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At least 775 records · Page 43

Language models for the prediction of SARS-CoV-2 inhibitors

The COVID-19 pandemic highlights the need for computational tools to automate and accelerate drug design for novel protein targets. We leverage deep learning language models to generate and score drug candidates based on predicted protein binding affinity. We pre-trained a deep learning language model (BERT) on ∼9.6 billion molecules and achieved peak performance of 603 petaflops in mixed precision. Our work reduces pre-training time from days to hours, compared to previous efforts with this architecture, while also increasing the dataset size by nearly an order of magnitude. For scoring, we fine-tuned the language model using an assembled set of thousands of protein targets with binding affinity data and searched for inhibitors of specific protein targets, SARS-CoV-2 Mpro and PLpro. We utilized a genetic algorithm approach for finding optimal candidates using the generation and scoring capabilities of the language model. Our generalizable models accelerate the identification of inhibitors for emerging therapeutic targets.

Blanchard, Andrew E.↗

Reactome and the Gene Ontology: digital convergence of data resources

Abstract Motivation Gene Ontology Causal Activity Models (GO-CAMs) assemble individual associations of gene products with cellular components, molecular functions and biological processes into causally linked activity flow models. Pathway databases such as the Reactome Knowledgebase create detailed molecular process descriptions of reactions and assemble them, based on sharing of entities between individual reactions into pathway descriptions. Results To convert the rich content of Reactome into GO-CAMs, we have developed a software tool, Pathways2GO, to convert the entire set of normal human Reactome pathways into GO-CAMs. This conversion yields standard GO annotations from Reactome content and supports enhanced quality control for both Reactome and GO, yielding a nearly seamless conversion between these two resources for the bioinformatics community. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Validation and demonstration of the AEFC as a practical safeguards tool for inventory verification

The Advanced Experimental Fuel Counter (AEFC) is a nondestructive assay (NDA) instrument designed to determine the residual fissile mass in irradiated fuel assemblies for safeguards verification purposes. This is done by actively interrogating an assembly with a neutron source and measuring the total (Singles) and correlated (Doubles) neutron count rates resulting from induced fissions in the irradiated nuclear fuel and relating those rates to the residual fissile mass using calibration curves. Comprehensive NDA measurements of the irradiated fuel inventory at Israeli Research Reactor 1 (IRR-1) were taken with the AEFC to validate a set of previously developed calibration curves. During the campaign, measurements were acquired of 32 standard fuel assemblies and three control assemblies in just nine days. This is a significant majority of the research reactor's irradiated fuel inventory and the largest data set gathered by the AEFC to date. Many of the fuel assemblies measured during the campaign had much shorter cooling times than those assemblies previously measured with the instrument. Calibration curves developed from previous AEFC deployments were used to determine the residual 235 U mass in the measured standard fuel assemblies. The results of the campaign demonstrated that the AEFC can be used to estimate the 235 U mass remaining in a large number of irradiated fuel assemblies with 1%–5% uncertainty in a reasonable amount of time despite operating in a high dose environment.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Calculated Drag of an Aerial Refueling Assembly Through Airplane Performance Analysis

The aerodynamic drag of an aerial refueling assembly was calculated during the Automated Aerial Refueling project at the NASA Dryden Flight Research Center. An F/A-18A airplane was specially instrumented to obtain accurate fuel flow measurements and to determine engine thrust. A standard Navy air refueling store with a retractable refueling hose and paradrogue was mounted to the centerline pylon of the F/A-18A airplane. As the paradrogue assembly was deployed and stowed, changes in the calculated thrust of the airplane occurred and were equated to changes in vehicle drag. These drag changes were attributable to the drag of the paradrogue assembly. The drag of the paradrogue assembly was determined to range from 200 to 450 lbf at airspeeds from 170 to 250 KIAS. Analysis of the drag data resulted in a single drag coefficient of 0.0056 for the paradrogue assembly that adequately matched the calculated drag for all flight conditions. The drag relief provided to the tanker airplane when a receiver airplane engaged the paradrogue is also documented from 35 to 270 lbf at the various flight conditions tested. The results support the development of accurate aerodynamic models to be used in refueling simulations and control laws for fully autonomous refueling.

