Using Machine Learning to Understand the Causes of Quantum Decoherence in Solution-Phase Bond-Breaking Reactions
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Results for “Materials science, Computer science, Physics - Atomic and molecular physics”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Roadmap on electronic structure codes in the exascale era
Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing.
36 MATERIALS SCIENCE↗
Determining best practices for using genetic algorithms in molecular discovery
Genetic algorithms (GAs) are a powerful tool to search large chemical spaces for inverse molecular design. However, GAs have multiple hyperparameters that have not been thoroughly investigated for chemical space searches. In this tutorial, we examine the general effects of a number of hyperparameters, such as population size, elitism rate, selection method, mutation rate, and convergence criteria, on key GA performance metrics. Here, we show that using a self-termination method with a minimum Spearman’s rank correlation coefficient of 0.8 between generations maintained for 50 consecutive generations along with a population size of 32, a 50% elitism rate, three-way tournament selection, and a 40% mutation rate provides the best balance of finding the overall champion, maintaining good coverage of elite targets, and improving relative speedup for general use in molecular design GAs.
36 MATERIALS SCIENCE↗
Modern chemical graph theory
Abstract Graph theory has a long history in chemistry. Yet as the breadth and variety of chemical data is rapidly changing, so too do graph encoding methods and analyses that yield qualitative and quantitative insights. Using illustrative cases within a basic mathematical framework, we showcase modern chemical graph theory's utility in Chemists' analysis and model development toolkit. The encoding of both experimental and simulation data is discussed at various levels of granularity of information. This is followed by a discussion of the two major classes of graph theoretical analyses: identifying connectivity patterns and partitioning methods. Measures, metrics, descriptors, and topological indices are then introduced with an emphasis upon enhancing interpretability and incorporation into physical models. Challenging data cases are described that include strategies for studying time dependence. Throughout, we incorporate recent advancements in computer science and applied mathematics that are propelling chemical graph theory into new domains of chemical study. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Structure and Mechanism > Computational Materials Science Structure and Mechanism > Molecular Structures
Leite, Leonardo S. G.↗
Studying light–matter interactions and energy transfer at the nanoscale with a trapped–ion quantum computer
A grand challenge in materials sciences is to control energy transduction, transfer and dissipation at the nanoscale. Meeting this challenge requires progress in nanoscale fabrication and synthesis, but equally importantly, also progress in our understanding of how nanoscale structure influences these phenomena. Although detailed quantum mechanical models exist that capture the structure and physics of materials and molecular species, solving these models to calculate the relevant emergent phenomena, which often occur over vastly different time and energy scales, has so far proven difficult. In this project, we studied how to model energy transfer and light-matter interactions using trapped-ion quantum computers. Our studies focused on emulation of critical processes in natural systems, such as the well-known photosynthetic pigment-protein complexes responsible for capturing and transducing light to electrons. In addition, we implemented proof-of-principle experiments demonstrating that such calculations are possible on trapped-ion quantum computing hardware. These studies and experiments pave the way to investigate energy transport and transduction in a detail not accessible with classical computing technologies. We expect that our studies will allow to extract important guiding principles on how to improve the efficiency of nano-scale light-harvesting and transduction devices.
36 MATERIALS SCIENCE↗
Plasma Surface Interactions: Predicting the Performance and Impact of Dynamic PFC Surfaces
The objective of this project is to develop, and integrate, high-performance simulation tools capable of predicting plasma-facing component (PFC) operating lifetime and the impact of the evolving surface morphology of tungsten-based PFCs on plasma contamination, including the dynamic recycling of fuel species and tritium retention, in future magnetic fusion devices. Establishing a fundamental physical understanding and developing predictive capabilities of plasma-surface interactions (PSI) requires simultaneously addressing complex and diverse physics occurring over a wide range of length (Angstroms to meters) and time (femtoseconds to years) scales, as well as integrating extensive physical processes across the plasma–surface interface. This requires development of not only detailed physics models and computational strategies at each scale, but also algorithms and methods to couple them effectively in a way that can be robustly validated. Deploying these tools requires the continued development and coupling of leadership-scale computational codes to describe the boundary plasma and the evolving PFC surface, as well as a host of simulations that bridge disparate scales to address complex physical and computational issues at the plasma–surface interface in multi-component materials systems for magnetic fusion energy development beyond ITER.
