorado 80303, USA
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2
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Geistfeld EC, Torres E, Schwartzentruber T. Quasi-classical trajectory analysis of three-body collision induced recombination in neutral nitrogen and oxygen. J Chem Phys 2023; 159:154111. [PMID: 37861123 DOI: 10.1063/5.0163942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
We present theory and a simulation framework to model three-body collisions and gas phase recombination in dilute atom/diatom mixtures of pure oxygen (O/O2) and nitrogen (N/N2) using the Quasi-Classical Trajectory method. We formulate a three-body collision rate constant based on the lifetimes of binary collisions and initialize three-body collisions by sampling the arrival time of a third body within the lifetimes of pre-simulated binary collisions. We use this method to calculate distributions of recombined product energies, probabilities of recombination, and recombination rate constants through different collision pathways. Long-lived binary atom-diatom collisions are observed, but are too rare to play a dominant role in the recombination process for shock-heated air near the equilibrium conditions studied. The resulting recombination rate constants are within an order of magnitude of the predictions of detailed balance. Notably, the recombination simulation framework does not appeal to the principle of detailed balance and could be useful for studying conditions far from equilibrium.
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Affiliation(s)
- Eric C Geistfeld
- Department of Aerospace Engineering and Mechanics, University of Minnesota Minneapolis, Minneapolis, Minnesota 55455, USA
| | - Erik Torres
- Department of Aerospace Engineering and Mechanics, University of Minnesota Minneapolis, Minneapolis, Minnesota 55455, USA
| | - Thomas Schwartzentruber
- Department of Aerospace Engineering and Mechanics, University of Minnesota Minneapolis, Minneapolis, Minnesota 55455, USA
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3
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Zanardi I, Venturi S, Panesi M. Adaptive physics-informed neural operator for coarse-grained non-equilibrium flows. Sci Rep 2023; 13:15497. [PMID: 37726349 PMCID: PMC10509218 DOI: 10.1038/s41598-023-41039-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 08/21/2023] [Indexed: 09/21/2023] Open
Abstract
This work proposes a new machine learning (ML)-based paradigm aiming to enhance the computational efficiency of non-equilibrium reacting flow simulations while ensuring compliance with the underlying physics. The framework combines dimensionality reduction and neural operators through a hierarchical and adaptive deep learning strategy to learn the solution of multi-scale coarse-grained governing equations for chemical kinetics. The proposed surrogate's architecture is structured as a tree, with leaf nodes representing separate neural operator blocks where physics is embedded in the form of multiple soft and hard constraints. The hierarchical attribute has two advantages: (i) It allows the simplification of the training phase via transfer learning, starting from the slowest temporal scales; (ii) It accelerates the prediction step by enabling adaptivity as the surrogate's evaluation is limited to the necessary leaf nodes based on the local degree of non-equilibrium of the gas. The model is applied to the study of chemical kinetics relevant for application to hypersonic flight, and it is tested here on pure oxygen gas mixtures. In 0-[Formula: see text] scenarios, the proposed ML framework can adaptively predict the dynamics of almost thirty species with a maximum relative error of 4.5% for a wide range of initial conditions. Furthermore, when employed in 1-[Formula: see text] shock simulations, the approach shows accuracy ranging from 1% to 4.5% and a speedup of one order of magnitude compared to conventional implicit schemes employed in an operator-splitting integration framework. Given the results presented in the paper, this work lays the foundation for constructing an efficient ML-based surrogate coupled with reactive Navier-Stokes solvers for accurately characterizing non-equilibrium phenomena in multi-dimensional computational fluid dynamics simulations.
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Affiliation(s)
- Ivan Zanardi
- Center for Hypersonics and Entry Systems Studies, Department of Aerospace Engineering, University of Illinois Urbana-Champaign, Urbana, 61801, IL, USA
| | - Simone Venturi
- Center for Hypersonics and Entry Systems Studies, Department of Aerospace Engineering, University of Illinois Urbana-Champaign, Urbana, 61801, IL, USA
| | - Marco Panesi
- Center for Hypersonics and Entry Systems Studies, Department of Aerospace Engineering, University of Illinois Urbana-Champaign, Urbana, 61801, IL, USA.
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4
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Del Val A, Chazot O. Stochastic determination of thermal reaction rate coefficients for air plasmas. J Chem Phys 2023; 159:064105. [PMID: 37565683 DOI: 10.1063/5.0160776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/24/2023] [Indexed: 08/12/2023] Open
Abstract
This work deals with the stochastic inference of gas-phase chemical reaction rates in high temperature air flows from plasma wind tunnel experimental data. First, a Bayesian approach is developed to include not only measurements but also additional information related to how the experiment is performed. To cope with the resulting computationally demanding likelihood, we use the Morris screening method to find the reactions that influence the solution to the stochastic inverse problem from a mechanism comprising 21 different reactions for an air mixture with seven species: O2, N2, NO, NO+, O, N, e-. A set of six reactions, mainly involving nitrogen dissociation and exchange, are the ones identified to impact the solution the most. As such, they are assumed to be uncertain and estimated along with the boundary conditions of the experiment and the catalytic recombination parameters of the materials involved in the testing. The remaining 15 reactions are set to their nominal values. The posterior distribution is then propagated through the proposed boundary layer model to produce the posterior predictive distributions of the temperature and mass fraction profiles along the boundary layer stagnation line. It is identified that NO concentrations have the largest increase in uncertainty levels compared to cases where the inference problem is carried out for fixed chemical model parameter values. This allows us to inform a new experimental campaign targeting the reduction of uncertainties affecting the chemical models.
