Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “model discovery”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Discovery of Pyridopyrimidinones that Selectively Inhibit the H1047R PI3Kα Mutant Protein

The H1047R mutation of PIK3CA is highly prevalent in breast cancers and other solid tumors. Selectively targeting PI3Kα H1047R over PI3Kα WT is crucial due to the role that PI3Kα WT plays in normal cellular processes, including glucose homeostasis. Currently, only one PI3Kα H1047R -selective inhibitor has progressed into clinical trials, while three pan mutant (H1047R, H1047L, H1047Y, E542K, and E545K) selective PI3Kα inhibitors have also reached the clinical stage. Herein, we report the design and discovery of a series of pyridopyrimidinones that inhibit PI3Kα H1047R with high selectivity over PI3Kα WT , resulting in the discovery of compound 17. When dosed in the HCC1954 tumor model in mice, 17 provided tumor regressions and a clear pharmacodynamic response. X-ray cocrystal structures from several PI3Kα inhibitors were obtained, revealing three distinct binding modes within PI3Kα H1047R including a previously reported cryptic pocket in the C-terminus of the kinase domain wherein we observe a ligand-induced interaction with Arg1047.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Discovery of Macrocyclic Myeloid Cell Leukemia 1 (Mcl-1)Inhibitors that Demonstrate Potent Cellular Efficacy and In Vivo Activity in a Mouse Solid Tumor Xenograft Model

Abstract The B cell lymphoma 2 (Bcl-2) family of proteins are key regulators of intrinsic apoptosis. The antiapoptotic protein myeloid cell leukemia 1 (Mcl-1), which is associated with high tumor grade, poor survival, and resistance to treatment, has emerged as a promising candidate for treating hematological and solid cancers. Herein, we report the structure-guided design of small molecule macrocyclic Mcl-1 inhibitors based on the (R)-methyl-dihydropyrazinoindolone scaffold our group has previously disclosed. The macrocyclic inhibitors bind Mcl-1 with subnanomolar affinity and offer improved potency in cell culture growth inhibition assays. Inhibitor 13 achieved tumor regression in a lung cancer-derived tumor xenograft model in mice as a monotherapy. The improved potency of the macrocyclic series allowed replacement of heretofore conserved indole carboxylic acid moiety, resulting in neutral inhibitors. Amide inhibitor 25 displayed a >10-fold increase in oral bioavailability as compared to acid-containing macrocyclic or acyclic inhibitors.

Pharmacology & Pharmacy↗
DOE OSTI2026

Bayesian Optimization of Catalysis with In-Context Learning

Large language models (LLMs) can perform accurate classification with zero or few examples through in-context learning (ICL), allowing the model to observe query-relevant examples at inference time and eliminating the need for additional weight updates to generalize beyond its original training data. We extend this capability to regression with uncertainty estimation using frozen LLMs (e.g., GPT-4o, Gemini), enabling Bayesian optimization (BO) in natural language without explicit model training or feature engineering. We apply this to materials discovery by representing materials as synthesis and testing procedures for use in natural language prompts. This Bayesian, design-first approach prioritizes optimization toward target material properties before detailed characterization, in contrast to conventional experimental workflows that often emphasize characterization of suboptimal materials. On benchmarks like aqueous solubility and oxidative coupling of methane (OCM), BO-ICL matches or outperforms Gaussian processes. In live experiments on the reverse water–gas shift (RWGS) reaction, BO-ICL identifies multimetallic catalysts that approach equilibrium CO yield within 6 and 10 iterations from a pool of 3,700 and 360,000 candidates, respectively. Our method redefines materials representation and accelerates discovery, with broad applications across catalysis, materials science, and AI.