Vachon, Michael Jacob↗

Birth of a Bipolar Active Region in a Small Coronal Hole

We report on an the emergence of an anemone active region in a very small coronal hole (about 120'' across), beginning at approximately 19:00 UT on March 3, 2016. The emergence was initially observed by an amateur astronomer (RW) in an H-alpha movie from the Global Oscillation Network Group (GONG); it attracted the attention of the observer because there was no active region at the site of the H-alpha brightening. To examine the region in detail, we use data from the Solar Dynamics Observatory (SDO), provided by the Atmospheric Imaging Assembly (AIA) in wavelengths 193 Å, 211 Å, 304 Å, and 94 Å, and with the Helioseismic and Magnetic Imager (HMI). Data analysis and calibration activities such as scaling, rotation so that north is up, and removal of solar rotation are accomplished with SunPy. The emergence seen in HMI data begins with the appearance of a bipole close to the center of the coronal hole, followed by the appearance and growth of a coronal anemone in AIA-EUV images; as the emergence proceeds, the anemone fills the coronal hole in AIA wavelengths. The interchange reconnection of the emerging closed field with ambient open field builds the anemone and shifts the coronal hole from one side of the anemone to the other. Eventually, a sunspot forms in one foot of the emerging field. To date, studies of observations with SDO of anemone emergence in on-disk coronal holes are rare. This bipolar flux emergence episode fits well with the standard picture for the production of coronal-anemone regions.

Adams, Mitzi↗

Final Report on Characterization of Irradiated Sensors and Coupling Adhesive Bonds

This report summarizes characterization via scanning/transmission electron microscopy of the microstructures of the unirradiated and irradiated piezoelectric ultrasonic sensor/aluminum substrate assemblies using four commercially available inorganic coupling adhesives to bond two types of piezoelectric crystals to the substrates. The sample assemblies were irradiated in the PULSTAR reactor at NC State University and ultrasonic data was collected in-situ. ORNL LAMDA Laboratory capabilities were utilized to perform pre- and post-irradiation examination of the sensor assemblies. This document summarizes the PIE performed at the ORNL LAMDA laboratory. The results of the PIE described in this report are consistent with the ultrasonic data collected during irradiation – in particular, high temperature epoxy adhesive seemed to provide the best coupling as compared to the refractory ceramic adhesives. It was determined that the quality of the sensor-adhesive-substrates governed the ultrasonic performance of the sensors. It was also apparent that irradiation did not significantly affect bond quality, which is also supported by the ultrasonic data collected during irradiation. A more comprehensive DOE NSUF Final Report including details of materials selection, sample fabrication, initial ultrasonic testing, irradiation and in-situ ultrasonic testing, positron annihilation lifetime spectroscopy and doppler broadening spectroscopy performed at EPRI and NC State University will be published at the conclusion of the project.

36 MATERIALS SCIENCE↗

Understanding the impact of nuclear-data covariances on various integral responses using adjustment

The EUCLID (Experiments Underpinned by Computational Learning for Improvements in Nuclear Data) project created a library of sensitivities for nine different integral responses with respect to nuclear data. These integral responses were obtained from measurements at LLNL (Lawrence Livermore National Laboratory) pulsed spheres, critical and sub-critical assemblies. At the same time, covariances for ENDF/B-VIII.0 were processed at LANL (Los Alamos National Laboratory). The combination of these data allow us to study the impact of nuclear-data covariances on various integral responses, either by forward-propagating covariances via sensitivities, or by using nuclear data, integral responses, and sensitivities for adjustment. Here, we will present: the impact of 1 H, 9 Be, 12 C, 27 Al, 56 Fe, 235,238 U, and 239,240 Pu ENDF/B-VIII.0 covariances on simulated bounds of the following integral responses: LLNL pulsed-spheres neutron-leakage spectra, the effective neutron multiplication factor, reaction rates, and reactivity coefficients of ICSBEP critical assemblies. Also, adjustment results with the same nuclear-data covariances and responses will be discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