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Affiliation(s)
- Anabel Del Val
- Aeronautics and Aerospace Department, von Karman Institute for Fluid Dynamics, Chaussée de Waterloo 72, 1640 Rhode-St-Genèse, Belgium
| | - Olivier Chazot
- Aeronautics and Aerospace Department, von Karman Institute for Fluid Dynamics, Chaussée de Waterloo 72, 1640 Rhode-St-Genèse, Belgium
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5
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Kubečka J, Knattrup Y, Engsvang M, Jensen AB, Ayoubi D, Wu H, Christiansen O, Elm J. Current and future machine learning approaches for modeling atmospheric cluster formation. NATURE COMPUTATIONAL SCIENCE 2023; 3:495-503. [PMID: 38177415 DOI: 10.1038/s43588-023-00435-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/16/2023] [Indexed: 01/06/2024]
Abstract
The formation of strongly bound atmospheric molecular clusters is the first step towards forming new aerosol particles. Recent advances in the application of machine learning models open an enormous opportunity for complementing expensive quantum chemical calculations with efficient machine learning predictions. In this Perspective, we present how data-driven approaches can be applied to accelerate cluster configurational sampling, thereby greatly increasing the number of chemically relevant systems that can be covered.
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Affiliation(s)
- Jakub Kubečka
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Yosef Knattrup
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | | | | | - Daniel Ayoubi
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Haide Wu
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | | | - Jonas Elm
- Department of Chemistry, Aarhus University, Aarhus, Denmark.
- iCLIMATE Aarhus University Interdisciplinary Centre for Climate Change, Aarhus, Denmark.
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6
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Priyadarshini MS, Venturi S, Zanardi I, Panesi M. Efficient quasi-classical trajectory calculations by means of neural operator architectures. Phys Chem Chem Phys 2023; 25:13902-13912. [PMID: 37183638 DOI: 10.1039/d2cp05506f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
An accurate description of non-equilibrium chemistry relies on rovibrational state-to-state (StS) kinetics data, which can be obtained through the quasi-classical trajectory (QCT) method for high-energy collisions. However, these calculations still represent one of the major computational bottlenecks in predictive simulations of non-equilibrium reacting gases. This work addresses this limitation by proposing SurQCT, a novel machine learning-based surrogate for efficiently and accurately predicting StS chemical reaction rate coefficients. The QCT emulator is constructed using three independent components: two deep operator networks (DeepONets) for inelastic and exchange processes and a feed-forward neural network (FNN) for the dissociation reactions. SurQCT is tested on the O2 + O system, showing a computational speed-up of 85%. Furthermore, we carry out a StS master equation analysis of an isochoric, isothermal heat bath simulation at various temperatures to study how the predicted rate coefficients impact the accuracy of multiple quantities of interest (QoIs) at the kinetics level (e.g., global quasi-steady state (QSS) dissociation rate coefficients and energy relaxation times). For all these QoIs, the master equation analysis relying on SurQCT data shows an accuracy within 15% across the entire temperature regime.
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Affiliation(s)
- Maitreyee Sharma Priyadarshini
- Center for Hypersonics and Entry Systems Studies, Department of Aerospace Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Simone Venturi
- Center for Hypersonics and Entry Systems Studies, Department of Aerospace Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Ivan Zanardi
- Center for Hypersonics and Entry Systems Studies, Department of Aerospace Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Marco Panesi
- Center for Hypersonics and Entry Systems Studies, Department of Aerospace Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
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7
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Yang Z, Chen H, Buren B, Chen M. Globally Accurate Gaussian Process Potential Energy Surface and Quantum Dynamics Studies on the Li(2S) + Na2 → LiNa + Na Reaction at Low Collision Energies. Molecules 2023; 28:molecules28072938. [PMID: 37049701 PMCID: PMC10096016 DOI: 10.3390/molecules28072938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
The LiNa2 reactive system has recently received great attention in the experimental study of ultracold chemical reactions, but the corresponding theoretical calculations have not been carried out. Here, we report the first globally accurate ground-state LiNa2 potential energy surface (PES) using a Gaussian process model based on only 1776 actively selected high-level ab initio training points. The constructed PES had high precision and strong generalization capability. On the new PES, the quantum dynamics calculations on the Li(2S) + Na2(v = 0, j = 0) → LiNa + Na reaction were carried out in the 0.001–0.01 eV collision energy range using an improved time-dependent wave packet method. The calculated results indicate that this reaction is dominated by a complex-forming mechanism at low collision energies. The presented dynamics data provide guidance for experimental research, and the newly constructed PES could be further used for ultracold reaction dynamics calculations on this reactive system.
