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Paláček S, Kalus R, Gadéa FX, Benhenni M, Leininger T, Yousfi M. Rotational Transitions in the N 2 + Ion Induced by Collisions with Helium Atoms in Cold Helium Plasmas. A Quasiclassical Trajectory Study. Chemphyschem 2024; 25:e202300469. [PMID: 37850571 DOI: 10.1002/cphc.202300469] [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: 07/03/2023] [Revised: 10/10/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Cross-sections of state-to-state rotational transitions in electronically ground-state 14N 2 + ${{\rm{N}}_2^ + }$ (X2Σ g + ${{\Sigma }_{g}^{+}}$ ) ions induced by collisions with 4 He atoms have been calculated using a quasiclassical trajectory method and a set of artificial neural networks representing theN 2 + ${{\rm{N}}_2^ + }$ /He potential energy surface. The training points for the neural networks have been calculated at a MCSCF (multi-configuration self-consistent field)/aug-cc-pVQZ level. A broad range of theN 2 + ${{\rm{N}}_2^ + }$ /He collision energy has been considered (E c o l l ≤ 100 ${{E}_{{\rm c}{\rm o}{\rm l}{\rm l}}\le 100}$ eV) and the efficiency of vibrational transitions in theN 2 + ${{\rm{N}}_2^ + }$ ion has also been analyzed. It has been found that vibrational transitions are negligible with respect to rotational transitions up toE c o l l ≈ 10 ${{E}_{{\rm c}{\rm o}{\rm l}{\rm l}}\approx 10}$ eV and that above this energy, both rotational and vibrational transitions inN 2 + ${{\rm{N}}_2^ + }$ are marginal in theN 2 + ${{\rm{N}}_2^ + }$ /He collisions.
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Affiliation(s)
- Stanislav Paláček
- IT4Innovations National Supercomputing Center and Department of Applied Mathematics, Faculty of Electrical Engineering and Computer Science, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, 708 00, Ostrava - Poruba, Czech Republic
| | - René Kalus
- Department of Applied Mathematics, Faculty of Electrical Engineering and Computer Science, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, 708 00, Ostrava - Poruba, Czech Republic
| | - Florent Xavier Gadéa
- Laboratoire de Chimie et Physique Quantiques, UMR5626 du CNRS, Université Toulouse III - Paul Sabatier, 31062, Toulouse Cedex 09, France
| | - Malika Benhenni
- Laboratoire Plasma et Conversion d'Energie, LAPLACE & UMR5213 du CNRS, Université Toulouse III - Paul Sabatier, 118 route de Narbonne, 31062, Toulouse Cedex, France
| | - Thierry Leininger
- Laboratoire de Chimie et Physique Quantiques, UMR5626 du CNRS, Université Toulouse III - Paul Sabatier, 31062, Toulouse Cedex 09, France
| | - Mohammed Yousfi
- Laboratoire Plasma et Conversion d'Energie, LAPLACE & UMR5213 du CNRS, Université Toulouse III - Paul Sabatier, 118 route de Narbonne, 31062, Toulouse Cedex, France
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2
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Ibrahim A, Roy PN. Three-body potential energy surface for para-hydrogen. J Chem Phys 2022; 156:044301. [PMID: 35105099 DOI: 10.1063/5.0076494] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Alexander Ibrahim
- Department of Physics and Astronomy, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Pierre-Nicholas Roy
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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3
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Unke O, Chmiela S, Sauceda HE, Gastegger M, Poltavsky I, Schütt KT, Tkatchenko A, Müller KR. Machine Learning Force Fields. Chem Rev 2021; 121:10142-10186. [PMID: 33705118 PMCID: PMC8391964 DOI: 10.1021/acs.chemrev.0c01111] [Citation(s) in RCA: 404] [Impact Index Per Article: 134.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Indexed: 12/27/2022]
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.