36 MATERIALS SCIENCE↗
Development of a Reactive Force Field for Simulating Photoinitiated Acrylate Polymerization
Light-driven and photo-curable polymer based additive manufacturing (AM) has enormous potential due to its excellent resolution and precision. Acrylated radical chain-growth polymerized resins are widely used in photopolymer AM due to their fast kinetics, and often serve as a departure point for developing other resin materials for photopolymer-based AM technologies. For successful control of the photopolymer resins, the molecular basis of the acrylate free-radical polymerization has to be understood in detail. We present an optimized reactive force field (ReaxFF) for molecular dynamics (MD) simulations of acrylate polymer resins that captures radical polymerization thermodynamics and kinetics. The force field is trained against an extensive training set including density functional theory (DFT) calculations of reaction pathways along the radical polymerization from methyl acrylate to methyl butyrate, bond dissociation energies, and structures and partial charges of several molecules and radicals. We also found that it was critical to train the force field against an incorrect, nonphysical reaction pathway observed in simulations that used parameters not optimized for acrylate polymerization. As a result, the parameterization process utilizes a parallelized search algorithm, and the resulting model can describe polymer resin formation, crosslinking density, conversion rate, and residual monomers of the complex acrylate mixtures.
36 MATERIALS SCIENCE↗
Particle-based simulations of electrophoretic deposition with adaptive physics models
Not Available
36 MATERIALS SCIENCE↗
Uncertainty quantification for molecular property predictions with graph neural architecture search
Graph Neural Networks (GNNs) have emerged as a prominent class of data-driven methods for molecular property prediction. However, a key limitation of typical GNN models is their inability to quantify uncertainties in the predictions. This capability is crucial for ensuring the trustworthy use and deployment of models in downstream tasks. To that end, we introduce AutoGNNUQ, an automated uncertainty quantification (UQ) approach for molecular property prediction. AutoGNNUQ leverages architecture search to generate an ensemble of high-performing GNNs, enabling the estimation of predictive uncertainties. Our approach employs variance decomposition to separate data (aleatoric) and model (epistemic) uncertainties, providing valuable insights for reducing them. In our computational experiments, we demonstrate that AutoGNNUQ outperforms existing UQ methods in terms of both prediction accuracy and UQ performance on multiple benchmark datasets, and generalizes well to out-of-distribution datasets. Additionally, we utilize t-SNE visualization to explore correlations between molecular features and uncertainty, offering insight for dataset improvement. AutoGNNUQ has broad applicability in domains such as drug discovery and materials science, where accurate uncertainty quantification is crucial for decision-making.
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Symposium: Quantum Theory, Quantum Materials, Quantum Computing (Final Report, DE-SC0022551)
Quantum mechanics is fundamental to understanding, predicting, and controlling many physical processes in a vast range of scientific and technological areas. In molecules and materials, the quantum mechanics of Coulombic many-body systems determines far more than the ground state and bulk properties. Quantum mechanics governs magnetism, electron and spin transport, chemical reactions and catalysis, superconductivity, photosynthesis, etc. Each plays a vital role in modern society. As digital technologies push both temporal and length-scale limits, fundamental quantum principles become the current focus for a new class of technologies: quantum computing, quantum sensing, quantum encryption, etc. This oncoming quantum information sciences wave is manifest recently in frontier foci of all six Department of Energy Office of Science programs. The Sanibel Symposium offers a proven, influential platform for facilitating and advancing cross-fertilization among theoretical and computational chemists and physicists, computer scientists, and materials engineers. The Symposia have a long, successful record of driving progress on theory and computation of materials, nanostructures, and their molecular constituents. The Symposia thus are well-suited for advancing the quantum information science thrust in the Office of Basic Energy Sciences (BES). With that QIS thrust as the focus, we propose five sessions of the 61st Sanibel Symposium on the theme Quantum Theory, Quantum Materials, Quantum Computing. From a longer perspective, this thematic program for 2022 is the second year of a five year plan of program segments addressed at challenges in quantum information sciences and quantum materials. The rest of the Symposium program will be of considerable relevance, with, for example, sessions on quantum molecular and material dynamics, and new directions in coupled cluster theory. New ideas for methods and applications can be expected to emerge from the stimulus of the formal presentations and informal discussions. The proposed award is targeted at students, post-docs, and junior scientists. Conscious effort, characteristic of the Sanibel Symposia, to stimulate the participation of women and under-represented minorities will continue.