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8
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Valentini P, Verhoff AM, Grover MS, Bisek NJ. First-principles predictions for shear viscosity of air components at high temperature. Phys Chem Chem Phys 2023; 25:9131-9139. [PMID: 36939072 DOI: 10.1039/d3cp00072a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
The direct molecular simulation (DMS) method is used to obtain shear viscosity data for non-reacting air and its components by simulating isothermal, plane Poiseuille subsonic flows. Shear viscosity is estimated at several temperatures, from 273 K to 10 000 K, by fitting the DMS velocity profiles using the analytic solution of the Navier-Stokes equations for this simple canonical flow. The ab initio potential energy surfaces (PESs) that describe the various atomic-level interactions are the only input in the simulations. Molecules involved in a collision within the flow can occupy any rovibrational state that is allowed by the effective diatomic potential. For molecular nitrogen, oxygen, and air at standard condition molar composition, the DMS shear viscosity predictions are in excellent agreement with the experimental data that are available up to about 2000 K. The results for pure molecular nitrogen and pure molecular oxygen also agree very well with previously published quasi-classical trajectory (QCT) calculations based on the same PESs. It is further shown that the ab initio shear viscosity data are generally lower than the corresponding values used in popular computational fluid dynamics codes, over a wide temperature range. Finally, Wilke's mixing rule is demonstrated to accurately predict the DMS air viscosity results from the pure molecular components data up to 4000 K.
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Affiliation(s)
- Paolo Valentini
- University of Dayton Research Institute, 1700 South Patterson Blvd, Dayton, Ohio 45469, USA.
| | - Ashley M Verhoff
- US Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, USA
| | - Maninder S Grover
- University of Dayton Research Institute, 1700 South Patterson Blvd, Dayton, Ohio 45469, USA.
| | - Nicholas J Bisek
- US Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, USA
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9
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Olatomiwa A, Adam T, Edet C, Adewale A, Chik A, Mohammed M, Gopinath SC, Hashim U. Recent advances in density functional theory approach for optoelectronics properties of graphene. Heliyon 2023; 9:e14279. [PMID: 36950613 PMCID: PMC10025043 DOI: 10.1016/j.heliyon.2023.e14279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Graphene has received tremendous attention among diverse 2D materials because of its remarkable properties. Its emergence over the last two decades gave a new and distinct dynamic to the study of materials, with several research projects focusing on exploiting its intrinsic properties for optoelectronic devices. This review provides a comprehensive overview of several published articles based on density functional theory and recently introduced machine learning approaches applied to study the electronic and optical properties of graphene. A comprehensive catalogue of the bond lengths, band gaps, and formation energies of various doped graphene systems that determine thermodynamic stability was reported in the literature. In these studies, the peculiarity of the obtained results reported is consequent on the nature and type of the dopants, the choice of the XC functionals, the basis set, and the wrong input parameters. The different density functional theory models, as well as the strengths and uncertainties of the ML potentials employed in the machine learning approach to enhance the prediction models for graphene, were elucidated. Lastly, the thermal properties, modelling of graphene heterostructures, the superconducting behaviour of graphene, and optimization of the DFT models are grey areas that future studies should explore in enhancing its unique potential. Therefore, the identified future trends and knowledge gaps have a prospect in both academia and industry to design future and reliable optoelectronic devices.
