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Molecular Simulation of Lithium Carbonate Reactive Vapor–Liquid Equilibria Using a Deep Potential Model
We developed a first-principles machine learning model for the reactive vapor–liquid phase behavior of molten Li 2 CO 3 . The model was trained on ab initio electronic density functional theory data using the Deep Potential (DP) methodology, and its accuracy was evaluated by comparing model predictions of density and viscosity to experimental measurements. Direct coexistence simulations with the DP model over time scales of tens of nanoseconds were used to observe equilibrium dissociation of Li 2 CO 3 into CO 2 residing primarily in the vapor phase and Li 2 O which remains dissolved in the liquid. The simulations covered a range of temperatures, overall system sizes, and vapor-to-liquid volume ratios. Results were analyzed in terms of the observed chemical composition of the liquid and vapor phases, product structure, and CO 2 partial pressures. In addition, we calculated equilibrium constants for the dissociation reaction by assuming ideal-solution behavior for the liquid. As expected on the basis of thermodynamic arguments and prior experiments for this system, the observed partial pressure of CO 2 in the gas phase depends on both the temperature and the ratio of vapor to liquid volumes, while the calculated equilibrium constants only depend on temperature. DP model predictions for the equilibrium constant of the reaction are generally consistent with the available experimental measurements. Furthermore, the present study establishes the validity of the DP methodology for the description of reactive, multiphase equilibria from first principles, with possible applications to many other systems of scientific and technological interest even in the absence of relevant experimental measurements.
De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM
Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates remains a significant challenge. Here, we introduce Cryo2Struct, a fully automated de novo cryo-EM structure modeling method. Cryo2Struct utilizes a 3D transformer to identify atoms and amino acid types in cryo-EM density maps, followed by an innovative Hidden Markov Model (HMM) to connect predicted atoms and build protein backbone structures. Cryo2Struct produces substantially more accurate and complete protein structural models than the widely used ab initio method Phenix. Additionally, its performance in building atomic structural models is robust against changes in the resolution of density maps and the size of protein structures.
Exploiting Machine Learning in Multiscale Modelling of Materials
Recent developments in efficient machine learning algorithms have spurred significant interest in the materials community. The inherently complex and multiscale problems in Materials Science and Engineering pose a formidable challenge. The present scenario of machine learning research in Materials Science has a clear lacunae, where efficient algorithms are being developed as a separate endeavour, while such methods are being applied as ‘black-box’ models by others. The present article aims to discuss pertinent issues related to the development and application of machine learning algorithms for various aspects of multiscale materials modelling. The authors present an overview of machine learning of equivariant properties, machine learning-aided statistical mechanics, the incorporation of ab initio approaches in multiscale models of materials processing and application of machine learning in uncertainty quantification. In addition to the above, the applicability of Bayesian approach for multiscale modelling will be discussed. Critical issues related to the multiscale materials modelling are also discussed.
Ab initio leading order effective potential for elastic proton scattering based on the symmetry-adapted no-core shell model
Calculating microscopic optical potentials for elastic scattering at intermediate energies from light nuclei in an ab initio fashion within the Watson expansion has been established within the last few years. Based on the Watson expansion of the multiple scattering series, we employ a nonlocal translationally invariant nuclear density derived within the symmetry-adapted no-core shell model (SA-NCSM) framework from a chiral next-to-next-to-leading order (NNLO) nucleon-nucleon interaction and the very same interaction for a consistent full-folding calculation of the effective (optical) potential for nucleon-nucleus scattering for medium-heavy nuclei. The leading order effective (optical) folding potential is computed by integrating over a translationally invariant SA-NCSM one-body scalar density, spin-projected momentum distribution, and the Wolfenstein amplitudes 𝐴, 𝐶, and 𝑀. The resulting nonlocal potentials serve as input for a momentum space Lippmann-Schwinger equation. In the SA-NCSM, the model space is systematically up-selected using Sp(3,ℝ) symmetry considerations. For the light nucleus of 6 He, we establish a systematic selection scheme in the SA-NCSM for scattering observables. Then, we apply this scheme to calculations of scattering observables, such as differential cross sections, analyzing powers, and spin rotation functions for elastic proton scattering from 20 Ne and 40 Ca in the energy regime between 65 and 200 MeV, and compare to available data. Furthermore, our calculations show that the leading order effective nucleon-nucleus potential in the Watson expansion of multiple scattering theory obtained from an up-selected SA-NCSM model space describes 40 Ca elastic scattering observables reasonably well to about 60 degrees in the center-of-mass frame, which coincides roughly with the validity of the NNLO chiral interaction used to calculate both the nucleon-nucleon amplitudes and the one-body scalar and spin nuclear densities.