36 MATERIALS SCIENCE↗
A Transferable Force Field for Simulating Adsorption in Metal–Organic Frameworks with Open Metal Sites Based on the 12–6–4 Lennard-Jones Potential
Metal−organic frameworks (MOFs) that contain coordinatively unsaturated open metal sites (OMSs) provide strong host− guest interactions, making them promising sorbents for low-concentration gas adsorption applications such as direct air capture and atmospheric water harvesting. However, accurately modeling host−guest interactions involving OMSs remains challenging for classical force fields (FFs) based on the 12−6 Lennard−Jones (LJ) potential, as the polarization effect of the guest molecule induced by the positively charged OMS is not considered. Here, we introduce an FF based on the 12−6−4 LJ potential, which incorporates charge−induced dipole interactions and is parametrized against a diverse set of host−guest potential energy surfaces (PESs) obtained from density functional theory (DFT). The resulting FF, trained on a generic trimetallic cluster, performs well in both host−guest binding energetics and gas adsorption isotherms across different OMS-containing MOFs, including MOF-74 series and Cu-BTC. These results highlight the excellent transferability of our approach and its potential to enhance the accuracy and robustness of high-throughput MOF discovery workflows, particularly for gas adsorption and separation in large and diverse MOF databases.
36 MATERIALS SCIENCE↗
One thousand soils for molecular understanding of belowground carbon cycling
While significant progress has been made in understanding global carbon (C) cycling, the mechanisms regulating belowground C fluxes and storage are still uncertain. New molecular technologies have the power to elucidate these processes, yet we have no widespread standardized implementation of molecular techniques. To address this gap, we introduce the Molecular Observation Network (MONet), a decadal vision from the Environmental Molecular Sciences Laboratory (EMSL), to develop a national network for understanding the molecular composition, physical structure, and hydraulic and biological properties of soil and water. These data are essential for advancing the next generation of multiscale Earth systems models. In this paper, we discuss the 1000 Soils Pilot for MONet, including a description of standardized sampling materials and protocols and a use case to highlight the utility of molecular-level and microstructural measurements for assessing the impacts of wildfire on soil. While the 1000 Soils Pilot generated a plethora of data, we focus on assessments of soil organic matter (SOM) chemistry via Fourier-transform ion cyclotron resonance-mass spectrometry and microstructural properties via X-ray computed tomography to highlight the effects of recent fire history in forested ecosystems on belowground C cycling. We observed decreases in soil respiration, microbial biomass, and potential enzyme activity in soils with high frequency burns. Additionally, the nominal oxidation state of carbon in SOM increased with burn frequency in surface soils. This results in a quantifiable shift in the molecular signature of SOM and shows that wildfire may result in oxidation of SOM and structural changes to soil pore networks that persist into deeper soils.
54 ENVIRONMENTAL SCIENCES↗
Machine Learning Framework for Modeling Exciton-Polaritons in Molecular Materials
Explore the source record for details and available documents.