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Affiliation(s)
- A.L. Olatomiwa
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
- Faculty of Electronic Engineering and Technology, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
| | - Tijjani Adam
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
- Faculty of Electronic Engineering and Technology, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
- Micro System Technology, Centre of Excellence (CoE), Universiti Malaysia Perlis (UniMAP), Pauh Campus, 02600, Arau, Perlis, Malaysia
| | - C.O. Edet
- Faculty of Electronic Engineering and Technology, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
- Institute of Engineering Mathematics, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
- Department of Physics, Cross River University of Technology, Calabar, Nigeria
| | - A.A. Adewale
- Department of Pure and Applied Physics, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Abdullah Chik
- Centre for Frontier Materials Research, Universiti Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
- Faculty of Chemical Engineering and Technology, Universiti Malaysia Perlis (UniMAP), Taman Muhibbah, Jejawi, 02600, Arau, Perlis, Malaysia
| | - Mohammed Mohammed
- Faculty of Chemical Engineering and Technology, Universiti Malaysia Perlis (UniMAP), Taman Muhibbah, Jejawi, 02600, Arau, Perlis, Malaysia
- Center of Excellence Geopolymer & Green Technology (CEGeoGTech), Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
| | - Subash C.B. Gopinath
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
- Micro System Technology, Centre of Excellence (CoE), Universiti Malaysia Perlis (UniMAP), Pauh Campus, 02600, Arau, Perlis, Malaysia
- Faculty of Chemical Engineering and Technology, Universiti Malaysia Perlis (UniMAP), Taman Muhibbah, Jejawi, 02600, Arau, Perlis, Malaysia
| | - U. Hashim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000, Kangar, Perlis, Malaysia
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10
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Jo SM, Venturi S, Kim JG, Panesi M. Rovibrational internal energy transfer and dissociation of high-temperature oxygen mixture. J Chem Phys 2023; 158:064305. [PMID: 36792518 DOI: 10.1063/5.0133463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
This work constructs a rovibrational state-to-state model for the O2 + O2 system leveraging high-fidelity potential energy surfaces and quasi-classical trajectory calculations. The model is used to investigate internal energy transfer and nonequilibrium reactive processes in a dissociating environment using a master equation approach, whereby the kinetics of each internal rovibrational state is explicitly computed. To cope with the exponentially large number of elementary processes that characterize reactive bimolecular collisions, the internal states of the collision partner are assumed to follow a Boltzmann distribution at a prescribed internal temperature. This procedure makes the problem tractable, reducing the computational cost to a comparable scale with the O2 + O system. The constructed rovibrational-specific kinetic database covers the temperature range of 7500-20 000 K. The reaction rate coefficients included in the database are parameterized in the function of kinetic and internal temperatures. Analysis of the energy transfer and dissociation process in isochoric and isothermal conditions reveals that significant departure from the equilibrium Boltzmann distribution occurs during the energy transfer and dissociation phase. Comparing the population distribution of the O2 molecules against the O2 + O case demonstrates a more significant extent of nonequilibrium characterized by a more diffuse distribution whereby the vibrational strands are more clearly identifiable. This is partly due to less efficient mixing of the rovibrational states, which results in more diffuse rovibrational distributions in the quasi-steady-state distribution of O2 + O2. A master equation analysis for the combined O2 + O and O2 + O2 system reveals that the O2 + O2 system governs the early stage of energy transfer, whereas the O2 + O system takes control of the dissociation dynamics. The findings of the present work will provide a strong physical foundation that can be exploited to construct an improved reduced-order model for oxygen chemistry.
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Affiliation(s)
- Sung Min Jo
- Center for Hypersonics and Entry Systems Studies (CHESS), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Simone Venturi
- Center for Hypersonics and Entry Systems Studies (CHESS), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jae Gang Kim
- Department of Aerospace System Engineering, Sejong University, Seoul 05006, Republic of Korea
| | - Marco Panesi
- Center for Hypersonics and Entry Systems Studies (CHESS), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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11
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Zhang Y, Lin Q, Jiang B. Atomistic neural network representations for chemical dynamics simulations of molecular, condensed phase, and interfacial systems: Efficiency, representability, and generalization. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Yaolong Zhang
- Department of Chemical Physics, School of Chemistry and Materials Science, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes University of Science and Technology of China Hefei Anhui China
| | - Qidong Lin
- Department of Chemical Physics, School of Chemistry and Materials Science, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes University of Science and Technology of China Hefei Anhui China
| | - Bin Jiang
- Department of Chemical Physics, School of Chemistry and Materials Science, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes University of Science and Technology of China Hefei Anhui China
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12
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Priyadarshini MS, Jo SM, Venturi S, Schwenke DW, Jaffe RL, Panesi M. Comprehensive Study of HCN: Potential Energy Surfaces, State-to-State Kinetics, and Master Equation Analysis. J Phys Chem A 2022; 126:8249-8265. [DOI: 10.1021/acs.jpca.2c03959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maitreyee Sharma Priyadarshini
- Center for Hypersonics & Entry Systems Studies, Department of Aerospace Engineering, University of Illinois, Urbana-Champaign, Urbana, Illinois61801, United States
| | - Sung Min Jo
- Center for Hypersonics & Entry Systems Studies, Department of Aerospace Engineering, University of Illinois, Urbana-Champaign, Urbana, Illinois61801, United States
| | - Simone Venturi
- Center for Hypersonics & Entry Systems Studies, Department of Aerospace Engineering, University of Illinois, Urbana-Champaign, Urbana, Illinois61801, United States
| | - David W. Schwenke
- NASA Ames Research Center, Moffett Field, California94035, United States
| | - Richard L. Jaffe
- NASA Ames Research Center, Moffett Field, California94035, United States
| | - Marco Panesi
- Center for Hypersonics & Entry Systems Studies, Department of Aerospace Engineering, University of Illinois, Urbana-Champaign, Urbana, Illinois61801, United States
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13
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Kuntz D, Wilson AK. Machine learning, artificial intelligence, and chemistry: how smart algorithms are reshaping simulation and the laboratory. PURE APPL CHEM 2022. [DOI: 10.1515/pac-2022-0202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Machine learning and artificial intelligence are increasingly gaining in prominence through image analysis, language processing, and automation, to name a few applications. Machine learning is also making profound changes in chemistry. From revisiting decades-old analytical techniques for the purpose of creating better calibration curves, to assisting and accelerating traditional in silico simulations, to automating entire scientific workflows, to being used as an approach to deduce underlying physics of unexplained chemical phenomena, machine learning and artificial intelligence are reshaping chemistry, accelerating scientific discovery, and yielding new insights. This review provides an overview of machine learning and artificial intelligence from a chemist’s perspective and focuses on a number of examples of the use of these approaches in computational chemistry and in the laboratory.