Two-photon double ionization with finite pulses: Application of the virtual sequential model to helium
As a step toward the full ab initio description of two-photon double ionization processes, we present a finite-pulse version of the virtual-sequential model for polyelectronic atoms. The model relies on the ab initio description of the single ionization scattering states of both the neutral and ionized target system. As a proof of principle and a benchmark, the model is applied to the helium atom using the newstock atomic photoionization code. The results of angularly integrated observables, which are in excellent agreement with existing time-dependent Schrödinger equation (TDSE) simulations, show how the model is able to capture the role of electron correlation in the nonsequential regime, and the influence of autoionizing states in the sequential regime, at a comparatively modest computational cost. The model also reproduces the two-particle interference with ultrashort pulses, which is within reach of current experimental technologies. Furthermore, the model shows the modulation of the joint energy distribution in the vicinity of autoionizing states, which can be probed with extreme-ultraviolet pulses of duration much longer than the characteristic lifetime of the resonance. Furthermore, the formalism discussed here applies also to polyelectronic atoms and molecules, thus opening a window on nonsequential and sequential double ionization in these more complex systems.
Towards Ab-Initio Simulations of Crystalline Defects at the Exascale Using Spectral Quadrature Density Functional Theory
Defects in crystalline solids play a crucial role in determining properties of materials at the nano, meso- and macroscales, such as the coalescence of vacancies at the nanoscale to form voids and prismatic dislocation loops or diffusion and segregation of solutes to nucleate precipitates, phase transitions in magnetic materials via disorder and doping. First principles Density Functional Theory (DFT) simulations can provide a detailed understanding of these phenomena. However, the number of atoms needed to correctly simulate these systems is often beyond the reach of many widely used DFT codes. The aim of this article is to discuss recent advances in first principles modeling of crystal defects using the spectral quadrature method. The spectral quadrature method is linear scaling with respect to the number of atoms, permits spatial coarse-graining, and is capable of simulating non-periodic systems embedded in a bulk environment, which allows the application of appropriate boundary conditions for simulations of crystalline defects. In this article, we discuss the state-of-the-art in ab-initio modeling of large metallic systems of the order of several thousand atoms that are suitable for utilizing exascale computing resourses.
MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction
Protein structure prediction is an important problem in bioinformatics and has been studied for decades. However, there are still few open-source comprehensive protein structure prediction packages publicly available in the field. In this paper, we present our latest open-source protein tertiary structure prediction system—MULTICOM2, an integration of template-based modeling (TBM) and template-free modeling (FM) methods. The template-based modeling uses sequence alignment tools with deep multiple sequence alignments to search for structural templates, which are much faster and more accurate than MULTICOM1. The template-free (ab initio or de novo) modeling uses the inter-residue distances predicted by DeepDist to reconstruct tertiary structure models without using any known structure as template. In the blind CASP14 experiment, the average TM-score of the models predicted by our server predictor based on the MULTICOM2 system is 0.720 for 58 TBM (regular) domains and 0.514 for 38 FM and FM/TBM (hard) domains, indicating that MULTICOM2 is capable of predicting good tertiary structures across the board. It can predict the correct fold for 76 CASP14 domains (95% regular domains and 55% hard domains) if only one prediction is made for a domain. The success rate is increased to 3% for both regular and hard domains if five predictions are made per domain. Moreover, the prediction accuracy of the pure template-free structure modeling method on both TBM and FM targets is very close to the combination of template-based and template-free modeling methods. This demonstrates that the distance-based template-free modeling method powered by deep learning can largely replace the traditional template-based modeling method even on TBM targets that TBM methods used to dominate and therefore provides a uniform structure modeling approach to any protein. Finally, on the 38 CASP14 FM and FM/TBM hard domains, MULTICOM2 server predictors (MULTICOM-HYBRID, MULTICOM-DEEP, MULTICOM-DIST) were ranked among the top 20 automated server predictors in the CASP14 experiment. After combining multiple predictors from the same research group as one entry, MULTICOM-HYBRID was ranked no. 5. The source code of MULTICOM2 is freely available at https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .