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Affiliation(s)
- Oliver
T. Unke
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
- DFG
Cluster of Excellence “Unifying Systems in Catalysis”
(UniSysCat), Technische Universität Berlin, 10623 Berlin, Germany
| | - Stefan Chmiela
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
| | - Huziel E. Sauceda
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
- BASLEARN,
BASF-TU Joint Lab, Technische Universität
Berlin, 10587 Berlin, Germany
| | - Michael Gastegger
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
- DFG
Cluster of Excellence “Unifying Systems in Catalysis”
(UniSysCat), Technische Universität Berlin, 10623 Berlin, Germany
- BASLEARN,
BASF-TU Joint Lab, Technische Universität
Berlin, 10587 Berlin, Germany
| | - Igor Poltavsky
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Kristof T. Schütt
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
| | - Alexandre Tkatchenko
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Klaus-Robert Müller
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
- BIFOLD−Berlin
Institute for the Foundations of Learning and Data, Berlin, Germany
- Department
of Artificial Intelligence, Korea University, Anam-dong, Seongbuk-gu, Seoul 02841, Korea
- Max Planck
Institute for Informatics, Stuhlsatzenhausweg, 66123 Saarbrücken, Germany
- Google
Research, Brain Team, Berlin, Germany
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4
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Hua Z, Zhao Y, Hu G, Feng S, Zhang Q, Chen Y, Zhao D. Probing the Charge-Transfer Potential Energy Surfaces by the Photodissociation of [Ar-N 2] . J Phys Chem Lett 2021; 12:4012-4017. [PMID: 33877828 DOI: 10.1021/acs.jpclett.1c00798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chemical reaction pathways and product state correlations of gas-phase ion-molecule reactions are governed by the involved potential energy surfaces (PESs). Here, we report the photodissociation dynamics of charge-transfer complex [Ar-N2]+, which is the intermediate of the model system of the Ar+ + N2 → Ar + N2+ reaction. High-resolution recoiling velocity images of photofragmented N2 and N2+ from different dissociation channels exhibit a vibrational state-specific correlation, revealing the nonadiabatic charge-transfer mechanisms upon the photodissociation of [Ar-N2]+. The state-resolved product branching ratios have yielded an accurate determination of the resonant charge-transfer probabilities. This work provides a powerful approach to elucidating the detailed dynamics of chemical events of charge-transfer complex [Ar-N2]+ and to probing the state-to-state charge-transfer PESs.
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Affiliation(s)
- Zefeng Hua
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yunxiao Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Gaoming Hu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Shaowen Feng
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Qiang Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yang Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Dongfeng Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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5
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Monte Carlo Simulation of a Modified Chi Distribution with Unequal Variances in the Generating Gaussians. A Discrete Methodology to Study Collective Response Times. MATHEMATICS 2020. [DOI: 10.3390/math9010077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Chi distribution is a continuous probability distribution of a random variable obtained from the positive square root of the sum of k squared variables, each coming from a standard Normal distribution (mean = 0 and variance = 1). The variable k indicates the degrees of freedom. The usual expression for the Chi distribution can be generalised to include a parameter which is the variance (which can take any value) of the generating Gaussians. For instance, for k = 3, we have the case of the Maxwell-Boltzmann (MB) distribution of the particle velocities in the Ideal Gas model of Physics. In this work, we analyse the case of unequal variances in the generating Gaussians whose distribution we will still represent approximately in terms of a Chi distribution. We perform a Monte Carlo simulation to generate a random variable which is obtained from the positive square root of the sum of k squared variables, but this time coming from non-standard Normal distributions, where the variances can take any positive value. Then, we determine the boundaries of what to expect when we start from a set of unequal variances in the generating Gaussians. In the second part of the article, we present a discrete model to calculate the parameter of the Chi distribution in an approximate way for this case (unequal variances). We also comment on the application of this simple discrete model to calculate the parameter of the MB distribution (Chi of k = 3) when it is used to represent the reaction times to visual stimuli of a collective of individuals in the framework of a Physics inspired model we have published in a previous work.
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6
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Machinery Failure Approach and Spectral Analysis to Study the Reaction Time Dynamics over Consecutive Visual Stimuli: An Entropy-Based Model. MATHEMATICS 2020. [DOI: 10.3390/math8111979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The reaction times of individuals over consecutive visual stimuli have been studied using an entropy-based model and a failure machinery approach. The used tools include the fast Fourier transform and a spectral entropy analysis. The results indicate that the reaction times produced by the independently responding individuals to visual stimuli appear to be correlated. The spectral analysis and the entropy of the spectrum yield that there are features of similarity in the response times of each participant and among them. Furthermore, the analysis of the mistakes made by the participants during the reaction time experiments concluded that they follow a behavior which is consistent with the MTBF (Mean Time Between Failures) model, widely used in industry for the predictive diagnosis of electrical machines and equipment.