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Affiliation(s)
- David Kuntz
- Department of Chemistry , University of North Texas , Denton , TX 76201 , USA
| | - Angela K. Wilson
- Department of Chemistry , Michigan State University , East Lansing , MI 48824 , USA
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14
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Nandi S, Busk J, Jørgensen PB, Vegge T, Bhowmik A. Cheap Turns Superior: A Linear Regression-Based Correction Method to Reaction Energy from the DFT. J Chem Inf Model 2022; 62:4727-4735. [DOI: 10.1021/acs.jcim.2c00760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Surajit Nandi
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej 301, Kongens Lyngby, Copenhagen 2800, Denmark
| | - Jonas Busk
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej 301, Kongens Lyngby, Copenhagen 2800, Denmark
| | - Peter Bjørn Jørgensen
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej 301, Kongens Lyngby, Copenhagen 2800, Denmark
| | - Tejs Vegge
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej 301, Kongens Lyngby, Copenhagen 2800, Denmark
| | - Arghya Bhowmik
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej 301, Kongens Lyngby, Copenhagen 2800, Denmark
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15
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Jo SM, Venturi S, Sharma MP, Munafò A, Panesi M. Rovibrational-Specific QCT and Master Equation Study on N 2(X 1Σ g+) + O( 3P) and NO(X 2Π) + N( 4S) Systems in High-Energy Collisions. J Phys Chem A 2022; 126:3273-3290. [PMID: 35604650 DOI: 10.1021/acs.jpca.1c10346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work presents a detailed investigation of the energy-transfer and dissociation mechanisms in N2(X1Σg+) + O(3P) and NO(X2Π) + N(4S) systems using rovibrational-specific quasiclassical trajectory (QCT) and master equation analyses. The complete set of state-to-state kinetic data, obtained via QCT, allows for an in-depth investigation of the Zel'dovich mechanism leading to the formation of NO molecules at microscopic and macroscopic scales. The master equation analysis demonstrates that the low-lying vibrational states of N2 and NO have dominant contributions to the NO formation and the corresponding extinction of N2 through the exchange process. For the considered temperature range, it is found that nearly 50% of the dissociation processes for N2 and NO molecules occur in the quasi-steady-state (QSS) regime, while for the Zel'dovich reaction, the distribution of the reactants does not reach the QSS conditions. Furthermore, using the QSS approximation to model the Zel'dovich mechanism leads to overestimating NO production by more than a factor of 4 in the high-temperature range. The breakdown of this well-known approximation has profound consequences for the approaches that heavily rely on the validity of QSS assumption in hypersonic applications. Finally, the investigation of the rovibrational state population dynamics reveals substantial similarities among different chemical systems for the energy-transfer and the dissociation processes, providing promising physical foundations for the use of reduced-order strategies in other chemical systems without significant loss of accuracy.
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Affiliation(s)
- Sung Min Jo
- Center for Hypersonics and Entry Systems Studies (CHESS), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Simone Venturi
- Center for Hypersonics and Entry Systems Studies (CHESS), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Maitreyee P Sharma
- Center for Hypersonics and Entry Systems Studies (CHESS), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Alessandro Munafò
- Center for Hypersonics and Entry Systems Studies (CHESS), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Marco Panesi
- Center for Hypersonics and Entry Systems Studies (CHESS), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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16
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Yang Z, Chen H, Chen M. Representing Globally Accurate Reactive Potential Energy Surfaces with Complex Topography by Combining Gaussian Process Regression and Neural Network. Phys Chem Chem Phys 2022; 24:12827-12836. [DOI: 10.1039/d2cp00719c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There has been increasing attention in using machine learning technologies, such as neural network (NN) and Gaussian process regression (GPR), to model multidimensional potential energy surfaces (PESs). NN PES features...