Calibration↗
DOE OSTI2025

A neural master equation framework for multiscale modeling of molecular processes: application to atomic-scale plasma processes

Plasma-surface interactions (PSI) play a crucial role in microelectronics fabrication; however, their multiscale nature and array of complex, often unknown interactions make computational modeling of PSIs extremely difficult. To this end, we propose a general neural master equation (NME) framework that uses master equations to describe the dynamics of a molecular process, wherein neural networks learned from atomistic simulations represent unknown transitions between different system states. By leveraging the physics-based structure of master equations and data-driven state transitions, the NME framework promotes generalizability and physics interpretability, and can bridge disparate length and time scales. The framework is demonstrated for multiscale modeling of Si atomic layer etching and reactive ion etching, where the learned NME-based surface kinetic models exhibit good predictive and extrapolative capabilities for predicting experimentally relevant observables as a function of process parameters. The NME-based surface kinetic models obey physical constraints, which are violated in models based on neural ordinary differential equations. The proposed NME framework for multiscale modeling of molecular processes can pave the way for the discovery of new chemistries and materials in atomic-scale plasma processes.

Chemical engineering↗
DOE OSTI2025

Solving sparse finite element problems on neuromorphic hardware

The finite element method (FEM) is one of the most important and ubiquitous numerical methods for solving partial differential equations (PDEs) on computers for scientific and engineering discovery. Applying the FEM to larger and more detailed scientific models has driven advances in high-performance computing for decades. Here we demonstrate that scalable spiking neuromorphic hardware can directly implement the FEM by constructing a spiking neural network that solves the large, sparse, linear systems of equations at the core of the FEM. We show that for the Poisson equation, a fundamental PDE in science and engineering, our neural circuit achieves meaningful levels of numerical accuracy and close to ideal scaling on modern, inherently parallel and energy-efficient neuromorphic hardware, specifically Intel’s Loihi 2 neuromorphic platform. We illustrate extensions to irregular mesh geometries in both two and three dimensions as well as other PDEs such as linear elasticity. Our spiking neural network is constructed from a recurrent network model of the brain’s motor cortex and, in contrast to black-box deep artificial neural network-based methods for PDEs, directly translates the well-understood and trusted mathematics of the FEM to a natively spiking neuromorphic algorithm.

Applied mathematics↗
DOE OSTI2021

Coordinated resource allocation to plant growth–defense tradeoffs

Summary Plant resource allocation patterns often reveal tradeoffs that favor growth (G) over defense (D), or vice versa. Ecologists most often explain G–D tradeoffs through principles of economic optimality, in which negative trait correlations are attributed to the reconciliation of fitness costs. Recently, researchers in molecular biology have developed ‘big data’ resources including multi‐omic (e.g. transcriptomic, proteomic and metabolomic) studies that describe the cellular processes controlling gene expression in model species. In this synthesis, we bridge ecological theory with discoveries in multi‐omics biology to better understand how selection has shaped the mechanisms of G–D tradeoffs. Multi‐omic studies reveal strategically coordinated patterns in resource allocation that are enabled by phytohormone crosstalk and transcriptional signal cascades. Coordinated resource allocation justifies the framework of optimality theory, while providing mechanistic insight into the feedbacks and control hubs that calibrate G–D tradeoff commitments. We use the existing literature to describe the coordinated resource allocation hypothesis (CoRAH) that accounts for balanced cellular controls during the expression of G–D tradeoffs, while sustaining stored resource pools to buffer the impacts of future stresses. The integrative mechanisms of the CoRAH unify the supply‐ and demand‐side perspectives of previous G–D tradeoff theories.

Monson, Russell K.↗
DOE OSTI2022

Machine learning enables interpretable discovery of innovative polymers for gas separation membranes

Polymer membranes perform innumerable separations with far-reaching environmental implications. Despite decades of research, design of new membrane materials remains a largely Edisonian process. To address this shortcoming, we demonstrate a generalizable, accurate machine learning (ML) implementation for the discovery of innovative polymers with ideal performance. Specifically, multitask ML models are trained on experimental data to link polymer chemistry to gas permeabilities of He, H 2 , O 2 , N 2 , CO 2 , and CH 4 . We interpret the ML models and extract valuable insights into the contributions of different chemical moieties to permeability and selectivity. We then screen over 9 million hypothetical polymers and identify thousands that lie well above current performance upper bounds, including hundreds of never-before-seen ultrapermeable polymer membranes with O 2 and CO 2 permeability greater than 10 4 and 10 5 Barrers, respectively. High-fidelity molecular dynamics simulations confirm the ML-predicted gas permeabilities of the promising candidates, which suggests that many can be translated to reality.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A cross-frontier quest to reveal the origin of the Universe [Slides]

