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At least 1,027 records · Page 57

Structure-Aware Unsupervised, Transformational Machine Learning for Drug Discovery (DTRA Basic Research Final Report)

The major goal of this project is to develop machine learning (ML) methods to enable improved predictive power on real drug discovery for novel targets. More specifically, we planned to demonstrate the capability and effectiveness of ML tools utilizing unlabeled large-volume protein-ligand datasets. We investigated multiple pre-training approaches for 3D protein-ligand structure-based foundation models, without relying on experimental binding data. We also addressed scenarios in which crystal structures are unavailable or binding data are limited. We also planned to develop a complete pipeline to screen novel compounds as well as to demonstrate the capability and effectiveness of the developed methods by testing on a realistic drug discovery task such as SARS-CoV-2. While the major goals and milestones remain consistent with the original proposal, certain technical details have been adjusted, based on the experimental results and related outcomes.

97 MATHEMATICS AND COMPUTING↗

Application of Machine Learning and Data Augmentation Algorithms in the Discovery of Metal Hydrides for Hydrogen Storage

The development of efficient and sustainable hydrogen storage materials is a key challenge for realizing hydrogen as a clean and flexible energy carrier. Among various options, metal hydrides offer high volumetric storage density and operational safety, yet their application is limited by thermodynamic, kinetic, and compositional constraints. In this work, we investigate the potential of machine learning (ML) to predict key thermodynamic properties—equilibrium plateau pressure, enthalpy, and entropy of hydride formation—based solely on alloy composition using Magpie-generated descriptors. We significantly expand an existing experimental dataset from ~400 to 806 entries and assess the impact of dataset size and data augmentation, using the PADRE algorithm, on model performance. Models including Support Vector Machines and Gradient Boosted Random Forests were trained and optimized via grid search and cross-validation. Results show a marked improvement in predictive accuracy with increased dataset size, while data augmentation benefits are limited to smaller datasets and do not improve accuracy in underrepresented pressure regimes. Furthermore, clustering and cross-validation analyses highlight the limited generalizability of models across different material classes, though high accuracy is achieved when training and testing within a single hydride family (e.g., AB2). The study demonstrates the viability and limitations of ML for accelerating hydride discovery, emphasizing the importance of dataset diversity and representation for robust property prediction.

augmentation↗

Science of the Van Allen Probes Science Operations Centers

The Van Allen Probes mission operations materialized through a distributed model in which operational responsibility was divided between the Mission Operations Center (MOC) and separate instrument specific SOCs. The sole MOC handled all aspects of telemetering and receiving tasks as well as certain scientifically relevant ancillary tasks. Each instrument science team developed individual instrument specific SOCs proficient in unique capabilities in support of science data acquisition, data processing, instrument performance, and tools for the instrument team scientists. In parallel activities, project scientists took on the task of providing a significant modeling tool base usable by the instrument science teams and the larger scientific community. With a mission as complex as Van Allen Probes, scientific inquiry occurred due to constant and significant collaboration between the SOCs and in concert with the project science team. Planned cross-instrument coordinated observations resulted in critical discoveries during the seven-year mission. Instrument cross-calibration activities elucidated a more seamless set of data products. Specific topics include post-launch changes and enhancements to the SOCs, discussion of coordination activities between the SOCs, SOC specific analysis software, modeling software provided by the Van Allen Probes project, and a section on lessons learned. One of the most significant lessons learned was the importance of the original decision to implement individual team SOCs providing timely and well-documented instrument data for the NASA Van Allen Probes Mission scientists and the larger magnetospheric and radiation belt scientific community.

47 OTHER INSTRUMENTATION↗

Stardust Interstellar Preliminary Examination X: Impact Speeds and Directions of Interstellar Grains on the Stardust Dust Collector

On the basis of an interstellar dust model compatible with Ulysses and Galileo observations, we calculate and predict the trajectories of interstellar dust (ISD) in the solar system and the distribution of the impact speeds, directions, and flux of ISD particles on the Stardust Interstellar Dust Collector during the two collection periods of the mission. We find that the expected impact velocities are generally low (less than 10 km per second) for particles with the ratio of the solar radiation pressure force to the solar gravitational force beta greater than 1, and that some of the particles will impact on the cometary side of the collector. If we assume astronomical silicates for particle material and a density of 2 grams per cubic centimeter, and use the Ulysses measurements and the ISD trajectory simulations, we conclude that the total number of (detectable) captured ISD particles may be on the order of 50. In companion papers in this volume, we report the discovery of three interstellar dust candidates in the Stardust aerogel tiles. The impact directions and speeds of these candidates are consistent with those calculated from our ISD propagation model, within the uncertainties of the model and of the observations.