TESS Lens-Bezel Assembly Modal Testing

The Transiting Exoplanet Survey Satellite (TESS) program, led by the Kavli Institute for Astrophysics and Space Research at the Massachusetts Institute of Technology (MIT) will be the first-ever spaceborne all-sky transit survey. MIT Lincoln Laboratory is responsible for the cameras, including the lens assemblies, detector assemblies, lens hoods, and camera mounts. TESS is scheduled to be launched in August of 2017 with the primary goal to detect small planets with bright host starts in the solar neighborhood, so that detailed characterizations of the planets and their atmospheres can be performed. The TESS payload consists of four identical cameras and a data handling unit. Each camera consists of a lens assembly with seven optical elements and a detector assembly with four charge-coupled devices (CCDs) including their associated electronics. The optical prescription requires that several of the lenses are in close proximity to a neighboring element. A finite element model (FEM) was developed to estimate the relative deflections between each lens-bezel assembly under launch loads to predict that there are adequate clearances preventing the lenses from making contact. Modal tests using non-contact response measurements were conducted to experimentally estimate the modal parameters of the lens-bezel assembly, and used to validate the initial FEM assumptions. Key Words Non-contact measurements, modal analysis, model validation

Modal Testing↗

Directory of aerospace safety specialized information sources

A directory is presented to make available to the aerospace safety community a handbook of organizations and experts in specific, well-defined areas of safety technology. It is designed for the safety specialist as an aid for locating both information sources and individual points of contact (experts) in engineering related fields. The file covers sources of data in aerospace design, tests, as well as information in hazard and failure cause identification, accident analysis, materials characteristics, and other related subject areas. These 171 organizations and their staff members, hopefully, should provide technical information in the form of documentation, data and consulting expertise. These will be sources that have assembled and collated their information, so that it will be useful in the solution of engineering problems. One of the goals of the project in the United States that have and are willing to share data of value to the aerospace safety community.

Fullerton, E. A.↗

Bistatic radar sea state monitoring field test

Recent advances in understanding the physical phenomena controlling the interaction of electromagnetic energy with the ocean surface have revealed the possiblity of remote measurement of the two-dimensional surface wave height spectrum of the ocean using bistatic radar techniques. The basic feasibility of such a technique operating at frequencies in the HF region (3 to 30 MHz) was examined during previous studies and hardware for an experimental verification experiment was specified. The activities have resulted in a determination of the required hardware and system parameters for both satellite and aircraft systems, the development, assembly, and testing of hardware for an experimental aircraft system, the development and initial testing of data processing procedures, and the conduct of an initial flight test experiment. Activities were devoted to completing the assembly and testing of the experimental hardware, completing the experiment planning, conducting a field test experiment, and the processing and analysis of the experimental data. Even though directional spectrum maps of the test area cannot be generated from the measured data, the hardware concept employed appears viable, and solutions to the problems encountered have been identified.

Ruck, G. T.↗

Real-Time Science Decisioning During High Tempo-High Intensity Mission Operations and the Role of Analogs