The Standard Model is one of the most well-tested theories in Particle Physics. The particle content was completed by the discovery of the Higgs boson. However, it does not explain the complete picture. This report discusses physics beyond the Standard Model (BSM Physics).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Quantum-centric Supercomputing for Materials Science: A Perspective on Challenges and Future Directions

Computational models are an essential tool for the design, characterization, and discovery of novel materials. Hard computational tasks in materials science stretch the limits of existing high-performance supercomputing centers, consuming much of their simulation, analysis, and data resources. Quantum computing, on the other hand, is an emerging technology with the potential to accelerate many of the computational tasks needed for materials science. In order to do that, the quantum technology must interact with conventional high-performance computing in several ways: approximate results validation, identification of hard problems, and synergies in quantum-centric supercomputing. In this paper, we provide a perspective on how quantum-centric supercomputing can help address critical computational problems in materials science, the challenges to face in order to solve representative use cases, and new suggested directions.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Radioisotope Identification with List-Mode Gamma Ray Data: A rigorous assessment on the value of temporal information applied to radioisotope identification.

This work explores the potential of utilizing temporal data from gamma-ray detectors, known as list-mode data, to enhance radioisotope identification. Traditional identification methods, which rely on full gamma-ray spectrum analysis, often require long dwell times and struggle with “confuser” sources, or spectra with similarly spaced spectral peaks. We hypothesize that by leveraging the probabilistic nature of nuclear decay and the time-encoded information from decay sequences and interactions with surrounding materials, we can improve classification accuracy over static spectral analysis. This research rigorously examines the temporal content of list-mode data through exploratory data analysis via correlation discovery and information theory. We further propose a basic classification model that can utilize spectral or temporal data (or both) to determine if the incorporation of temporal information can improve radioisotope identification. The findings suggest that the temporal information present in list-mode gamma-ray data has merit and should be further investigated.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Weinberg’s Compositeness

Nearly 60 years ago, Weinberg suggested a criterion for particle “compositeness”, which has acquired a new life with the discovery of new, exotic hadrons. His idea resonates with model-based intuition. I discuss the role it plays in the context of another of Weinberg’s creations, the model-independent framework of effective field theories.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

High Entropy Alloys: Advanced Synchrotron X-Ray and Neutron Scattering Studies

Synchrotron high energy X-rays and neutrons are powerful complementary tools for structure-property relationship studies by probing materials under complex external stimuli and measuring the bulk-average materials properties and response mechanism, thanks to the high brightness and advanced instrumentations. The research of using the high energy X-ray or neutron scattering instruments at large facilities in high entropy alloys has greatly increased in alloy design, synthesis, property evaluation, performance testing, and predictive model validation, and thus accelerates the next generation structural material discoveries.

An, Ke↗
DOE OSTI2023

Quantum-centric Supercomputing for Materials Science: A Perspective on Challenges and Future Directions

Computational models are an essential tool for the design, characterization, and discovery of novel materials. Hard computational tasks in materials science stretch the limits of existing high-performance supercomputing centers, consuming much of their simulation, analysis, and data resources. Quantum computing, on the other hand, is an emerging technology with the potential to accelerate many of the computational tasks needed for materials science. In order to do that, the quantum technology must interact with conventional high-performance computing in several ways: approximate results validation, identification of hard problems, and synergies in quantum-centric supercomputing. In this paper, we provide a perspective on how quantum-centric supercomputing can help address critical computational problems in materials science, the challenges to face in order to solve representative use cases, and new suggested directions.