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17
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Xu M, Zhu T, Zhang JZH. Automated Construction of Neural Network Potential Energy Surface: The Enhanced Self-Organizing Incremental Neural Network Deep Potential Method. J Chem Inf Model 2021; 61:5425-5437. [PMID: 34752095 DOI: 10.1021/acs.jcim.1c01125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In recent years, the use of deep learning (neural network) potential energy surface (NNPES) in molecular dynamics simulation has experienced explosive growth as it can be as accurate as quantum chemistry methods while being as efficient as classical mechanic methods. However, the development of NNPES is highly nontrivial. In particular, it has been troubling to construct a dataset that is as small as possible yet can cover the target chemical space. In this work, an ESOINN-DP method is developed, which has the enhanced self-organizing incremental neural network (ESOINN) and a newly proposed error indicator at its core. With ESOINN-DP, one can construct the NNPES with little human intervention, and this method ensures that the constructed reference dataset covers the target chemical space with minimum redundancy. The performance of the ESOINN-DP method has been well validated by developing neural network potential energy surfaces for water clusters, tripeptides, and by de-redundancy of a sub-dataset of the ANI-1 database. We believe that the ESOINN-DP method provides a novel idea for the construction of NNPES and, especially, the reference datasets, and it can be used for molecular dynamics (MD) simulations of various gas-phase and condensed-phase chemical systems.
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Affiliation(s)
- Mingyuan Xu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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18
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Schwalbe-Koda D, Tan AR, Gómez-Bombarelli R. Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks. Nat Commun 2021; 12:5104. [PMID: 34429418 PMCID: PMC8384857 DOI: 10.1038/s41467-021-25342-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 08/02/2021] [Indexed: 12/14/2022] Open
Abstract
Neural network (NN) interatomic potentials provide fast prediction of potential energy surfaces, closely matching the accuracy of the electronic structure methods used to produce the training data. However, NN predictions are only reliable within well-learned training domains, and show volatile behavior when extrapolating. Uncertainty quantification methods can flag atomic configurations for which prediction confidence is low, but arriving at such uncertain regions requires expensive sampling of the NN phase space, often using atomistic simulations. Here, we exploit automatic differentiation to drive atomistic systems towards high-likelihood, high-uncertainty configurations without the need for molecular dynamics simulations. By performing adversarial attacks on an uncertainty metric, informative geometries that expand the training domain of NNs are sampled. When combined with an active learning loop, this approach bootstraps and improves NN potentials while decreasing the number of calls to the ground truth method. This efficiency is demonstrated on sampling of kinetic barriers, collective variables in molecules, and supramolecular chemistry in zeolite-molecule interactions, and can be extended to any NN potential architecture and materials system.
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Affiliation(s)
- Daniel Schwalbe-Koda
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aik Rui Tan
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rafael Gómez-Bombarelli
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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19
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Abstract
Machine learning (ML) techniques applied to chemical reactions have a long history. The present contribution discusses applications ranging from small molecule reaction dynamics to computational platforms for reaction planning. ML-based techniques can be particularly relevant for problems involving both computation and experiments. For one, Bayesian inference is a powerful approach to develop models consistent with knowledge from experiments. Second, ML-based methods can also be used to handle problems that are formally intractable using conventional approaches, such as exhaustive characterization of state-to-state information in reactive collisions. Finally, the explicit simulation of reactive networks as they occur in combustion has become possible using machine-learned neural network potentials. This review provides an overview of the questions that can and have been addressed using machine learning techniques, and an outlook discusses challenges in this diverse and stimulating field. It is concluded that ML applied to chemistry problems as practiced and conceived today has the potential to transform the way with which the field approaches problems involving chemical reactions, in both research and academic teaching.
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Affiliation(s)
- Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland.,Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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20
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Beć KB, Grabska J, Huck CW. Current and future research directions in computer-aided near-infrared spectroscopy: A perspective. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 254:119625. [PMID: 33706116 DOI: 10.1016/j.saa.2021.119625] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
The present review aims to draw a perspective on the vibrational spectroscopy combined with the tools of computational chemistry. This includes an overview of the accomplishments made so far, the assessment of the present development trends and the prospects for continuing these advances. State-of-the-art methods, current challenges and the expected future advances are evaluated from the point-of-view of the practical application in vibrational spectroscopy. A special attention is given to near-infrared (NIR) spectroscopy, which occupies a distinct position among the techniques of vibrational spectroscopy. As the result of intrinsically complex spectra, reliance on the anharmonicity as well as keen interest given to complex materials, NIR spectroscopy may particularly benefit from computational chemistry. The present key limitations hindering development of NIR spectroscopy are identified; these constitute primarily the limit in the treatable system size and the inability to effectively include chemical matrix effects. Given the expanding role of NIR spectroscopy in science and industry, lifting these limitations would directly enhance the general potential of this technique.
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Affiliation(s)
- Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, CCB-Center for Chemistry and Biomedicine, Innrain 80/82, 6020 Innsbruck, Austria
| | - Justyna Grabska
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, CCB-Center for Chemistry and Biomedicine, Innrain 80/82, 6020 Innsbruck, Austria.