Material Science↗
Ligand Controls Excited Charge Carrier Dynamics in Metal-Rich CdSe Quantum Dots: Computational Insights
Small metal-rich semiconducting quantum dots (QDs) are promising for solid-state lighting and single-photon emission due to their highly tunable yet narrow emission line widths. Nonetheless, the anionic ligands commonly employed to passivate these QDs exert a substantial influence on the optoelectronic characteristics, primarily owing to strong electron–phonon interactions. In this work, we combine time-domain density functional theory and nonadiabatic molecular dynamics to investigate the excited charge carrier dynamics of Cd 28 Se 17 X 22 QDs (X = HCOO – , OH – , Cl – , and SH – ) at ambient conditions. These chemically distinct but regularly used molecular groups influence the dynamic surface-ligand interfacial interactions in Cd-rich QDs, drastically modifying their vibrational characteristics. The strong electron–phonon coupling leads to substantial transient variations at the band edge states. The strength of these interactions closely depends on the physicochemical characteristics of passivating ligands. Consequently, the ligands largely control the nonradiative recombination rates and emission characteristics in these QDs. Our simulations indicate that Cd 28 Se 17 (OH) 22 has the fastest nonradiative recombination rate due to the strongest electron–phonon interactions. Conversely, QDs passivated with thiolate or chloride exhibit considerably longer carrier lifetimes and suppressed nonradiative processes. The ligand-controlled electron–phonon interactions further give rise to the broadest and narrowest intrinsic optical line widths for OH and Cl-passivated single QDs, respectively. Finally, obtained computational insights lay the groundwork for designing appropriate passivating ligands on metal-rich QDs, making them suitable for a wide range of applications, from blue LEDs to quantum emitters.
36 MATERIALS SCIENCE↗
Creating and Interfacing Designer Chemical Qubits (Final Technical Report)
The Final Technical Report describes a multi‑institution effort to develop programmable molecular qubits as precision quantum sensors for probing quantum materials. The team created chemically tunable qubits with optical addressability and practical coherence, integrated them into thin films and frameworks while preserving functionality, and established new magnetic and electric sensing methods suited to two‑dimensional magnets, ferroelectrics, and multiferroics. They also built computational models and spectroscopic tools that connect molecular design to material behavior, enabling access to quantum phenomena that previously could not be measured. The project produced more than 40 publications and trained a large cohort of graduate students and postdocs, strengthening the workforce and infrastructure needed for DOE's quantum information science mission.
2D Quantum Materials↗
Molecular properties controlling chirality transfer to halide perovskite: computational insights
Computationally investigate chirality transfer effect from chiral ligands bound to the surface of a lead-halide perovskite nanomaterial. By changing the molecular polarity of the chiral molecules, the chirality of the system can be tuned.
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Deep kernel methods learn better: from cards to process optimization
Abstract The ability of deep learning methods to perform classification and regression tasks relies heavily on their capacity to uncover manifolds in high-dimensional data spaces and project them into low-dimensional representation spaces. In this study, we investigate the structure and character of the manifolds generated by classical variational autoencoder (VAE) approaches and deep kernel learning (DKL). In the former case, the structure of the latent space is determined by the properties of the input data alone, while in the latter, the latent manifold forms as a result of an active learning process that balances the data distribution and target functionalities. We show that DKL with active learning can produce a more compact and smooth latent space which is more conducive to optimization compared to previously reported methods, such as the VAE. We demonstrate this behavior using a simple cards dataset and extend it to the optimization of domain-generated trajectories in physical systems. Our findings suggest that latent manifolds constructed through active learning have a more beneficial structure for optimization problems, especially in feature-rich target-poor scenarios that are common in domain sciences, such as materials synthesis, energy storage, and molecular discovery. The Jupyter Notebooks that encapsulate the complete analysis accompany the article.
97 MATHEMATICS AND COMPUTING↗
Transferring a Molecular Foundation Model for Polymer Property Predictions
Transformer-based large language models have remarkable potential to accelerate design optimization for applications such as drug development and material discovery. Self-supervised pretraining of transformer models requires large-scale data sets, which are often sparsely populated in topical areas such as polymer science. Further, state-of-the-art approaches for polymers conduct data augmentation to generate additional samples but unavoidably incur extra computational costs. In contrast, large-scale open-source data sets are available for small molecules and provide a potential solution to data scarcity through transfer learning. In this work, we show that using transformers pretrained on small molecules and fine-tuned on polymer properties achieves comparable accuracy to those trained on augmented polymer data sets for a series of benchmark prediction tasks.
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