Introduction: NASA’s VIPER mission presents a unique operational paradigm within the history of robotic spaceflight. The proximity of the Moon to the Earth and the terrain elements (surface characteristics, light/shadow dynamics, communication links) of the lunar South Polar landing site create unprecedented operational conditions between these two planetary bodies. Apollo era lunar science and exploration included humans in situ to operate instruments and assimilate observational inputs in real-time. Previous lunar orbital missions have worked to operational timescales, e.g., decisional timelines and communication exchanges, that were weeks in length. Mars rover missions have worked to operational timescales, e.g., decisional timelines and communication exchanges between Mars and Earth, that were hours, days, and weeks in length. In the case of the VIPER mission, our operational decisioning for rover driving and instrument commanding will be compressed to minute-scale timeframes. These operational conditions directly impact the manner and speed with which the VIPER Science Team (VST) is required to synthesize and analyze data and produce timely science-driven decisions throughout surface mission operations. The VST shall provide mission enhancing scientific input to guide rover traverse planning and drill site confirmation and selection throughout surface operations. Further, the VST input will be of vital importance to the mission’s ability to maximize science return and to meet broader NASA objectives for future lunar in-situ resource utilization (ISRU)and exploration activities. The VST co-located in the Mission Science Center (MSC) will be responsive to the tactical operational cadence of the Mission Operations Center (MOC) and will provide further strategic and Long-Term Planning (LTP) guidance to the mission. The VIPER Science Operations & Integration(SO&I)team has developed an architecture that is focused on the infusion of science-decisioning into the operational framework and execution cadence of VIPER. NASA analog research has played a significant role in the construction of the VIPER science operations systems. As an example, the SO&I team has led analog missions that have focused on bringing together expertise in the sciences (natural, applied and social) and in operations in service of learning how to build and hold together interdisciplinary work environments and what tools are needed to support high tempo, high intensity integrated decisioning. These experiences have provided an essential foundation of knowledge to the VIPER team. Those analogs that specifically influenced the VIPER science operations construct were identified through a process of comparative analysis to prioritize those that offered relevance in whole or in part, and those that did not. The analog research output that provided extensibility to the VIPER science operations architecture included remote teams of humans and robots in cooperation (synchronous and asynchronous) with simulated earthbound systems, engineering and science teams, and the integrated assembly of tools that supported scientific analysis and data synthesis and provided infrastructure for the remote testing framework. Analogs which included real-time data monitoring, synthesis, visualization and access in a democratized and operationalized manner were of particular interest to the development of the VIPER MSC toolset both in terms of the technology and the processes used to develop the supporting infrastructure. We anticipate that each subsequent mission to the lunar south pole, whether with robots or humans, will be able to optimize science and exploration return by evolving strategies to infuse real-time collaborative science-decisioning. Furthermore, these efforts will result in a foundation for science operations development in support of human-robotic exploration of deep space and Mars. NASA analogs can continue to provide the opportunity to prepare, test and iterate on the operational concepts and tools that will support these ever-expanding space exploration efforts. Our presentation will include an overview of the VIPER Science Operations & Integration development process and specifics on what aspects of analog research have had a significant impact on our work systems.

D S S Lim↗

Optical processing for landmark identification

A study of optical pattern recognition techniques, available components and airborne optical systems for use in landmark identification was conducted. A data base of imagery exhibiting multisensor, seasonal, snow and fog cover, exposure, and other differences was assembled. These were successfully processed in a scaling optical correlator using weighted matched spatial filter synthesis. Distinctive data classes were defined and a description of the data (with considerable input information and content information) emerged from this study. It has considerable merit with regard to the preprocessing needed and the image difference categories advanced. A optical pattern recognition airborne applications was developed, assembled and demontrated. It employed a laser diode light source and holographic optical elements in a new lensless matched spatial filter architecture with greatly reduced size and weight, as well as component positioning toleranced.

Casasent, D.↗

HipBone: A performance-portable graphics processing unit-accelerated C++ version of the NekBone benchmark

We present hipBone, an open-source performance-portable proxy application for the Nek5000 (and NekRS) computational fluid dynamics applications. HipBone is a fully GPU-accelerated C++ implementation of the original NekBone CPU proxy application with several novel algorithmic and implementation improvements which optimize its performance on modern fine-grain parallel GPU accelerators. Our optimizations include a conversion to store the degrees of freedom of the problem in assembled form in order to reduce the amount of data moved during the main iteration and a portable implementation of the main Poisson operator kernel. We demonstrate near-roofline performance of the operator kernel on three different modern GPU accelerators from two different vendors. We present a novel algorithm for splitting the application of the Poisson operator on GPUs which aggressively hides MPI communication required for both halo exchange and assembly. Our implementation of nearest-neighbor MPI communication then leverages several different routing algorithms and GPU-Direct RDMA capabilities, when available, which improves scalability of the benchmark. We demonstrate the performance of hipBone on three different clusters housed at Oak Ridge National Laboratory, namely, the Summit supercomputer and the Frontier early-access clusters, Spock and Crusher. Our tests demonstrate both portability across different clusters and very good scaling efficiency, especially on large problems.