Alexeev, Yuri↗
DOE OSTI2020

Application and assessment of deep learning for the generation of potential NMDA receptor antagonists

Uncompetitive antagonists of the N-methyl D-aspartate receptor (NMDAR) have demonstrated therapeutic benefit in the treatment of neurological diseases such as Parkinson's and Alzheimer's, but some also cause dissociative effects that have led to the synthesis of illicit drugs. The ability to generate NMDAR antagonists in silico is therefore desirable for both new medication development and preempting and identifying new designer drugs. Recently, generative deep learning models have been applied to de novo drug design as a means to expand the amount of chemical space that can be explored for potential drug-like compounds. In this study, we assess the application of a generative model to the NMDAR to achieve two primary objectives: (i) the creation and release of a comprehensive library of experimentally validated NMDAR phencyclidine (PCP) site antagonists to assist the drug discovery community and (ii) an analysis of both the advantages conferred by applying such generative artificial intelligence models to drug design and the current limitations of the approach. We apply, and provide source code for, a variety of ligand- and structure-based assessment techniques used in standard drug discovery analyses to the deep learning-generated compounds. Overall, we present twelve candidate antagonists that are not available in existing chemical databases to provide an example of what this type of workflow can achieve, though synthesis and experimental validation of these compounds are still required.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

bnl/pub-Maffettone_2020_08

The application of the XCA package as first demonstrated in aXiv:2008.00283. ABSTRACT: The discovery of new structural and functional materials is driven by phase identification, often using X-ray diffraction (XRD). Automation has accelerated the rate of XRD measurements, greatly outpacing XRD analysis techniques that remain manual, time consuming, error prone, and impossible to scale. With the advent of autonomous robotic scientists or self-driving labs, contemporary techniques prohibit the integration of XRD. Here, we describe a computer program for the autonomous characterization of XRD data, driven by artificial intelligence (AI), for the discovery of new materials. Starting from structural databases, we train an ensemble model using a physically accurate synthetic dataset, which output probabilistic classifications --- rather than absolutes --- to overcome the overconfidence in traditional neural networks. This AI agent behaves as a companion to the researcher, improving accuracy and offering unprecedented time savings, and is demonstrated on a diverse set of organic and inorganic materials challenges. This innovation is directly applicable to inverse design approaches, robotic discovery systems, and can be immediately considered for other forms of characterization such as spectroscopy and the pair distribution function.

Maffettone, PhillipM [Brookhaven National Lab. (BN↗
DOE OSTI2021

Crystallography companion agent for high-throughput materials discovery

The discovery of new structural and functional materials is driven by phase identification, often using X-ray diffraction (XRD). Automation has accelerated the rate of XRD measurements, greatly outpacing XRD analysis techniques that remain manual, time-consuming, error-prone and impossible to scale. With the advent of autonomous robotic scientists or self-driving laboratories, contemporary techniques prohibit the integration of XRD. Here, we describe a computer program for the autonomous characterization of XRD data, driven by artificial intelligence (AI), for the discovery of new materials. Starting from structural databases, we train an ensemble model using a physically accurate synthetic dataset, which outputs probabilistic classifications—rather than absolutes—to overcome the overconfidence in traditional neural networks. This AI agent behaves as a companion to the researcher, improving accuracy and offering substantial time savings. It is demonstrated on a diverse set of organic and inorganic materials characterization challenges. This method is directly applicable to inverse design approaches and robotic discovery systems, and can be immediately considered for other forms of characterization such as spectroscopy and the pair distribution function.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Advances in relaxation and memory effects of magnetic nanoparticles for biomedical applications

Functionalized magnetic nanoparticles are pivotal in magnetic resonance imaging, computed tomography, controlled drug delivery, and hyperthermia treatments due to their exceptional magnetic relaxation and functional properties. The magnetic core composition and structure significantly affects the complex magnetic properties of these nanoparticles necessitating a thorough examination of magnetism fundamentals related to these systems. One important aspect is the ability of magnetic nanoparticles to retain previous magnetic state configurations known as memory effect, primarily governed by domain structure and magnetic anisotropy. Despite its relevance to advanced applications, comprehensive studies on magnetic relaxation and memory effects remain limited. Here, the present review aims to bridge this gap by investigating relaxation mechanisms, synthesis strategies, and applications, fostering further innovation. It investigates the memory effects and their dependence on particle composition and morphology along with key synthesis techniques for large-scale production in industrial adoption. Structured into focused sections on magnetic properties and their influence on biomedical and technological applications, this review provides essential insights into memory effects, magneto-relaxation mechanisms, influencing factors, and both experimental and theoretical methodologies. It also delves into computational modelling and AI-driven design, which are revolutionizing the prediction, discovery, and optimization of materials with tailored properties.

36 MATERIALS SCIENCE↗