Spectroscopy-Guided Discovery of Three-Dimensional Structures of Disordered Materials with Diffusion Models (2312.05472v1)
Abstract: The ability to rapidly develop materials with desired properties has a transformative impact on a broad range of emerging technologies. In this work, we introduce a new framework based on the diffusion model, a recent generative machine learning method to predict 3D structures of disordered materials from a target property. For demonstration, we apply the model to identify the atomic structures of amorphous carbons ($a$-C) as a representative material system from the target X-ray absorption near edge structure (XANES) spectra--a common experimental technique to probe atomic structures of materials. We show that conditional generation guided by XANES spectra reproduces key features of the target structures. Furthermore, we show that our model can steer the generative process to tailor atomic arrangements for a specific XANES spectrum. Finally, our generative model exhibits a remarkable scale-agnostic property, thereby enabling generation of realistic, large-scale structures through learning from a small-scale dataset (i.e., with small unit cells). Our work represents a significant stride in bridging the gap between materials characterization and atomic structure determination; in addition, it can be leveraged for materials discovery in exploring various material properties as targeted.
- “Materials for electrochemical capacitors” In Nature materials 7.11 Nature Publishing Group UK London, 2008, pp. 845–854
- “Li-ion battery materials: present and future” In Materials today 18.5 Elsevier, 2015, pp. 252–264
- “Fluids and Electrolytes under Confinement in Single-Digit Nanopores” In Chemical reviews 123.6 ACS Publications, 2023, pp. 2737–2831
- “Accelerating materials development via automation, machine learning, and high-performance computing” In Joule 2.8 Elsevier, 2018, pp. 1410–1420
- “A high-throughput infrastructure for density functional theory calculations” In Computational Materials Science 50.8 Elsevier, 2011, pp. 2295–2310
- “Commentary: The Materials Project: A materials genome approach to accelerating materials innovation” In APL materials 1.1 AIP Publishing, 2013
- “Inverse molecular design using machine learning: Generative models for matter engineering” In Science 361.6400 American Association for the Advancement of Science, 2018, pp. 360–365
- “Inverse design of solid-state materials via a continuous representation” In Matter 1.5 Elsevier, 2019, pp. 1370–1384
- “Inverse design of nanoporous crystalline reticular materials with deep generative models” In Nature Machine Intelligence 3.1 Nature Publishing Group UK London, 2021, pp. 76–86
- Baekjun Kim, Sangwon Lee and Jihan Kim “Inverse design of porous materials using artificial neural networks” In Science advances 6.1 American Association for the Advancement of Science, 2020, pp. eaax9324
- “Machine-enabled inverse design of inorganic solid materials: promises and challenges” In Chemical Science 11.19 Royal Society of Chemistry, 2020, pp. 4871–4881
- “Deep unsupervised learning using nonequilibrium thermodynamics” In International Conference on Machine Learning, 2015, pp. 2256–2265 PMLR
- Jonathan Ho, Ajay Jain and Pieter Abbeel “Denoising diffusion probabilistic models” In Advances in Neural Information Processing Systems 33, 2020, pp. 6840–6851
- “Score-based generative modeling through stochastic differential equations” In arXiv preprint arXiv:2011.13456, 2020
- “Estimation of non-normalized statistical models by score matching.” In Journal of Machine Learning Research 6.4, 2005
- Pascal Vincent “A connection between score matching and denoising autoencoders” In Neural computation 23.7 MIT Press, 2011, pp. 1661–1674
- “Equivariant diffusion for molecule generation in 3d” In International conference on machine learning, 2022, pp. 8867–8887 PMLR
- “Torsional diffusion for molecular conformer generation” In Advances in Neural Information Processing Systems 35, 2022, pp. 24240–24253
- “Digress: Discrete denoising diffusion for graph generation” In arXiv preprint arXiv:2209.14734, 2022
- “Geodiff: A geometric diffusion model for molecular conformation generation” In arXiv preprint arXiv:2203.02923, 2022
- “Guided Diffusion for Inverse Molecular Design”, 2023
- “Crystal diffusion variational autoencoder for periodic material generation” In arXiv preprint arXiv:2110.06197, 2021
- “Towards Predicting Equilibrium Distributions for Molecular Systems with Deep Learning” In arXiv preprint arXiv:2306.05445, 2023
- Tuan Anh Pham, Yuan Ping and Giulia Galli “Modelling heterogeneous interfaces for solar water splitting” In Nature materials 16.4 Nature Publishing Group UK London, 2017, pp. 401–408
- “Beyond idealized models of nanoscale metal hydrides for hydrogen storage” In Industrial & Engineering Chemistry Research 59.13 ACS Publications, 2020, pp. 5786–5796
