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NASA NTRSDate not supplied

Developing Open-Source Training Materials for AI/ML and Space Biological Sciences Using NASA Cloud-Based Data

Artificial Intelligence (AI) and Machine Learning (ML) has gained significant traction in the biological and biomedical research fields in the last two decades, in part thanks to an increasing culture of open data sharing and reuse. Due to its capability for identifying complex relationships and patterns, AI/ML methodology is particularly well suited to recognize and predict biological patterns from high-dimensional next-generation sequencing data (e.g. whole genome sequencing, transcriptomic sequencing), as well as from biological or medical imaging data (e.g. microscopy, computed tomography, ultrasound, magnetic resonance imaging, radiography). These methodologies hold particular promise for space biosciences research and automated space health monitoring systems. However, there are many key considerations for properly training, validating, and testing a machine learning model in biological research or clinical application. Even with the positive culture of Open Science and data sharing, inexperienced researchers working quickly without proper checks can produce models that perform poorly outside of the immediate training dataset. Lessons learned from biological AI/ML research indicate that Open Science principles such as data sharing and open-source code must go hand-in-hand with publicly available, high-quality training curricula in best practices, with modules centered on real-life scientific use cases and data so future AI/ML practitioners gain experience on real problems. Here we present the development of open-source training materials for AI/ML and space biosciences, as part of the NASA Transform to Open Science Training (TOPST) initiative. We develop 4 independent training programs, focused on the following topics: 1) Fundamentals of Machine Learning and Space Biosciences Domain, 2) Open Science, Artificial Intelligence, and Ethical Best Practices for Data Sharing and Analysis, 3) Using AI/ML Classification to Identify Gene Networks Affected By Space Exposure in Mouse Liver, and 4) Using Neural Networks to Find DNA Damage Patterns in Immune Cells after Radiation. All programs leverage cloud-based NASA biological datasets. The curriculum we present will enable worldwide access to training in AI/ML and scientific analysis.

James Andrew Casaletto↗

NASA NTRSDate not supplied

Developing Open-Source Training Materials for AI/ML and Space Biological Sciences Using NASA Cloud-Based Data

Artificial Intelligence (AI) and Machine Learning (ML) has gained significant traction in the biological and biomedical research fields, in part due to a culture of open data sharing and reuse. AI/ML methodology is well-suited to recognize and predict biological patterns from high-dimensional next-generation sequencing data (e.g. whole genome sequencing, transcriptomic sequencing), as well as from biological or medical imaging data (e.g. microscopy, computed tomography, ultrasound, magnetic resonance imaging, radiography). These methodologies hold particular promise for space biosciences research and automated space health monitoring systems. However, there are key considerations for properly training, validating, and testing a machine learning model in biological research or clinical application. Inexperienced researchers can produce models that perform poorly outside of the training dataset. Open Science principles such as data sharing and open-source code must go hand-in-hand with publicly available, high-quality training curricula in best practices, with modules centered on real-life scientific use cases and data so future AI/ML practitioners gain experience on real problems. Here we present the development of open-source training materials for AI/ML and space biosciences, as part of the NASA Transform to Open Science Training (TOPST) initiative. We develop 4 independent training programs, focused on the following topics: 1) Fundamentals of Machine Learning and Space Biosciences Domain, 2) Open Science, Artificial Intelligence, and Ethical Best Practices for Data Sharing and Analysis, 3) Using AI/ML Classification to Identify Gene Networks Affected By Space Exposure in Mouse Liver, and 4) Using Neural Networks to Find DNA Damage Patterns in Immune Cells after Radiation. All programs leverage cloud-based NASA biological datasets. The curriculum we present will enable worldwide access to training in AI/ML and scientific analysis.