Computer Science↗

Poisson hurdle model-based method for clustering microbiome features

Abstract Motivation High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality. Results We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. Availability and implementation R package is freely available for download at https://cran.r-project.org/package=PHclust. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Data from Rossi-α and Pulsed Neutron Prompt Neutron Time Decay Measurements at the Oak Ridge Critical Experiments Facility

This report briefly describes the prompt neutron decay measurements by the Rossi-α and pulsed neutron methods performed at the Oak Ridge Critical Experiments Facility. It briefly describes the measurement equipment, the type of data, and how to access the actual data from the Laboratory Records Department at Oak Ridge National Laboratory and the International Nuclear Criticality Safety Benchmark Evaluation Program at Idaho National Laboratory. Most of the data was acquired between 1960 and 1975 with weapons-grade enriched uranium metal assemblies. It also includes measurement of these types performed at Los Alamos National Laboratory by Oak Ridge National Laboratory with the JEZEBEL and FLATTOP criticality assemblies and other plutonium metal parts. The purpose of this report is to support future mining of the data for publication of additional information that can be used to verify calculational methods and nuclear cross sections. Present calculational methods can be used to directly calculate the measured data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Artemis I Flight Instrumentation Data Quality Assessment and Processing

This paper is in support of the SciTech 2024 Space Launch System Aerosciences Special Sessions being organized by Brent Pomeroy and Jeremy Pinier. On November 16th, 2022, NASA launched an inaugural test flight of the Space Launch System (SLS) carrying the Orion capsule around the moon. The vehicle was instrumented with thousands of Developmental Flight Instrumentation (DFI) sensors, which monitored aerodynamic, acoustic, structural, and thermal environments. These data are used to validate experimental and numerical tools used to predict conditions the vehicle experiences during ascent. Prior to launch, a set of tests were performed to quantify the expected quality of the DFI flight data. These included testing of individual components, such as data acquisition units, at the Systems Integration Laboratory (SIL) and testing of integrated vehicle components at the Vehicle Assembly Building (VAB). This paper summarizes these tests. Some aspects of post processing of data are also discussed.

Developmental Flight Instrumentation↗

metabCombiner 2.0: Disparate Multi-Dataset Feature Alignment for LC-MS Metabolomics

Liquid chromatography–high-resolution mass spectrometry (LC-HRMS), as applied to untargeted metabolomics, enables the simultaneous detection of thousands of small molecules, generating complex datasets. Alignment is a crucial step in data processing pipelines, whereby LC-MS features derived from common ions are assembled into a unified matrix amenable to further analysis. Variability in the analytical factors that influence liquid chromatography separations complicates data alignment. This is prominent when aligning data acquired in different laboratories, generated using non-identical instruments, or between batches from large-scale studies. Previously, we developed metabCombiner for aligning disparately acquired LC-MS metabolomics datasets. Here, we report significant upgrades to metabCombiner that enable the stepwise alignment of multiple untargeted LC-MS metabolomics datasets, facilitating inter-laboratory reproducibility studies. To accomplish this, a “primary” feature list is used as a template for matching compounds in “target” feature lists. We demonstrate this workflow by aligning four lipidomics datasets from core laboratories generated using each institution’s in-house LC-MS instrumentation and methods. We also introduce batchCombine, an application of the metabCombiner framework for aligning experiments composed of multiple batches. metabCombiner is available as an R package on Github and Bioconductor, along with a new online version implemented as an R Shiny App.