A microscopic Kondo lattice model for the heavy fermion antiferromagnet CeIn 3
Electrons at the border of localization generate exotic states of matter across all classes of strongly correlated electron materials and many other quantum materials with emergent functionality. Heavy electron metals are a model example, in which magnetic interactions arise from the opposing limits of localized and itinerant electrons. This remarkable duality is intimately related to the emergence of a plethora of novel quantum matter states such as unconventional superconductivity, electronic-nematic states, hidden order and most recently topological states of matter such as topological Kondo insulators and Kondo semimetals and putative chiral superconductors. The outstanding challenge is that the archetypal Kondo lattice model that captures the underlying electronic dichotomy is notoriously difficult to solve for real materials. Here we show, using the prototypical strongly-correlated antiferromagnet CeIn 3 , that a multi-orbital periodic Anderson model embedded with input from ab initio bandstructure calculations can be reduced to a simple Kondo-Heisenberg model, which captures the magnetic interactions quantitatively. We validate this tractable Hamiltonian via high-resolution neutron spectroscopy that reproduces accurately the magnetic soft modes in CeIn 3 , which are believed to mediate unconventional superconductivity. Our study paves the way for a quantitative understanding of metallic quantum states such as unconventional superconductivity.
A = 3 ( e , e ' ) x B ≥ 1 cross-section ratios and the isospin structure of short-range correlations
We study the relation between measured high-x B , high-Q 2 , helium-3 to tritium, (e,e') inclusive-scattering cross-section ratios and the relative abundance of high-momentum neutron-proton (np) and proton-proton (pp) short-range correlated (SRC) nucleon pairs in three-body (A=3) nuclei. In this study, analysis of this data using a simple pair-counting cross-section model suggested a much smaller np/pp ratio than previously measured in heavier nuclei, questioning our understanding of A=3 nuclei and, by extension, all other nuclei. Here we examine this finding using spectral-function-based cross-section calculations, with both an ab initio A=3 spectral function and effective Generalized Contact Formalism (GCF) spectral functions using different nucleon-nucleon interaction models. The ab initio calculation agrees with the data, showing good understanding of the structure of A=3 nuclei. An 8% uncertainty on the simple pair-counting model, as implied by the difference between it and the ab initio calculation, gives a factor of 5 uncertainty in the extracted np/pp ratio. Thus we see no evidence for the claimed "unexpected structure in the high-momentum wavefunction for hydrogen-3 and helium-3."
Number of sites-based solver for determining coverages from steady-state mean-field micro-kinetic models
Kinetic models parameterized by ab-initio calculations have led to significant improvements in understanding chemical reactions in heterogeneous catalysis. These studies have been facilitated by implementations which determine steady-state coverages and rates of mean-field micro-kinetic models. As implemented in the open-source kinetic modeling program, CatMAP, the conventional solution strategy is to use a root-finding algorithm to determine the coverage of all intermediates through the steady-state expressions, constraining all coverages to be non-negative and to properly sum to unity. Though intuitive, this root-finding strategy causes issues with convergence to solution due to these imposed constraints. In this work, we avoid explicitly imposing these constraints, solving the mean-field steady-state micro-kinetic model in the space of number of sites instead of solving it in the space of coverages. Here, we transform the constrained root-finding problem to an unconstrained least-squares minimization problem, leading to significantly improved convergence in solving micro-kinetic models and thus enabling the efficient study of more complex catalytic reactions.
Uncertainty-aware molecular dynamics from Bayesian active learning for phase transformations and thermal transport in SiC
Abstract Machine learning interatomic force fields are promising for combining high computational efficiency and accuracy in modeling quantum interactions and simulating atomistic dynamics. Active learning methods have been recently developed to train force fields efficiently and automatically. Among them, Bayesian active learning utilizes principled uncertainty quantification to make data acquisition decisions. In this work, we present a general Bayesian active learning workflow, where the force field is constructed from a sparse Gaussian process regression model based on atomic cluster expansion descriptors. To circumvent the high computational cost of the sparse Gaussian process uncertainty calculation, we formulate a high-performance approximate mapping of the uncertainty and demonstrate a speedup of several orders of magnitude. We demonstrate the autonomous active learning workflow by training a Bayesian force field model for silicon carbide (SiC) polymorphs in only a few days of computer time and show that pressure-induced phase transformations are accurately captured. The resulting model exhibits close agreement with both ab initio calculations and experimental measurements, and outperforms existing empirical models on vibrational and thermal properties. The active learning workflow readily generalizes to a wide range of material systems and accelerates their computational understanding.
