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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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At least 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

AI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no significant change in detection

Protein-ligand docking is a computational method for identifying drug leads. The method is capable of narrowing a vast library of compounds down to a tractable size for downstream simulation or experimental testing and is widely used in drug discovery. While there has been progress in accelerating scoring of compounds with artificial intelligence, few works have bridged these successes back to the virtual screening community in terms of utility and forward-looking development. We demonstrate the power of high-speed ML models by scoring 1 billion molecules in under a day (50 k predictions per GPU seconds). We showcase a workflow for docking utilizing surrogate AI-based models as a pre-filter to a standard docking workflow. Our workflow is ten times faster at screening a library of compounds than the standard technique, with an error rate less than 0.01% of detecting the underlying best scoring 0.1% of compounds. Our analysis of the speedup explains that another order of magnitude speedup must come from model accuracy rather than computing speed. In order to drive another order of magnitude of acceleration, we share a benchmark dataset consisting of 200 million 3D complex structures and 2D structure scores across a consistent set of 13 million “in-stock” molecules over 15 receptors, or binding sites, across the SARS-CoV-2 proteome. We believe this is strong evidence for the community to begin focusing on improving the accuracy of surrogate models to improve the ability to screen massive compound libraries 100 × or even 1000 × faster than current techniques and reduce missing top hits. The technique outlined aims to be a fast drop-in replacement for docking for screening billion-scale molecular libraries.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Enabling reactive microscopy with MicroMator

Microscopy image analysis has recently made enormous progress both in terms of accuracy and speed thanks to machine learning methods and improved computational resources. This greatly facilitates the online adaptation of microscopy experimental plans using real-time information of the observed systems and their environments. Applications in which reactiveness is needed are multifarious. Here we report MicroMator, an open and flexible software for defining and driving reactive microscopy experiments. It provides a Python software environment and an extensible set of modules that greatly facilitate the definition of events with triggers and effects interacting with the experiment. We provide a pedagogic example performing dynamic adaptation of fluorescence illumination on bacteria, and demonstrate MicroMator’s potential via two challenging case studies in yeast to single-cell control and single-cell recombination, both requiring real-time tracking and light targeting at the single-cell level.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica

Abstract Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli , use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica . A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide’s ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A 2D/3D Heterostructure Perovskite Solar Cell with a Phase‐Pure and Pristine 2D Layer

Abstract Interface engineering plays a critical role in advancing the performance of perovskite solar cells. As such, 2D/3D perovskite heterostructures are of particular interest due to their optoelectrical properties and their further potential improvements. However, for conventional solution‐processed 2D perovskites grown on an underlying 3D perovskite, the reaction stoichiometry is normally unbalanced with excess precursors. Moreover, the formed 2D perovskite is impure, leading to unfavorable energy band alignment at the interface. Here a simple method is presented that solves both issues simultaneously. The 2D formation reaction is taken first to completion, fully consuming excess PbI 2 . Then, isopropanol is utilized to remove excess organic ligands, control the 2D perovskite thickness, and obtain a phase‐pure, n = 2, 2D perovskite. The outcome is a pristine (without residual 2D precursors) and phase‐pure 2D perovskite heterostructure with improved surface passivation and charge carrier extraction compared to the conventional solution process. PSCs incorporating this treatment demonstrate a notable improvement in both stability and power conversion efficiency, with negligible hysteresis, compared to the conventional process.

14 SOLAR ENERGY↗
DOE OSTI2026

FLAG review 2024

We review lattice results related to pion, kaon, 𝐷-meson, 𝐵-meson, and nucleon physics with the aim of making them easily accessible to the nuclear and particle physics communities. More specifically, we report on the determination of the light-quark masses, the form factor 𝑓+⁡(0) arising in the semileptonic 𝐾 → 𝜋 transition at zero momentum transfer, as well as the decay-constant ratio 𝑓 𝐾 ⁡/𝑓 𝜋 and its consequences for the Cabibbo–Kobayashi–Maskawa (CKM) matrix elements 𝑉 𝑢⁢𝑠 and 𝑉 𝑢⁢𝑑 . We review the determination of the 𝐵 𝐾 parameter of neutral kaon mixing as well as the additional four 𝐵 parameters that arise in theories of physics beyond the Standard Model. For the heavy-quark sector, we provide results for 𝑚 𝑐 and 𝑚 𝑏 as well as those for the decay constants, form factors, and mixing parameters of charmed and bottom mesons and baryons. These are the heavy-quark quantities most relevant for the determination of CKM matrix elements and the global CKM unitarity-triangle fit. We review the status of lattice determinations of the strong coupling constant 𝛼 𝑠 . We review the determinations of nucleon charges from the matrix elements of both isovector and flavor-diagonal axial, scalar and tensor local quark bilinears, and momentum fraction, helicity moment and the transversity moment from one-link quark bilinears. We also review determinations of scale-setting quantities. Finally, in this review we have added a new section on the general definition of the low-energy limit of the Standard Model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Decoy selection for protein structure prediction via extreme gradient boosting and ranking