James Casaletto↗

DOE OSTI2025

GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning interpretability

Aptamers are oligonucleotide receptors that bind to their targets with high affinity. Here, we consider aptamers comprised of single-stranded DNA that undergo target-binding-induced conformational changes, giving rise to unique secondary and tertiary structures. Given a specific aptamer primary sequence, there are well-established computational tools (notably mfold) to predict the secondary structure via free energy minimization algorithms. While mfold generates secondary structures for individual sequences, there is a need for a high-throughput process whereby thousands of DNA structures can be predicted in real-time for use in an interactive setting, when combined with aptamer selections that generate candidate pools that are too large to be experimentally interrogated. We developed a new Python code for high-throughput aptamer secondary structure determination (GMfold). GMfold uses subgraph matching methods to group aptamer candidates by secondary structure similarities. We also improve an open-source code, SeqFold, to incorporate subgraph matching concepts. We represent each secondary structure as a lowest-energy bipartite subgraph matching of the DNA graph to itself. These new tools enable thousands of DNA sequences to be compared based on their secondary structures, using machine-learning algorithms. This process is advantageous when analyzing sequences that arise from aptamer selections via systematic evolution of ligands by exponential enrichment (SELEX). This work is a building block for future machine-learning-informed DNA-aptamer selection processes to identify aptamers with improved target affinity and selectivity and advance aptamer biosensors and therapeutics.

Aptamer↗

NASA NTRSDate not supplied

Exploring Blockchain to Support Open Science Practices

Open science aims to foster transparent sharing of scientific processes including open access, incentivization, provenance, open source code and tools, metrics, and resource sharing. However, effective management of these processes remains a challenge. This paper explores the application of blockchain technology to address these key aspects of open science. Blockchain offers a decentralized and secureplatform for information exchange and verification. By leveraging blockchain, open science can enhance transparency and reproducibility. In this paper, we present an implementation of blockchain for Earth science data synchronization across organizations, enabling tracking of data copying, citation, anddownload. The findings highlight the potential of blockchain in supporting open science objectives.

Iksha Gurung↗

NASA NTRSDate not supplied

An Integrated Design Tool for Tow-Steered Laminates of Composites in Abaqus and MSC.Patran/Nastran

Tow-steered composites can be tailored for optimal mechanical performance of lightweight structures. However, there are no commercial-grade design tools for tow-steered composite structures, which hinders the design innovation of tow-steered composites in realistic structures. The novelty of this paper is to develop an integrated design framework along with the development of graphical user interface (GUI) plug-ins in commercial finite element (FE) software Abaqus and MSC.Patran/Nastran. The GUI plug-ins take all the design setups and communicate with external codes for the material modeling and optimization, and hence provide a unified design environment within the FE codes. The mechanics of structure genome (MSG) plate model computes shell element properties based on user-defined fiber paths and layup, which are defined via the GUI plug-ins. The optimization is performed by an open-source code, Dakota, from Sandia National Laboratories (Sandia), which also coordinates the structural analysis, material modeling, and optimization in design iterations. Two examples are presented to demonstrate the user-friendliness and versatility of the developed GUI plug-ins. The developed tools will ease the design process and facilitate the application of tow-steered composites in realistic aerospace structures.

Xin Liu↗

NASA NTRSDate not supplied

An Integrated Design Tool for Tow-Steered Laminates of Composites in Abaqus and MSC.Patran/Nastran

Xin Liu↗

DOE OSTI2022

Automated Crystal Orientation Mapping in py4DSTEM using Sparse Correlation Matching

Crystalline materials used in technological applications are often complex assemblies composed of multiple phases and differently oriented grains. Robust identification of the phases and orientation relationships from these samples is crucial, but the information extracted from the diffraction condition probed by an electron beam is often incomplete. We have developed an automated crystal orientation mapping (ACOM) procedure which uses a converged electron probe to collect diffraction patterns from multiple locations across a complex sample. We provide an algorithm to determine the orientation of each diffraction pattern based on a fast sparse correlation method. We demonstrate the speed and accuracy of our method by indexing diffraction patterns generated using both kinematical and dynamical simulations. We have also measured orientation maps from an experimental dataset consisting of a complex polycrystalline twisted helical AuAgPd nanowire. From these maps we identify twin planes between adjacent grains, which may be responsible for the twisted helical structure. All of our methods are made freely available as open source code, including tutorials which can be easily adapted to perform ACOM measurements on diffraction pattern datasets.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Stellarator Design Exploration Using Symbolic-Regression Neutronics Surrogates

Systems codes require fast, simplified models to rapidly evaluate fusion power plant concepts, but neutronics analyses are often a computational bottleneck. Here, to address this, surrogate models for key neutronics responses have been developed using 3-D neutronics-ready models built with the open-source code ParaStell from a database of stellarator equilibria. Neutronics responses such as tritium breeding ratio (TBR), nuclear heating, and neutron-induced radiation damage displacements per atom (dpa) were simulated using OpenMC. Through sensitivity analysis and symbolic regression (SR), simple power-law formulas were derived connecting these neutronics responses to global stellarator parameters, including fusion power, plasma surface area, and plasma elongation. Validation shows these formulas can predict the simulation results with low error, enabling quick and accurate assessment of neutronics requirements in stellarator design exploration activities with systems codes.