Experimentally informed structure optimization of amorphous TiO 2 films grown by atomic layer deposition
Amorphous titanium dioxide TiO 2 (a-TiO 2 ) has been widely studied, particularly as a protective coating layer on semiconductors to prevent corrosion and promote electron–hole conduction in photoelectrochemical reactions. The stability and longevity of a-TiO 2 is strongly affected by the thickness and structural heterogeneity, implying that understanding the structure properties of a-TiO 2 is crucial for improving the performance. This study characterized the structural and electronic properties of a-TiO 2 thin films (~17 nm) grown on Si by atomic layer deposition (ALD). Fluctuation spectra V(k) and angular correlation functions were determined with 4-dimensional scanning transmission electron microscopy (4D-STEM), which revealed the distinctive medium-range ordering in the a-TiO 2 film. A realistic atomic model of a-TiO 2 was established guided by the medium-range ordering and the previously reported short-range ordering of a-TiO 2 film, as well as the interatomic potential. The structure was optimized by the StructOpt code using a genetic algorithm that simultaneously minimizes energy and maximizes the match to experimental short- and medium-range ordering. The StructOpt a-TiO 2 model presents improved agreements with the medium-range ordering and the k-space location of the dominant 2-fold angular correlations compared with a traditional melt-quenched model. The electronic structure of the StructOpt a-TiO 2 model was studied by ab initio calculations and compared to the crystalline phases and experimental results. Finally, this work uncovered the medium-range ordering in a-TiO 2 thin films and provided a realistic a-TiO 2 structure model for further investigation of structure–property relationships and materials design. In addition, the improved multi-objective optimization package StructOpt was provided for structure determination of complex materials guided by experiments and simulations.
ab initio Sub-Mechanism Development for Cyclopentene Oxidation
To accurately predict low-temperature oxidation behavior, chemical kinetics mechanisms must contain complete reaction networks that include detailed consumption reactions of intermediates produced directly from hydroperoxyalkyl radicals, Q̇OOH, which undergo competing unimolecular reactions and bimolecular reactions with O2. Rates of chain-branching are governed by the flux between the two competing pathways, and inherently depend on temperature, pressure, and oxygen concentration. Neglect of consumption pathways for major oxidation intermediates leads to mechanism truncation error that is ameliorated by expanding the level of detail included in sub-mechanisms and employing ab initio methods for computing rates of elementary reactions and thermochemical properties of species involved. In the present work, an ab initio-derived sub-mechanism is developed using AutoMech to model the chemical kinetics of cyclopentene, a major product of cyclopentane oxidation. The ab initio sub-mechanism builds on a detailed mechanism developed using Reaction Mechanism Generator (RMG) for the specific purpose of determining the extent to which replacing cyclopentene-specific reactions and species with quantum chemical computations reduces model inaccuracies resulting from mechanism truncation error. In an effort to minimize interference from other reactions present during the formation of cyclopentene from cyclopentyl + O2, providing a narrower experimental scope, the model is compared against speciation measurements from jet-stirred reactor (JSR) experiments on cyclopentene oxidation. The experiments utilize vacuum ultraviolet-absorption spectroscopy and mass spectrometry for isomer-resolved speciation of intermediates at 835 Torr from 700 – 950 K. [O2]-dependent experiments were also conducted from 0.057 – 2.01 · 1018 molecules cm–3 at 825 K to examine the influence of oxygen on species profiles. Model predictions using the ab initio-revised mechanism yielded significant improvements in species profiles for both the temperature- and [O2]-dependent measurements, owing in part to increased rates of HOȮ and H2O2 production, which underscores the influence of theoretical calculations of reaction rates involving species produced from Ṙ + O2 such as cyclopentene.