Background: Identifying one or more biologically-active/native decoys from millions of non-native decoys is one of the major challenges in computational structural biology. The extreme lack of balance in positive and negative samples (native and non-native decoys) in a decoy set makes the problem even more complicated. Consensus methods show varied success in handling the challenge of decoy selection despite some issues associated with clustering large decoy sets and decoy sets that do not show much structural similarity. Recent investigations into energy landscape-based decoy selection approaches show promises. However, lack of generalization over varied test cases remains a bottleneck for these methods. Results: We propose a novel decoy selection method, ML-Select, a machine learning framework that exploits the energy landscape associated with the structure space probed through a template-free decoy generation. The proposed method outperforms both clustering and energy ranking-based methods, all the while consistently offering better performance on varied test-cases. Moreover, ML-Select shows promising results even for the decoy sets consisting of mostly low-quality decoys. Conclusions: ML-Select is a useful method for decoy selection. This work suggests further research in finding more effective ways to adopt machine learning frameworks in achieving robust performance for decoy selection in template-free protein structure prediction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Deep reinforcement learning for predicting kinetic pathways to surface reconstruction in a ternary alloy

Abstract The majority of computational catalyst design focuses on the screening of material components and alloy composition to optimize selectivity and activity for a given reaction. However, predicting the metastability of the alloy catalyst surface at realistic operating conditions requires an extensive sampling of possible surface reconstructions and their associated kinetic pathways. We present CatGym, a deep reinforcement learning (DRL) environment for predicting the thermal surface reconstruction pathways and their associated kinetic barriers in crystalline solids under reaction conditions. The DRL agent iteratively changes the positions of atoms in the near-surface region to generate kinetic pathways to accessible local minima involving changes in the surface compositions. We showcase our agent by predicting the surface reconstruction pathways of a ternary Ni 3 Pd 3 Au 2 (111) alloy catalyst. Our results show that the DRL agent can not only explore more diverse surface compositions than the conventional minima hopping method, but also generate the kinetic surface reconstruction pathways. We further demonstrate that the kinetic pathway to a global minimum energy surface composition and its associated transition state predicted by our agent is in good agreement with the minimum energy path predicted by nudged elastic band calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A machine-learning inverse model framework for rapid forecasting and history matching in unconventional reservoirs

Model-based optimization for real-time forecasting in unconventional reser-voirs requires novel methods and work?ows since the strategies and work?ows used in conventional reservoirs are either inapplicable, or prohibitively expen-sive and time-consuming. Insu?cient site data and computational expense of high-?delity simulations mean that work?ows with high-?delity simulations are not ideal for usage in comprehensive uncertainty quanti?cation stud-ies that require 1000s of forward model runs. We present an alternative, novel work?ow for unconventional reservoirs, based on the interplay between reduced-order models and machine-learning. Our physics-informed machine-learning (PIML) work?ow addresses the challenges to real-time reservoir management in uncoventionals, namely lack of data (the time-frame for which the wells have been producing), and computational expense of high-?delity modeling. We use the machine-learning paradigm of transfer-learning to bind together fast but less accurate reduced-order models with slow, but accurate high-?delity models and circumvent the di?culties inherent in the current state-of-the-art for unconventionals. Such a PIML work?ow, grounded in physics, is a viable candidate for real-time history matching and production forecasting in a fractured shale gas reservoir. The signi?cance of our approach is that while it is developed for a particu-lar well and site in the Marcelus Shale gas reservoir of the Appalachian basin (MSEEL), it is not wedded to it. We expect the same work?ow can be ap-plied to other shale formations (e.g., Woodford, Barnett, Utica, EagleFord) should site-data become available, using the same set of machine-learning techniques from transfer learning. Some ?ne-tuning (or minimal retraining of the neural networks) will be required to transfer knowledge across shale gas sites/formations but it is a clearly superior alternative to developing a new machine-learning model altogether when considering a di?erent site.

Srinivasan, Shriram↗
DOE OSTI2025

The design space of E(3)-equivariant atom-centred interatomic potentials

Abstract Molecular dynamics simulation is an important tool in computational materials science and chemistry, and in the past decade it has been revolutionized by machine learning. This rapid progress in machine learning interatomic potentials has produced a number of new architectures in just the past few years. Particularly notable among these are the atomic cluster expansion, which unified many of the earlier ideas around atom-density-based descriptors, and Neural Equivariant Interatomic Potentials (NequIP), a message-passing neural network with equivariant features that exhibited state-of-the-art accuracy at the time. Here we construct a mathematical framework that unifies these models: atomic cluster expansion is extended and recast as one layer of a multi-layer architecture, while the linearized version of NequIP is understood as a particular sparsification of a much larger polynomial model. Our framework also provides a practical tool for systematically probing different choices in this unified design space. An ablation study of NequIP, via a set of experiments looking at in- and out-of-domain accuracy and smooth extrapolation very far from the training data, sheds some light on which design choices are critical to achieving high accuracy. A much-simplified version of NequIP, which we call BOTnet (for body-ordered tensor network), has an interpretable architecture and maintains its accuracy on benchmark datasets.