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, CCB-Center for Chemistry and Biomedicine, Innrain 80/82, 6020 Innsbruck, Austria
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21
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Ferguson AL, Hachmann J, Miller TF, Pfaendtner J. The Journal of Physical Chemistry A/ B/ C Virtual Special Issue on Machine Learning in Physical Chemistry. J Phys Chem A 2021; 124:9113-9118. [PMID: 33147969 DOI: 10.1021/acs.jpca.0c09205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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San Vicente Veliz JC, Koner D, Schwilk M, Bemish RJ, Meuwly M. The C( 3P) + O 2( 3Σ g-) → CO 2 ↔ CO( 1Σ +) + O( 1D)/O( 3P) reaction: thermal and vibrational relaxation rates from 15 K to 20 000 K. Phys Chem Chem Phys 2021; 23:11251-11263. [PMID: 33949507 PMCID: PMC8133592 DOI: 10.1039/d1cp01101d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/10/2021] [Indexed: 11/24/2022]
Abstract
Thermal rates for the C(3P) + O2(3Σg-) ↔ CO(1Σ+)+ O(1D)/O(3P) reaction are investigated over a wide temperature range based on quasi classical trajectory (QCT) simulations on 3-dimensional, reactive potential energy surfaces (PESs) for the 1A', (2)1A', 1A'', 3A' and 3A'' states. These five states are the energetically low-lying states of CO2 and their PESs are computed at the MRCISD+Q/aug-cc-pVTZ level of theory using a state-average CASSCF reference wave function. Analysis of the different electronic states for the CO2 → CO + O dissociation channel rationalizes the topography of this region of the PESs. The forward rates from QCT simulations match measurements between 15 K and 295 K whereas the equilibrium constant determined from the forward and reverse rates is consistent with that derived from statistical mechanics at high temperature. Vibrational relaxation, O + CO(ν = 1,2) → O + CO(ν = 0), is found to involve both, non-reactive and reactive processes. The contact time required for vibrational relaxation to take place is τ ≥ 150 fs for non-reacting and τ ≥ 330 fs for reacting (oxygen atom exchange) trajectories and the two processes are shown to probe different parts of the global potential energy surface. In agreement with experiments, low collision energy reactions for the C(3P) + O2(3Σg-, ν = 0) → CO(1Σ+) + O(1D) lead to CO(1Σ+, ν' = 17) with an onset at Ec ∼ 0.15 eV, dominated by the 1A' surface with contributions from the 3A' surface. Finally, the barrier for the COA(1Σ+) + OB(3P) → COB(1Σ+) + OA(3P) atom exchange reaction on the 3A' PES yields a barrier of ∼7 kcal mol-1 (0.300 eV), consistent with an experimentally reported value of 6.9 kcal mol-1 (0.299 eV).
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Affiliation(s)
| | - Debasish Koner
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Max Schwilk
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland. and University of Vienna, Faculty of Physics, 1090 Vienna, Austria
| | - Raymond J Bemish
- Air Force Research Laboratory, Space Vehicles Directorate, Kirtland AFB, New Mexico 87117, USA
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland. and Brown University, Providence, RI 02912, USA
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23
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Lin Q, Zhang L, Zhang Y, Jiang B. Searching Configurations in Uncertainty Space: Active Learning of High-Dimensional Neural Network Reactive Potentials. J Chem Theory Comput 2021; 17:2691-2701. [PMID: 33904718 DOI: 10.1021/acs.jctc.1c00166] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Neural network (NN) potential energy surfaces (PESs) have been widely used in atomistic simulations with ab initio accuracy. While constructing NN PESs, their training data points are often sampled by molecular dynamics trajectories. This strategy can be however inefficient for reactive systems involving rare events. Here, we develop an uncertainty-driven active learning strategy to automatically and efficiently generate high-dimensional NN-based reactive potentials, taking a gas-surface reaction as an example. The difference between two independent NN models is used as a simple and differentiable uncertainty metric, allowing us to quickly search in the uncertainty space and place new samples at which the PES is less reliable. By interfacing this algorithm with the first-principles simulation package, we demonstrate that a globally accurate NN potential of the H2 + Ag(111) system can be constructed with merely ∼150 data points. This PES can be further refined to describe H2 dissociation on Ag(100) by adding ∼130 more configurations on this facet. The entire process is completely automatic and self-terminated once the relative error criterion is fulfilled. Impressively, data points sampled by this uncertainty-driven strategy are substantially fewer than by the traditional trajectory-based sampling. The final NN PES not only converges well the quantum dissociation probability of the molecule but also well-reproduces the phonon properties of the substrate and is capable of describing surface temperature effects. These results show the potential of this active learning approach in developing high-dimensional NN reactive potentials in gas and condensed phases.