Accelerating Ab Initio Simulation via Nested Monte Carlo and Machine Learned Reference Potentials
As a corollary of the rapid advances in computing, ab initio simulation is playing an increasingly important role in modeling materials at the atomic scale. Two strategies are possible, ab initio Monte Carlo (AIMC) and molecular dynamics (AIMD) simulation. The former benefits from exact sampling from the correct thermodynamic distribution, while the latter is typically more efficient with its collective all-atom coordinate updates. In this study, using a relatively simple test model comprised of helium and argon, we show that AIMC can be brought up to, and even above, the performance levels of AIMD via a hybrid nested sampling/machine learning (ML) strategy. Here, ML provides an accurate classical reference potential (up to three-body explicit interactions) that can pilot long collective Monte Carlo moves that are accepted or rejected in toto à la nested Monte Carlo (NMC); this is in contrast to the single move nature of a naive implementation. Our proposed method only requires a small up front expense from evaluating the ab initio energies and forces of (100) random configurations for training. Importantly, our method does not totally rely on the trained, assuredly imperfect, interaction. We show that high performance and exact sampling at the desired level of theory can be realized even when the trained interaction has appreciable differences from the ab initio potential. Remarkably, at the highest levels of performance realized via our approach, a pair of statistically uncorrelated atomic configurations can be generated with (1) ab initio calculations.
Breaking the Million-Electron and 1 EFLOP/s Barriers: Biomolecular-Scale Ab Initio Molecular Dynamics Using MP2 Potentials
The accurate simulation of complex biochemical phenomena has historically been hampered by the computational requirements of high-fidelity molecular-modeling techniques. Quantum mechanical methods, such as ab initio wave-function (WF) theory, deliver the desired accuracy, but have impractical scaling for modeling biosystems with thousands of atoms. Combining molecular fragmentation with MP2 perturbation theory, this study presents an innovative approach that enables biomolecular-scale ab initio molecular dynamics (AIMD) simulations at WF theory level. Leveraging the resolution-of-the-identity approximation for Hartree-Fock and MP2 gradients, our approach eliminates computationally intensive four-center integrals and their gradients, while achieving near-peak performance on modern GPU architectures. The introduction of asynchronous time steps minimizes time step latency, overlapping computational phases and effectively mitigating load imbalances. Utilizing up to 9,400 nodes of Frontier and achieving 59% (1006.7 PFLOP/s) of its double-precision floating-point peak, our method enables us to break the million-electron and 1EFLOP/s barriers for AIMD simulations with quantum accuracy.
A Deep Potential model for liquid–vapor equilibrium and cavitation rates of water
Computational studies of liquid water and its phase transition into vapor have traditionally been performed using classical water models. Here, we utilize the Deep Potential methodology—a machine learning approach—to study this ubiquitous phase transition, starting from the phase diagram in the liquid–vapor coexistence regime. The machine learning model is trained on ab initio energies and forces based on the SCAN density functional, which has been previously shown to reproduce solid phases and other properties of water. Here, we compute the surface tension, saturation pressure, and enthalpy of vaporization for a range of temperatures spanning from 300 to 600 K and evaluate the Deep Potential model performance against experimental results and the semiempirical TIP4P/2005 classical model. Moreover, by employing the seeding technique, we evaluate the free energy barrier and nucleation rate at negative pressures for the isotherm of 296.4 K. Further, we find that the nucleation rates obtained from the Deep Potential model deviate from those computed for the TIP4P/2005 water model due to an underestimation in the surface tension from the Deep Potential model. From analysis of the seeding simulations, we also evaluate the Tolman length for the Deep Potential water model, which is (0.091 ± 0.008) nm at 296.4 K. Finally, we identify that water molecules display a preferential orientation in the liquid–vapor interface, in which H atoms tend to point toward the vapor phase to maximize the enthalpic gain of interfacial molecules. We find that this behavior is more pronounced for planar interfaces than for the curved interfaces in bubbles. This work represents the first application of Deep Potential models to the study of liquid–vapor coexistence and water cavitation.
Ab initio translationally invariant nucleon-nucleus optical potentials
We combine the ab initio symmetry-adapted no-core shell model (SA-NCSM) with the single-particle Green's function approach to construct optical potentials rooted in first principles. Specifically, we show that total cross sections and phase shifts for neutron elastic scattering from a 4 He target with projectile energies between 0.5 and 10 MeV closely reproduce the experiment. In addition, we discuss an important new development that resolves a long-standing issue with spurious center-of-mass motion in the Green's function formalism for many-body approaches. Furthermore, the new development opens a path for first-principle predictions of cross sections for elastic scattering of single-nucleon projectiles, nucleon capture, and deuteron breakup reactions, feasible for a broad range of open-shell spherical and deformed nuclei in the SA-NCSM approach.