Computer Science↗
DOE OSTI2025

The hierarchical growth of bright central galaxies and intracluster light as traced by the magnitude gap

Using a sample of 2800 galaxy clusters identified in the Dark Energy Survey across the redshift range 0.20 < z < 0.60, we characterize the hierarchical assembly of bright central galaxies (BCGs) and the surrounding intracluster light (ICL). To quantify hierarchical formation we use the stellar mass–halo mass (SMHM) relation, comparing the halo mass, estimated via the mass–richness relation, to the stellar mass within the BCG + ICL system. Moreover, we incorporate the magnitude gap (M14), the difference in brightness between the BCG (measured within 30 kpc) and fourth brightest cluster member galaxy within 0.5 $R_{200,c}$, as a third parameter in this linear relation. The inclusion of M14, which traces BCG hierarchical growth, increases the slope and decreases the intrinsic scatter, highlighting that it is a latent variable within the BCG + ICL SMHM relation. Moreover, the correlation with M14 decreases at large radii. However, the stellar light within the BCG + ICL transition region (30 –80 kpc) most strongly correlates with halo mass and has a statistically significant correlation with M14. Since the transition region and M14 are independent measurements, the transition region may grow due to the BCG’s hierarchical formation. Additionally, as M14 and ICL result from hierarchical growth, we use a stacked sample and find that clusters with large M14 values are characterized by larger ICL and BCG + ICL fractions, which illustrates that the merger processes that build the BCG stellar mass also grow the ICL. Furthermore, this may suggest that M14 combined with the ICL fraction can identify dynamically relaxed clusters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Cusps enable line attractors for neural computation

Here, line attractors in neuronal networks have been suggested to be the basis of many brain functions, such as working memory, oculomotor control, head movement, locomotion, and sensory processing. In this paper, we make the connection between line attractors and pulse gating in feed-forward neuronal networks. In this context, because of their neutral stability along a one-dimensional manifold, line attractors are associated with a time-translational invariance that allows graded information to be propagated from one neuronal population to the next. To understand how pulse-gating manifests itself in a high-dimensional, nonlinear, feedforward integrate-and-fire network, we use a Fokker-Planck approach to analyze system dynamics. We make a connection between pulse-gated propagation in the Fokker-Planck and population-averaged mean-field (firing rate) models, and then identify an approximate line attractor in state space as the essential structure underlying graded information propagation. An analysis of the line attractor shows that it consists of three fixed points: a central saddle with an unstable manifold along the line and stable manifolds orthogonal to the line, which is surrounded on either side by stable fixed points. Along the manifold defined by the fixed points, slow dynamics give rise to a ghost. We show that this line attractor arises at a cusp catastrophe, where a fold bifurcation develops as a function of synaptic noise; and that the ghost dynamics near the fold of the cusp underly the robustness of the line attractor. Understanding the dynamical aspects of this cusp catastrophe allows us to show how line attractors can persist in biologically realistic neuronal networks and how the interplay of pulse gating, synaptic coupling, and neuronal stochasticity can be used to enable attracting one-dimensional manifolds and, thus, dynamically control the processing of graded information.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Growing field of materials informatics: databases and artificial intelligence

The paradigm of molecular discovery in the chemical and pharmaceutical industry has followed a repetitive succession of screening and synthesis, involving the analysis of individual molecules that were both natural and produced. This ability to generate and screen libraries of compounds has found an echo in solid-state physics with the demand to explore and produce new materials for testing. In response to this demand, a golden age of materials discovery is being developed, with progress on important areas of both basic science and device applications. The confluence of theoretical and simulation methods, together with the availability of computation resources, has established the “materials genome” approach that is used by a growing number of research groups around the world with the goal of innovating on materials through systematic discovery. Here, an overview of this group of methodologies in tackling the ever-increasing complexity of computational materials science simulations is provided. Computational simulation is highlighted as a major component of rational design and synthesis of new materials with targeted properties, describing progress on databases and large data treatment. Tools for new materials discovery, including progress on the deployment of new data repositories, the implementation of high-throughput simulation approaches, and the development of artificial intelligence algorithms, are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2024