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7
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Koner D, Bemish RJ, Meuwly M. Dynamics on Multiple Potential Energy Surfaces: Quantitative Studies of Elementary Processes Relevant to Hypersonics. J Phys Chem A 2020; 124:6255-6269. [DOI: 10.1021/acs.jpca.0c01870] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debasish Koner
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Raymond J. Bemish
- Air Force Research Laboratory, Space Vehicles Directorate, Kirtland AFB, New Mexico 87117, United States
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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8
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Venturi S, Jaffe RL, Panesi M. Bayesian Machine Learning Approach to the Quantification of Uncertainties on Ab Initio Potential Energy Surfaces. J Phys Chem A 2020; 124:5129-5146. [DOI: 10.1021/acs.jpca.0c02395] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- S. Venturi
- University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - R. L. Jaffe
- NASA Ames Research Center, Moffett Field, California 94035-1000, United States
| | - M. Panesi
- University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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9
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Koner D, Bemish RJ, Meuwly M. The C( 3P) + NO(X 2Π) → O( 3P) + CN(X 2Σ +), N( 2D)/N( 4S) + CO(X 1Σ +) reaction: Rates, branching ratios, and final states from 15 K to 20 000 K. J Chem Phys 2018; 149:094305. [PMID: 30195287 DOI: 10.1063/1.5046906] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The C + NO collision system is of interest in the area of high-temperature combustion and atmospheric chemistry. In this work, full dimensional potential energy surfaces for the 2A', 2A″, and 4A″ electronic states of the [CNO] system have been constructed following a reproducing kernel Hilbert space approach. For this purpose, more than 50 000 ab initio energies are calculated at the MRCI+Q/aug-cc-pVTZ level of theory. The dynamical simulations for the C(3P) + NO(X2Π) → O(3P) + CN(X2Σ+), N(2D)/N(4S) + CO(X1Σ+) reactive collisions are carried out on the newly generated surfaces using the quasiclassical trajectory (QCT) calculation method to obtain reaction probabilities, rate coefficients, and the distribution of product states. Preliminary quantum calculations are also carried out on the surfaces to obtain the reaction probabilities and compared with QCT results. The effect of nonadiabatic transitions on the dynamics for this title reaction is explored within the Landau-Zener framework. QCT simulations have been performed to simulate molecular beam experiment for the title reaction at 0.06 and 0.23 eV of relative collision energies. Results obtained from theoretical calculations are in good agreement with the available experimental as well as theoretical data reported in the literature. Finally, the reaction is studied at temperatures that are not practically achievable in the laboratory environment to provide insight into the reaction dynamics at temperatures relevant to hypersonic flight.
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Affiliation(s)
- Debasish Koner
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - 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
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10
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Meuwly M. Reactive molecular dynamics: From small molecules to proteins. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1386] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Markus Meuwly
- Department of Chemistry University of Basel Basel Switzerland
- Department of Chemistry Brown University Providence Rhode Island
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11
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Karandashev K, Xu ZH, Meuwly M, Vaníček J, Richardson JO. Kinetic isotope effects and how to describe them. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061501. [PMID: 29282447 PMCID: PMC5729036 DOI: 10.1063/1.4996339] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 08/23/2017] [Indexed: 06/01/2023]
Abstract
We review several methods for computing kinetic isotope effects in chemical reactions including semiclassical and quantum instanton theory. These methods describe both the quantization of vibrational modes as well as tunneling and are applied to the ⋅H + H2 and ⋅H + CH4 reactions. The absolute rate constants computed with the semiclassical instanton method both using on-the-fly electronic structure calculations and fitted potential-energy surfaces are also compared directly with exact quantum dynamics results. The error inherent in the instanton approximation is found to be relatively small and similar in magnitude to that introduced by using fitted surfaces. The kinetic isotope effect computed by the quantum instanton is even more accurate, and although it is computationally more expensive, the efficiency can be improved by path-integral acceleration techniques. We also test a simple approach for designing potential-energy surfaces for the example of proton transfer in malonaldehyde. The tunneling splittings are computed, and although they are found to deviate from experimental results, the ratio of the splitting to that of an isotopically substituted form is in much better agreement. We discuss the strengths and limitations of the potential-energy surface and based on our findings suggest ways in which it can be improved.
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Affiliation(s)
- Konstantin Karandashev
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Zhen-Hao Xu
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jeremy O Richardson
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich (ETHZ), CH-8093 Zürich, Switzerland
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12
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Bircher MP, Liberatore E, Browning NJ, Brickel S, Hofmann C, Patoz A, Unke OT, Zimmermann T, Chergui M, Hamm P, Keller U, Meuwly M, Woerner HJ, Vaníček J, Rothlisberger U. Nonadiabatic effects in electronic and nuclear dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061510. [PMID: 29376108 PMCID: PMC5760266 DOI: 10.1063/1.4996816] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/19/2017] [Indexed: 05/25/2023]
Abstract
Due to their very nature, ultrafast phenomena are often accompanied by the occurrence of nonadiabatic effects. From a theoretical perspective, the treatment of nonadiabatic processes makes it necessary to go beyond the (quasi) static picture provided by the time-independent Schrödinger equation within the Born-Oppenheimer approximation and to find ways to tackle instead the full time-dependent electronic and nuclear quantum problem. In this review, we give an overview of different nonadiabatic processes that manifest themselves in electronic and nuclear dynamics ranging from the nonadiabatic phenomena taking place during tunnel ionization of atoms in strong laser fields to the radiationless relaxation through conical intersections and the nonadiabatic coupling of vibrational modes and discuss the computational approaches that have been developed to describe such phenomena. These methods range from the full solution of the combined nuclear-electronic quantum problem to a hierarchy of semiclassical approaches and even purely classical frameworks. The power of these simulation tools is illustrated by representative applications and the direct confrontation with experimental measurements performed in the National Centre of Competence for Molecular Ultrafast Science and Technology.