interstellar↗

Modeling and Performance Analysis of the LUVOIR Coronagraph Instrument

Future space missions such as the Large UV/Optical/Infrared Surveyor (LUVOIR) and the Habitable Exoplanet Observatory, when equipped with coronagraphs with active wavefront control to suppress starlight, will allow the discovery and characterization of habitable exoplanets. The Extreme Coronagraph for Living Planetary Systems (ECLIPS) is the coronagraph instrument on the LUVOIR Surveyor mission concept, an 8- to 15-m segmented telescope. ECLIPS is split into three channels, namely, UV (200 to 400 nm), optical (400 to 850 nm), and near IR (850 nm to 2 μm), with each channel equipped with two deformable mirrors for wavefront control, a suite of coronagraph masks, a low-order/out-of-band wavefront sensor, and separate science imagers and spectrographs. The apodized pupil Lyot coronagraph and the vector vortex coronagraph are the baselined mask technologies for ECLIPS to enable the required 10−10 contrast for observations in the habitable zones of nearby stars for LUVOIR-A (15-m telescope) and LUVOIR-B (8-m telescope), respectively. Their performance depends on active wavefront sensing and control, as well as metrology subsystems to compensate for aberrations induced by segment errors (e.g., piston and tip/tilt), secondary mirror misalignment, and global low-order wavefront errors. Here, we present the latest results of the simulation of these effects for the LUVOIR coronagraph instrument and discuss the achieved contrast for exoplanet detection and characterization after closed-loop wavefront estimation and control algorithms have been applied. Finally, we show simulated observations using high-fidelity spatial and spectral input models of complete planetary systems generated with the Haystacks code framework.

Roser Juanola-Parramon↗

Unsupervised discovery of nonlinear plasma physics using differentiable kinetic simulations

Plasma supports collective modes and particle–wave interactions that lead to complex behaviour in, for example, inertial fusion energy applications. While plasma can sometimes be modelled as a charged fluid, a kinetic description is often crucial for studying nonlinear effects in the higher-dimensional momentum–position phase space that describes the full complexity of the plasma dynamics. We create a differentiable solver for the three-dimensional partial-differential equation describing the plasma kinetics and introduce a domain-specific objective function. Using this framework, we perform gradient-based optimization of neural networks that provide forcing function parameters to the differentiable solver given a set of initial conditions. We apply this to an inertial-fusion-relevant configuration and find that the optimization process exploits a novel physical effect.

plasma nonlinear phenomena↗

Scenario storyline discovery for complex multi-actor human-natural systems

This poster was presented at the AGU Fall Meeting 2024. Abstract:Scenario analysis is a useful tool for assessing the impacts of future conditions or alternative strategies. However, the common practice of focusing on a small number of predetermined scenarios can limit our understanding of key uncertainties, and fail to represent diverse stakeholder impacts. Exploratory modeling approaches have been developed to address these issues by simulating a wide range of possible futures and system perspectives. A challenge with these approaches is that they often involve large ensemble experiments which limit interpretability and usability. We recently introduced the FRamework for Narrative Storylines and Impact Classification (FRNSIC; pronounced ``forensic''), a scenario discovery framework that helps users identify scenario storylines that capture key system dynamics and as well as important outcomes. In this poster presentation, we present training materials to support the generalizable application of the framework to other multi-actor systems with complex dynamics. Specifically, we will present a step-by-step methodological typology of tools and methods that can be used to generate and classify plausible states of the world on key metrics and consequential dynamics. The typology will also discuss potential implications of these choices and their applicability to different systems.