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Affiliation(s)
- Qidong Lin
- Hefei National Laboratory for Physical Science at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Liang Zhang
- Hefei National Laboratory for Physical Science at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yaolong Zhang
- Hefei National Laboratory for Physical Science at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bin Jiang
- Hefei National Laboratory for Physical Science at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
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24
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Ferguson AL, Hachmann J, Miller TF, Pfaendtner J. The Journal of Physical Chemistry A/ B/ C Virtual Special Issue on Machine Learning in Physical Chemistry. J Phys Chem B 2021; 124:9767-9772. [PMID: 33147970 DOI: 10.1021/acs.jpcb.0c09206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Geistfeld E, Schwartzentruber TE. QCT calculations of O 2 + O collisions: Comparison to molecular beam experiments. J Chem Phys 2020; 153:184302. [DOI: 10.1063/5.0024870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- E. Geistfeld
- Department of Aerospace Engineering and Mechanics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - T. E. Schwartzentruber
- Department of Aerospace Engineering and Mechanics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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26
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Venturi S, Sharma MP, Lopez B, Panesi M. Data-Inspired and Physics-Driven Model Reduction for Dissociation: Application to the O 2 + O System. J Phys Chem A 2020; 124:8359-8372. [PMID: 32886505 DOI: 10.1021/acs.jpca.0c04516] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work presents an in-depth discussion on the nonequilibrium dissociation of O2 molecules colliding with O atoms, combining quasi-classical trajectory calculations, master equation, and dimensionality reduction. A rovibrationally resolved database for all of the elementary collisional processes is constructed by including all nine adiabatic electronic states of O3 in the QCT calculations. A detailed analysis of the ab initio data set reveals that for a rovibrational level, the probability of dissociating is mostly dictated by its deficit in internal energy compared to the centrifugal barrier. Because of the assumption of rotational equilibrium, the conventional vibrational-specific calculations fail to characterize such a dependence. Based on this observation, a new physics-based grouping strategy for application to coarse-grained models is proposed. By relying on a hybrid technique made of rovibrationally resolved excitation coupled to coarse-grained dissociation, the new approach is compared to the vibrational-specific model and the direct solution of the rovibrational state-to-state master equation. Simulations are performed in a zero-dimensional isothermal and isochoric chemical reactor for a wide range of temperatures (1500-20,000 K). The study shows that the main contribution to the model inadequacy of vibrational-specific approaches originates from the incapability of characterizing dissociation, rather than the energy transfers. Even when constructed with only twenty groups, the new reduced-order model outperforms the vibrational-specific one in predicting all of the QoIs related to dissociation kinetics. At the highest temperature, the accuracy in the mole fraction is improved by 2000%.
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Affiliation(s)
- S Venturi
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - M P Sharma
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - B Lopez
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - M Panesi
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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27
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Manzhos S, Carrington T. Neural Network Potential Energy Surfaces for Small Molecules and Reactions. Chem Rev 2020; 121:10187-10217. [PMID: 33021368 DOI: 10.1021/acs.chemrev.0c00665] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We review progress in neural network (NN)-based methods for the construction of interatomic potentials from discrete samples (such as ab initio energies) for applications in classical and quantum dynamics including reaction dynamics and computational spectroscopy. The main focus is on methods for building molecular potential energy surfaces (PES) in internal coordinates that explicitly include all many-body contributions, even though some of the methods we review limit the degree of coupling, due either to a desire to limit computational cost or to limited data. Explicit and direct treatment of all many-body contributions is only practical for sufficiently small molecules, which are therefore our primary focus. This includes small molecules on surfaces. We consider direct, single NN PES fitting as well as more complex methods that impose structure (such as a multibody representation) on the PES function, either through the architecture of one NN or by using multiple NNs. We show how NNs are effective in building representations with low-dimensional functions including dimensionality reduction. We consider NN-based approaches to build PESs in the sums-of-product form important for quantum dynamics, ways to treat symmetry, and issues related to sampling data distributions and the relation between PES errors and errors in observables. We highlight combinations of NNs with other ideas such as permutationally invariant polynomials or sums of environment-dependent atomic contributions, which have recently emerged as powerful tools for building highly accurate PESs for relatively large molecular and reactive systems.
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Affiliation(s)
- Sergei Manzhos
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650, Boulevard Lionel-Boulet, Varennes, Québec City, Québec J3X 1S2, Canada
| | - Tucker Carrington
- Chemistry Department, Queen's University, Kingston Ontario K7L 3N6, Canada
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28
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Koner D, San Vicente Veliz JC, Bemish RJ, Meuwly M. Accurate reproducing kernel-based potential energy surfaces for the triplet ground states of N2O and dynamics for the N + NO ↔ O + N2 and N2 + O → 2N + O reactions. Phys Chem Chem Phys 2020; 22:18488-18498. [DOI: 10.1039/d0cp02509g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Reproducing kernel-based potential energy surface based on MRCI+Q/aug-cc-pVTZ energies for the triplet states of N2O and quasiclassical dynamical study for the reaction, dissociation and vibrational relaxation.
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Affiliation(s)
- Debasish Koner
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | | | - Raymond J. Bemish
- Air Force Research Laboratory
- Space Vehicles Directorate
- Kirtland AFB
- USA
| | - Markus Meuwly
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
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