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Affiliation(s)
- Martin P Bircher
- Laboratory of Computational Chemistry and Biochemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Elisa Liberatore
- Laboratory of Computational Chemistry and Biochemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Nicholas J Browning
- Laboratory of Computational Chemistry and Biochemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | | | - Aurélien Patoz
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Oliver T Unke
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Tomáš Zimmermann
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide (LSU) and Lausanne Centre for Ultrafast Science (LACUS), Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zürich, Switzerland
| | - Ursula Keller
- Physics Department, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Hans-Jakob Woerner
- Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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13
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Unke OT, Meuwly M. Toolkit for the Construction of Reproducing Kernel-Based Representations of Data: Application to Multidimensional Potential Energy Surfaces. J Chem Inf Model 2017; 57:1923-1931. [PMID: 28666387 DOI: 10.1021/acs.jcim.7b00090] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the early days of computation, slow processor speeds limited the amount of data that could be generated and used for scientific purposes. In the age of big data, the limiting factor usually is the method with which large amounts of data are analyzed and useful information is extracted. A typical example from chemistry are high-level ab initio calculations for small systems, which have nowadays become feasible even if energies at many different geometries are required. Molecular dynamics simulations often require several thousand distinct trajectories to be run. Under such circumstances suitable analytical representations of potential energy surfaces (PESs) based on ab initio calculations are required to propagate the dynamics at an acceptable cost. In this work we introduce a toolkit which allows the automatic construction of multidimensional PESs from gridded ab initio data based on reproducing kernel Hilbert space (RKHS) theory. The resulting representations require no tuning of parameters and allow energy and force evaluations at ab initio quality at the same cost as empirical force fields. Although the toolkit is primarily intended for constructing multidimensional potential energy surfaces for molecular systems, it can also be used for general machine learning purposes. The software is published under the MIT license and can be downloaded, modified, and used in other projects for free.
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Affiliation(s)
- Oliver T Unke
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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14
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Denis-Alpizar O, Bemish RJ, Meuwly M. Communication: Vibrational relaxation of CO(1Σ) in collision with Ar(1S) at temperatures relevant to the hypersonic flight regime. J Chem Phys 2017; 146:111102. [DOI: 10.1063/1.4978498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Otoniel Denis-Alpizar
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - 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
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
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15
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Denis-Alpizar O, Bemish RJ, Meuwly M. Reactive collisions for NO(2Π) + N(4S) at temperatures relevant to the hypersonic flight regime. Phys Chem Chem Phys 2017; 19:2392-2401. [DOI: 10.1039/c6cp07142b] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rate coefficients for the NO(2Π) + N(4S) reaction at high temperatures from quasiclassical trajectories using MRCI+Q PESs of the lowest triplet states.
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Affiliation(s)
- Otoniel Denis-Alpizar
- Department of Chemistry
- University of Basel
- Klingelbergstrasse 80
- 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
- Department of Chemistry
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16
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Denis-Alpizar O, Unke OT, Bemish RJ, Meuwly M. Quantum and quasiclassical trajectory studies of rotational relaxation in Ar–N2+ collisions. Phys Chem Chem Phys 2017; 19:27945-27951. [DOI: 10.1039/c7cp05036d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum and classical study of the Ar–N2+ collision based on a new potential energy surface.
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Affiliation(s)
- Otoniel Denis-Alpizar
- Department of Chemistry
- University of Basel
- Klingelbergstrasse 80
- CH-4056 Basel
- Switzerland
| | - Oliver T. Unke
- Department of Chemistry
- University of Basel
- Klingelbergstrasse 80
- CH-4056 Basel
- Switzerland
| | - Raymond J. Bemish
- Air Force Research Laboratory
- Space Vehicles Directorate
- New Mexico 87117
- USA
| | - Markus Meuwly
- Department of Chemistry
- University of Basel
- Klingelbergstrasse 80
- CH-4056 Basel
- Switzerland
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