Colorado River↗

Multi-top signals of vectorlike quarks at the LHC

We point out that events with 6 or more top quarks may be observed at the LHC if certain particles exist at the TeV scale. In a model where a vectorlike quark of charge 2/3 decays into a top quark and a pseudoscalar particle, which subsequently decays into a top-antitop pair, the LHC production cross section for events with 6 top quarks may be above 10 fb. If the pseudoscalar is part of a complex scalar field, then longer cascade decays, involving the scalar partner, may lead to events with 8 or even 10 top quarks. We show that for a region of parameter space the dominant LHC signal in this model is 8 top quarks (i.e., four $t\bar{t}$ pairs). The ensuing signals would be spectacular, including many leptons and b jets. A discovery in that case would allow several cross section measurements that may determine the masses of all three new particles.

Specific BSM Phenomenology↗

Accelerating the discovery of low-energy structure configurations: A computational approach that integrates first-principles calculations, Monte Carlo sampling, and Machine Learning

Finding Minimum Energy Configurations (MECs) is essential in fields such as physics, chemistry, and materials science, as they represent the most stable states of the systems. In particular, identifying such MECs in multi-component alloys considered candidate PFMs is key because it determines the most stable arrangement of atoms within the alloy, directly influencing its phase stability, structural integrity, and thermo-mechanical properties. However, since the search space grows exponentially with the number of atoms considered, obtaining such MECs using computationally expensive first-principles DFT calculations often results in a cumbersome task. To escape the above compromise between physical fidelity and computational efficiency, we have developed a novel physics-based data-driven approach that combines Monte Carlo sampling, first-principles DFT calculations, and Machine Learning to accelerate the discovery of MECs in multi-component alloys. More specifically, we have leveraged well-established Cluster Expansion (CE) techniques with Local Outlier Factor models to establish strategies that enhance the reliability of the CE method. In this work, we demonstrated the capabilities of the proposed approach for the particular case of a tungsten-based quaternary high-entropy alloy. However, the method is applicable to other types of alloys and enables a wide range of applications.

36 MATERIALS SCIENCE↗

Leveraging unlabeled SEM datasets with self-supervised learning for enhanced particle segmentation

Scanning Electron Microscopes (SEMs) are widely used in experimental science laboratories, often requiring cumbersome and repetitive user analysis. Automating SEM image analysis processes is highly desirable to address this challenge. In particle sample analysis, Machine Learning (ML) has emerged as the most effective approach for particle segmentation. However, the time-intensive process of manually annotating thousands of SEM images limits the applicability of supervised learning approaches. Self-Supervised Learning (SSL) offers a promising alternative by enabling knowledge extraction from raw, unlabeled data. This study presents a framework for evaluating SSL techniques in SEM image analysis, focusing on novel methods leveraging the ConvNeXtV2 architecture for particle detection. A dataset comprising 25,000 SEM images is curated to benchmark these proposed SSL methods. The results demonstrate that ConvNeXtV2 models, with varying parameter counts, consistently outperform other techniques in particle detection across different length scales, achieving up to a 34% reduction in relative error compared to established SSL methods. Furthermore, an ablation study explores the relationship between dataset size and SSL performance, providing actionable insights for practitioners regarding model selection and resource efficiency. This research advances the integration of SSL into autonomous analysis pipelines and supports its application in accelerating materials science discovery.

Rettenberger, Luca↗

High-throughput screening of the ReFRAME, Pandemic Box, and COVID Box drug repurposing libraries against SARS-CoV-2 nsp15 endoribonuclease to identify small-molecule inhibitors of viral activity

SARS-CoV-2 has caused a global pandemic, and has taken over 1.7 million lives as of mid-December, 2020. Although great progress has been made in the development of effective countermeasures, with several pharmaceutical companies approved or poised to deliver vaccines to market, there is still an unmet need of essential antiviral drugs with therapeutic impact for the treatment of moderate-to-severe COVID-19. Towards this goal, a high-throughput assay was used to screen SARS-CoV-2 nsp15 uracil-dependent endonuclease (endoU) function against 13 thousand compounds from drug and lead repurposing compound libraries. While over 80% of initial hit compounds were pan-assay inhibitory compounds, three hits were confirmed as nsp15 endoU inhibitors in the 1–20 μM range in vitro. Furthermore, Exebryl-1, a ß-amyloid anti-aggregation molecule for Alzheimer’s therapy, was shown to have antiviral activity between 10 to 66 μM, in Vero 76, Caco-2, and Calu-3 cells. Although the inhibitory concentrations determined for Exebryl-1 exceed those recommended for therapeutic intervention, our findings show great promise for further optimization of Exebryl-1 as an nsp15 endoU inhibitor and as a SARS-CoV-2 antiviral.