- Massimiliano Comin and Laurent J Lewis “Deep-learning approach to the structure of amorphous silicon” In Physical Review B 100.9 APS, 2019, pp. 094107
- “Wasserstein auto-encoders” In arXiv preprint arXiv:1711.01558, 2017
- “Hydrogen in disordered titania: connecting local chemistry, structure, and stoichiometry through accelerated exploration” In Journal of Materials Chemistry A 11.16 Royal Society of Chemistry, 2023, pp. 8670–8683
- “Molecular dynamics simulations of gas selectivity in amorphous porous molecular solids” In Journal of the American Chemical Society 135.47 ACS Publications, 2013, pp. 17818–17830
- “Molecular dynamics modeling of interfacial interactions between flattened carbon nanotubes and amorphous carbon: Implications for ultra-lightweight composites” In ACS applied nano materials 5.4 ACS Publications, 2022, pp. 5915–5924
- “ReaxFF molecular dynamics simulation for the graphitization of amorphous carbon: a parametric study” In Journal of chemical theory and computation 14.5 ACS Publications, 2018, pp. 2322–2331
- Paul J Steinhardt, David R Nelson and Marco Ronchetti “Bond-orientational order in liquids and glasses” In Physical Review B 28.2 APS, 1983, pp. 784
- Miguel A Caro “GAP interatomic potential for amorphous carbon (2.0) [Data set]” DOI: 10.5281/zenodo.5243184
- Volker L Deringer and Gábor Csányi “Machine learning based interatomic potential for amorphous carbon” In Physical Review B 95.9 APS, 2017, pp. 094203
- “Harnessing Neural Networks for Elucidating X-ray Absorption Structure–Spectrum Relationships in Amorphous Carbon” In The Journal of Physical Chemistry C 127.33 ACS Publications, 2023, pp. 16473–16484
- “Structural and elastic properties of amorphous carbon from simulated quenching at low rates” In Modelling and Simulation in Materials Science and Engineering 27.8 IOP Publishing, 2019, pp. 085009
- Xuerong Mao “The truncated Euler–Maruyama method for stochastic differential equations” In Journal of Computational and Applied Mathematics 290 Elsevier, 2015, pp. 370–384
- Jörg Behler “Atom-centered symmetry functions for constructing high-dimensional neural network potentials” In The Journal of chemical physics 134.7 AIP Publishing, 2011
- Albert P Bartók, Risi Kondor and Gábor Csányi “On representing chemical environments” In Physical Review B 87.18 APS, 2013, pp. 184115
- “Unified representation of molecules and crystals for machine learning” In arXiv preprint arXiv:1704.06439, 2017
- “Diffusion Posterior Sampling for General Noisy Inverse Problems” In The Eleventh International Conference on Learning Representations, 2022
- “Pytorch: An imperative style, high-performance deep learning library” In Advances in neural information processing systems 32, 2019, pp. 8026–8037
- Matthias Fey and Jan Eric Lenssen “Fast graph representation learning with PyTorch Geometric” Preprint at https://arxiv.org/abs/1903.02428, 2019
- “Fourier features let networks learn high frequency functions in low dimensional domains” In Advances in Neural Information Processing Systems 33, 2020, pp. 7537–7547
- “Learning mesh-based simulation with graph networks” In arXiv preprint arXiv:2010.03409, 2020
- “Restart Sampling for Improving Generative Processes” In arXiv preprint arXiv:2306.14878, 2023
- “X-ray absorption spectra of water from first principles calculations” In Phys. Rev. Lett. 96.21 APS, 2006, pp. 215502
- “QUANTUM ESPRESSO: A modular and open-source software project for quantum simulations of materials” In J. Phys. Condens. Matter 21.39 IOP Publishing, 2009, pp. 395502
- David Prendergast and Steven G Louie “Bloch-state-based interpolation: An efficient generalization of the Shirley approach to interpolating electronic structure” In Phys. Rev. B 80.23 APS, 2009, pp. 235126
- John P Perdew, Kieron Burke and Matthias Ernzerhof “Generalized gradient approximation made simple” In Phys. Rev. Lett. 77.18 APS, 1996, pp. 3865
- David Vanderbilt “Soft self-consistent pseudopotentials in a generalized eigenvalue formalism” In Phys. Rev. B 41.11 APS, 1990, pp. 7892
- “Trends in carbon, oxygen, and nitrogen core in the X-ray absorption spectroscopy of carbon nanomaterials: a guide for the perplexed” In J. Phys. Chem. C 125.1 ACS Publications, 2020, pp. 973–988
- Eric L Shirley “Ab initio inclusion of electron-hole attraction: Application to X-ray absorption and resonant inelastic X-ray scattering” In Phys. Rev. Lett. 80.4 APS, 1998, pp. 794
- “Theoretical optical and X-ray spectra of liquid and solid H2subscriptH2\text{H}_{2}H start_POSTSUBSCRIPT 2 end_POSTSUBSCRIPTO” In Phys. Rev. B 85.4 APS, 2012, pp. 045101
- “Linear-response and real-time time-dependent density functional theory studies of core-level near-edge X-ray absorption” In J. Chem. Theory Comput. 8.9 ACS Publications, 2012, pp. 3284–3292