Abstract
Chemistry dynamics simulation is widely used in quantitative structure activity relationship QSAR, virtual screening, protein structure prediction, quantum chemistry, materials design, and property prediction, etc. This chapter explores the idea of integrating Long Short-Term Memory (LSTM) with chemistry dynamics simulations to enhance the performance of the simulation and improve its usability for research and education. The idea is successfully used to predict the location, energy, and Hessian of atoms in a H2O reaction system. The results demonstrate that the artificial neural network–based memory model successfully learns the desired features associated with the atomic trajectory and rapidly generates predictions that are in excellent agreement with the results from chemistry dynamics simulations. The accuracy of the prediction is better than expected.
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References
D.L. Bunker, Classical trajectory methods. Comput. Phys., 10, 287–324 (1971, 1971)
J.M. Millam, V. Bakken, W. Chen, W.L. Hase, Ab initio classical trajectories on the Born–Oppenheimer surface: Hessian-based integrators using fifth-order polynomial and rational function fits. J. Chem. Phys. 111, 3800–3805 (1999)
N. Sathyamurthy, Computational fitting of AB initio potential energy surfaces. Comput. Phys. Rep. 3, 1–69 (1985)
H.-M. Keller, H. Floethmann, A.J. Dobbyn, R. Schinke, H.-J. Werner, C. Bauer, P. Rosmus, The unimolecular dissociation of HCO. II. Comparison of calculated resonance energies and widths with high-resolution spectroscopic data. J. Chem. Phys. 105, 4983–5004 (1996)
X. Zhang, S. Zou, L.B. Harding, J.M. Bowman, A global ab initio potential energy surface for formaldehyde. J. Phys. Chem. 108, 8980–8986 (2004)
A.P. Bartók, M.J. Gillan, F.R. Manby, G. Csányi, Machine-learning approach for one- and two-body corrections to density functional theory: applications to molecular and condensed water. Phys. Rev. B 88, 054104 (August 2013)
NIH., https://ncats.nih.gov/news/releases/2015/tox21-challenge-2014-winners (2014)
M. Rupp, A. Tkatchenko, K.-R. MĂĽller, O.A. von Lilienfeld, Fast and accurate modeling of molecular atomization energies with machine learning. Phys. Rev. Lett. 108, 058301 (2012)
R. Ramakrishnan, P.O. Dral, M. Rupp, O.A. von Lilienfeld, J. Chem. Theor. Comput. 11, 2087 (2015)
S. Lu, Q. Zeng, H. Wu, A New Power Load Forecasting Model (SIndRNN): independently recurrent neural network based on softmax kernel function. IEEE 21st International Conference on High Performance Computing and Communications , https://doi.org/10.1109/HPCC/SmartCity/DSS.2019.00320, 2019
H. Wu, S. Lu, A. Lopez-Aeamburo, J. She, Temperature Prediction Based on Long Short-Term Memory Networks, CSCI'19, 2019
V. Botu, R. Ramprasad, Adaptive machine learning framework to accelerate ab initio molecular dynamics. Int. J. Quantum Chem. 115(16), 1074–1083 (2015)
E. Apra, T.L. Windus, T.P. Straatsma, et al., NWChem, A computational chemistry package for parallel computers, version 5.0, Pacific Northwest National Laboratory, Richland, Washington, 2007
H. Wu et al., Higher-accuracy schemes for approximating the Hessian from electronic structure calculations in chemical dynamics simulations. J. Chem. Phys. 133, 074101, 2010
H. Wu, et al., A High Accuracy Computing Reduction Algorithm Based on Data Reuse for Direct Dynamics Simulations, CSCI 2016
H. Wu and S. Lu, Evaluating the accuracy of a third order hessian-based predictor-corrector integrator, Europe Simulation Conference, 2016
H. Wu, S. Lu, et al., Evaluating the accuracy of Hessian-based predictor-corrector integrators. J. Cent. South Univ. 24(7), 1696–1702 (2017)
Acknowledgments
This work was supported by Dr. Hase research group and Chemdynm cluster at Texas Tech University, as well as the Industrial Internet Innovation and Development Project of China: Digital twin system for automobile welding and casting production lines and its application demonstration (TC9084DY).
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Wu, H., Lu, S., Eduardo, CD., Liang, J., She, J., Tan, X. (2021). Long Short-Term Memory in Chemistry Dynamics Simulation. In: Arabnia, H.R., Ferens, K., de la Fuente, D., Kozerenko, E.B., Olivas Varela, J.A., Tinetti, F.G. (eds) Advances in Artificial Intelligence and Applied Cognitive Computing. Transactions on Computational Science and Computational Intelligence. Springer, Cham. https://doi.org/10.1007/978-3-030-70296-0_9
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