60 APPLIED LIFE SCIENCES↗

Harnessing the power of ab initio calculations, distributed computing and machine learning to efficiently locate extreme molecules for use in carbon-based solar cells (Final Technical Report)

The use of high-throughput virtual screening (HTVS) tools is a powerful tool to expedite the materials discovery of commercially relevant materials. In previous years, our group has developed a molecular discovery platform to generate libraries in order to obtain suitable candidates for different applications, starting from the Harvard Clean Energy Project. This platform is suitable to test in-silico on traditional supercomputing clusters and shared resources, for example, in the IBM World Community Grid. In this project, we used the molecular discovery platform to create and screen a library of candidates of organic photovoltaic (OPVs) molecules. Based on a set of candidates created with combinations of molecular moieties, we were able to filter, by conformation stability, the energy of electronic orbitals and approximated power conversion efficiencies (PCE). To improve the predictions of orbital energies calculated and the PCEs, we used Gaussian Process regression and two sets of molecules. These sets correspond to electronic structure calculations of a higher level of theory and experimental PCE values, respectively. Finally, we selected a subset of the best candidates (molecules with a PCE higher than 10%) to understand its absorbance properties with TD-DFT. This project has demonstrated the capabilities of our molecular discovery platform for HTVS. Finally, machine learning can help us to introduce more complex effects included in bulk conditions and computational intensive calculations on models.

14 SOLAR ENERGY↗

S-193 impulse response cross correlation

The author has identified the following significant results. A significant result was the realization that the phase information, normally lost in envelope detection and sampling, could have been preserved if the samples were taken at the peaks of the carrier frequency at intervals equal to a twice or an integral multiple of the integral number of its period. Thus the Skylab S193 Model 1 altimeter data does not contain phase information in accordance with the technical information obtained from NASA and Lockheed technical personnel. Another significant discovery was to learn that the eight return pulse samples don't belong to the same pulse but represent an average over many pulses.

Hayre, H. S.↗

Using FT-IR Spectroscopy to Elucidate the Structures of Ablative Polymers

The composition and structure of an ablative polymer has a multifaceted influence on its thermal, mechanical and ablative properties. Understanding the molecular level information is critical to the optimization of material performance because it helps to establish correlations with the macroscopic properties of the material, the so-called structure-property relationship. Moreover, accurate information of molecular structures is also essential to predict the thermal decomposition pathways as well as to identify decomposition species that are fundamentally important to modeling work. In this presentation, I will describe the use of infrared transmission spectroscopy (FT-IR) as a convenient tool to aid the discovery and development of thermal protection system materials.

Fan, Wendy↗

Global earth mineral inventory: A data legacy

Minerals contain important clues to understanding the complex geologic history of Earth and other planetary bodies. Therefore, geologists have been collecting mineral samples and compiling data about these samples for centuries. These data have been used to better understand the movement of continental plates, the oxidation of Earth's atmosphere and the water regime of ancient martian landscapes. Datasets found at ‘RRUFF.info/Evolution’ and ‘mindat.org’ have documented a wealth of mineral occurrences around the world. One of the main goals in geoinformatics has been to facilitate discovery by creating and merging datasets from various scientific fields and using statistical methods and visualization tools to inspire and test hypotheses applicable to modelling Earth's past environments. To help achieve this goal, we have compiled physical, chemical and geological properties of minerals and linked them to the above-mentioned mineral occurrence datasets. As a part of the Deep Time Data Infrastructure, funded by the W.M. Keck Foundation, with significant support from the Deep Carbon Observatory (DCO) and the A.P. Sloan Foundation, GEMI (‘Global Earth Mineral Inventory’) was developed from the need of researchers to have all of the required mineral data visible in a single portal, connected by a robust, yet easy to understand schema. Our data legacy integrates these resources into a digestible format for exploration and analysis and has allowed researchers to gain valuable insights from mineralogical data. GEMI can be considered a network, with every node representing some feature of the datasets, for example, a node can represent geological parameters like colour, hardness or lustre. Exploring subnetworks gives the researcher a specific view of the data required for the task at hand. GEMI is accessible through the DCO Data Portal (https://dx.deepcarbon.net/11121/6200-6954-6634-8243-CC). We describe our efforts in compiling GEMI, the Data Policies for usage and sharing, and the evaluation metrics for this data legacy.