97 MATHEMATICS AND COMPUTING↗

CFD 2030 Grand Challenge: CFD-in-the-Loop Monte Carlo Flight Simulation for Space Vehicle Design

Flight qualification of space vehicles is markedly different from those typically employed for aircraft. The concept of an extensive flight test campaign for a space vehicle does not exist, and vehicle designers must look to alternative techniques for demonstrating robust and reliable performance of their vehicles prior to operational flight. A space vehicle may undergo only a handful of flight tests in its development cycle, with each flight representing a drastically different flight phase or flight configuration. For instance, NASA’s Space Launch System (SLS) launch vehicle and Orion spacecraft will only see a total of four flight demonstrations before flying a crew on its first operational mission, and each flight demonstrates a unique vehicle configuration and/or set of flight conditions. The SLS will be flown only one time before it becomes operational (Artemis 1). The Orion spacecraft Crew Module (CM) will have been tested twice, once on a Delta IV launch vehicle (Exploration Flight Test 1) and once as a fully integrated system with the SLS launch vehicle (Artemis 1). The Orion Launch abort system will have been tested twice, once in a pad abort scenario (Pad Abort 1) and once in an inflight abort scenario (Ascent Abort 2) on a modified Peacekeeper booster. Both of these latter tests involve only a boiler plate CM, not a functional Orion spacecraft. Thus, unlike aircraft, there is very little opportunity for engineers to assess and evaluate their preflight predictions. Instead, space vehicle designers rely on Monte Carlo flight simulations with detailed dispersions of predicted nominal flight behavior to determine how robust their design is to errors and uncertainties in the flight conditions their vehicle may encounter. These Monte Carlo analyses entail thousands of trajectory simulations to demonstrate that the vehicle can meet design requirements at a specified level of reliability. From an aerodynamics and aerothermodynamics perspective, these trajectory simulations are fueled by an extensive aerodynamic database that covers the complete range of expected flight conditions, vehicle configurations, and flight attitudes expected in a given mission. Today, these databases amount to a table of engineering parameters that can be quickly interrogated by the trajectory simulator. The aerodynamic and aerothermodynamic databases are assembled via a series of ground tests, empirical and analytical analysis, physics-based computational analysis, applicable past flight performance data, and in some cases, engineering judgment. These databases generally take years to assemble for a new space vehicle system and in the case of SLS/Orion, over a decade of test and analysis have been expended to develop the extensive databases required to cover the myriad of configurations and potential flight conditions required for the system. Recently, it has been proposed that Computational Fluid Dynamic (CFD) and computing capability may be reaching a point where it is foreseeable that CFD could be integrated directly into the production trajectory simulation tools used to design NASA’s space vehicles. To demonstrate this, NASA has embarked on two demonstrations of this type of capability, one where six degree of freedom flight trajectory simulation equations are embedded in an existing CFD solver and another where a production CFD solver is loosely coupled with a production trajectory simulation tool. These efforts represent an initial demonstration of a future approach to flight trajectory simulation, but they are a far cry from the capability required to perform a full-up CFD-in-the-loop Monte Carlo trajectory simulation. Therefore, this represents a viable grand challenge for computational methods addressing space vehicle design and development. The final paper/presentation will discuss the many hurdles, beyond simply raw computational power, to realizing this grand challenge and how they map directly to the CFD Vision 2030 ojectives. Among these are the wide range of flight conditions, including accelerating/decelerating flight, encountered by a space vehicle during launch and/or entry. The vehicle can also encounter numerous configuration changes, some of which can be quite drastic, during the course of its flight, so robust, automated geometry modeling, grid generation, and adaptation will play a huge role in reaching this goal. Multiply this by 1000’s of trajectory simulations occurring simultaneously in a given Monte Carlo analysis, and the problem readily scales to absorb virtually any size of supercomputer envisioned today. The concept of CFD-in-the-loop Monte Carlo trajectory simulation poses a formidable challenge for emerging and future computing systems, and it has the potential to shave years off the development cycle for aerodynamic and aerothermodynamic performance predictions as compared to today’s space vehicle design approach.

CFD 2030↗