SOMA: Observability, monitoring, and in situ analytics for exascale applications

With the rise of exascale systems and large, data-centric workflows, the need to observe and analyze high performance computing (HPC) applications during their execution is becoming increasingly important. HPC applications are typically not designed with online monitoring in mind, therefore, the observability challenge lies in being able to access and analyze interesting events with low overhead while seamlessly integrating such capabilities into existing and new applications. We explore how our service-based observation, monitoring, and analytics (SOMA) approach to collecting and aggregating both application-specific diagnostic data and performance data addresses these needs. Furthermore, we present our SOMA framework and demonstrate its viability with LULESH, a hydrodynamics proxy application. Then we focus on Astaroth, a multi-GPU library for stencil computations, highlighting the integration of the TAU and APEX performance tools and SOMA for application and performance data monitoring.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Property Prediction of Organic Donor Molecules for Photovoltaic Applications Using Extremely Randomized Trees

Organic solar cells are an inexpensive, flexible alternative to traditional silicon-based solar cells but disadvantaged by low power conversion efficiency due to empirical design and complex manufacturing processes. This process can be accelerated by generating a comprehensive set of potential candidates. However, this would require a laborious trial and error method of modeling all possible polymer configurations. A machine learning model has the potential to accelerate the process of screening potential donor candidates by associating structural features of the compound using molecular fingerprints with their highest occupied molecular orbital energies. In this paper, extremely randomized tree learning models are employed for the prediction of HOMO values for donor compounds, and a web application is developed. Finally, the proposed models outperform neural networks trained on molecular fingerprints as well as SMILES, as well as other state-of-the-art architectures such as Chemception and Molecular Graph Convolution on two datasets of varying sizes.

42 ENGINEERING↗
DOE OSTI2017

MIRAGE: A Framework for Data-Driven Collaborative High-Resolution Simulation

Information about how human populations shift in response to various stimuli is limited because no single model is capable of addressing these stimuli simultaneously, and integration of the best existing models has been challenging because of the vast disparity among constituent model purposes, architectures, scales, and execution environments. To demonstrate a potential model coupling for approaching this problem, three major model components are integrated into a fully coupled system that executes a worldwide infection-infected routine where a human population requires a food source for sustenance and an infected population can spread an infection when it is in contact with the remaining healthy population. To enable high-resolution data-driven model federation and an ability to capture dynamics and behaviors of billions of humans, a high-performance computing agent-based framework has been created and is demonstrated in this chapter.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

PDE-constrained high-order mesh optimization

Here, we present a novel framework for PDE-constrained r-adaptivity of high-order meshes. The proposed method formulates mesh movement as an optimization problem, with an objective function defined as a convex combination of a mesh quality metric and a measure of the accuracy of the PDE solution obtained via finite element discretization. The proposed formulation achieves optimized, well-defined high-order meshes by integrating mesh quality control, PDE solution accuracy, and robust gradient regularization. We adopt the Target-Matrix Optimization Paradigm to control geometric properties across the mesh, independent of the PDE of interest. To incorporate the accuracy of the PDE solution, we introduce error measures that control the finite element discretization error. The implicit dependence of these error measures on the mesh nodal positions is accurately captured by adjoint sensitivity analysis. Additionally, a convolution-based gradient regularization strategy is used to ensure stable and effective adaptation of high-order meshes. We demonstrate that the proposed framework can improve mesh quality and reduce the error by up to 10 times for the solution of Poisson and linear elasto-static problems. The approach is general with respect to the dimensionality, the order of the mesh, the types of mesh elements, and can be applied to any PDE that admits well-defined adjoint operators.

Computer science↗
DOE OSTI2016

Present-day and future Antarctic ice sheet climate and surface mass balance in the Community Earth System Model

Here, we present climate and surface mass balance (SMB) of the Antarctic ice sheet (AIS) as simulated by the global, coupled ocean–atmosphere–land Community Earth System Model (CESM) with a horizontal resolution of ~1° in the past, present and future (1850–2100). CESM correctly simulates present-day Antarctic sea ice extent, large-scale atmospheric circulation and near-surface climate, but fails to simulate the recent expansion of Antarctic sea ice. The present-day Antarctic ice sheet SMB equals 2280 ± 131Gtyear –1 , which concurs with existing independent estimates of AIS SMB. When forced by two CMIP5 climate change scenarios (high mitigation scenario RCP2.6 and high-emission scenario RCP8.5), CESM projects an increase of Antarctic ice sheet SMB of about 70 Gtyear –1 per degree warming. This increase is driven by enhanced snowfall, which is partially counteracted by more surface melt and runoff along the ice sheet’s edges. This intensifying hydrological cycle is predominantly driven by atmospheric warming, which increases (1) the moisture-carrying capacity of the atmosphere, (2) oceanic source region evaporation, and (3) summer AIS cloud liquid water content.

54 ENVIRONMENTAL SCIENCES↗