data legacy↗

A Scalable Parallel Hypergraph Generator (HyGen)

Graphs are extensively used to model real-world complex systems. An edge in a graph can model pairwise relationships. However, multiway relationships (connections between three or more vertices) are common in many complex systems such as cellular process, image segmentation, and circuit design. A graph edge cannot model multiway relationships. A hypergraph, which can connect more than two vertices, is thus a better option to model multiway relationships. A large-scale hypergraph analysis has the potential to find useful insights from a complex system and assist in knowledge discovery. Currently a limited number of hypergraphs exists that are representative of real-world datasets. Moreover, real-world hypergraph datasets are small in size and inadequate to incorporate future needs. A graph generator that can produce large-scale synthetic hypergraphs can solve the above mentioned problems. In this paper, we present a scalable parallel hypergraph generator (HyGen) based on the Message Passing Interface (MPI) standard. To generate hypergraphs, HyGen takes the following parameter values as inputs: i) number of vertices, ii) number of hyperedges, iii) number of clusters, iv) vertex distribution, v) hyperedge distribution, vi) local cluster cardinality, and vii) global cluster cardinality. We have demonstrated that HyGen can generate hypergraphs of various sizes in a scalable fashion. HyGen takes approximately four minutes to generate a hypergraph with 4.8 million vertices, 1.6 million hyperedges, and 800 clusters using 1,024 processes on a leadership class computing platform. Our strong and weak scaling experiments on supercomputers demonstrate that HyGen can quickly create large-scale hypergraphs in a parallel manner, thus providing a useful capability for hypergraph analysis.

Hasan, S M Shamimul↗

Global Modeling of Mineral Dust and its Optical Thickness

Global distribution of dust in the atmosphere has been simulated using the NASA Goddard chemical transport model (GEOS-CTM) to help retrieve the aerosol optical thickness from TOMS absorbing aerosol index. The model contains a dust module which accounts for sources and removal processes. The transport is driven by the assimilated meteorological fields generated by the NASA Goddard Earth Observing System Data Assimilation System (GEOS DAS). One of the key parameters, in the retrieval algorithm of optical thickness from Total Ozone Mapping Spectrometer (TOMS) data, is the vertical profile of aerosols. During the period 10- 19 September 1994, Lidar on-space Technology Experiment (LITE) was flown on space shuttle Discovery. The 53 hours of data collected cover the lower atmosphere from the earth surface to 20 kilometers altitude and from 57 N to 57 S with a high resolution of about 15 meters. The model results are compared with LITE data over the source regions of dust (Africa, Middle East, Asia, Australia) and in the remote troposphere (Atlantic and Pacific). The simulated horizontal distribution is compared with TOMS absorbing aerosol index. Finally the calculated optical thickness will be assessed with ground based sun-photometers (AERONET).

Ginoux, Paul A.↗

Derivation of physical equations for high-speed laser welding using large language models

It is challenging to formulate complex physical phenomena that occur in a manufacturing process, particularly when the available data are limited, rendering conventional data-driven approaches ineffective. This study aims to predict humping onset in high-speed laser welding by introducing a novel framework, namely text-to-equations generative pre-trained transformer (T2EGPT). This method leverages the capabilities of large language models (LLMs), in combination with sparse experimental data and enriched literature data, to derive an interpretable and generalizable equation for predicting humping initiation. By capturing key correlations among physical parameters, T2EGPT generates a compact and dimensionless expression that accurately predicts hump formation. The equation reveals that humping arises from the interplay between inertia-driven backward melt flow and capillary-driven surface stabilization, where inertial forces drive molten metal backward and capillary forces resist surface deformation. Furthermore, compared to traditional data-driven models, T2EGPT demonstrates enhanced predictive accuracy and cross-material transferability. More broadly, this study highlights the potential of LLMs to integrate textual information with data-driven discovery, enabling the extraction of physical laws in data-scarce scientific domains.

36 MATERIALS SCIENCE↗