Modeling↗

NASA NTRSDate not supplied

NASA Operational Simulator for SmallSats (NOS3): Design Reference Mission

The NASA Operational Simulator for Small Satellites (NOS3) has undergone significant advances including updating the framework to be “component” based and expanding the open-source code to include a generic design reference mission to enable advanced technologies. This paper details the changes to the framework as well as a number of innovative use-cases the team is currently supporting such as 1) the expansion of NOS3 to support distributed systems missions in collaboration with NASA GSFC, 2) the integration of NASA JPL’s Science Yield improvement via Onboard Prioritization and Summary of Information Systems (SYNOPSIS) for on-orbit science data prioritization, and 3) the inclusion of NASA IV&V’s software-only CCSDS encryption library (CryptoLib). NOS3 continues to serve the SmallSat community by providing an open-source digital twin that can significantly reduce costs associated with spacecraft software development, test, and operations. The NOS3 team hopes to continue to expand the resources available to the community and partner with others to resolve issues and add new features requested via the NASA GitHub.

SmallSats↗

DOE OSTI2023

Viscoplastic selfconsistent (VPSC) code (version 8, open source)

VPSC is a mean-field polycrystal plasticity code for the prediction of the mechanical response and microstructure evolution of polycrystalline aggregates. The VPSC code is the computational realization of the visco-plastic self-consistent theory of polycrystal deformation. Both the theory and details of its numerical implementation were originally reported by R.A. Lebensohn and C.N. Tomé: "A self-consistent approach for the simulation of plastic deformation and texture development of polycrystals: application to Zirconium alloys", Acta Metallurgica et Materialia 41, 2611 (1993). Since then, the VPSC code has experienced several improvements and extensions and it is nowadays extensively used to simulate plastic deformation of polycrystalline aggregates and to interpret experimental evidence on metals, minerals and polymers.

Lebensohn, Ricardo↗

DOE OSTI2024

Optical second harmonic generation in anisotropic multilayers with complete multireflection of linear and nonlinear waves using ♯SHAARP.ml package

Abstract Optical second harmonic generation (SHG) is a nonlinear optical effect widely used for nonlinear optical microscopy and laser frequency conversion. Closed-form analytical solution of the nonlinear optical responses is essential for evaluating materials whose optical properties are unknown a priori. A recent open-source code, ♯SHAARP. si , can provide such closed form solutions for crystals with arbitrary symmetries, orientations, and anisotropic properties at a single interface. However, optical components are often in the form of slabs, thin films on substrates, and multilayer heterostructures with multiple reflections of both the fundamental and up to ten different SHG waves at each interface, adding significant complexity. Many approximations have therefore been employed in the existing analytical approaches, such as slowly varying approximation, weak reflection of the nonlinear polarization, transparent medium, high crystallographic symmetry, Kleinman symmetry, easy crystal orientation along a high-symmetry direction, phase matching conditions and negligible interference among nonlinear waves, which may lead to large errors in the reported material properties. To avoid these approximations, we have developed an open-source package named Second Harmonic Analysis of Anisotropic Rotational Polarimetry in Multilayers (♯SHAARP. ml ). The reliability and accuracy are established by experimentally benchmarking with both the SHG polarimetry and Maker fringes using standard and commonly used nonlinear optical materials as well as twisted 2-dimensional heterostructures.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Enhancing ChatPORT with CUDA-to-SYCL Kernel Translation Capability

Large Language Models (LLMs) have shown strong capabilities in general code translation. However, code translation involving parallel programming models remains largely unexplored. This work enhances the capabilities of code LLMs in CUDA-to-SYCL kernel translation with parameter-efficient fine-tuning. The resultant fine-tuned LLM, called ChatPORT, is an effort to provide high-fidelity translations from one programming model to another. We describe the preparation of datasets from heterogeneous computing benchmarks for model fine-tuning and testing, the parameter-efficient fine-tuning of 19 open-source code models ranging in size from 0.5 to 34 billion parameters and evaluate the correctness rates of the SYCL kernels by the fine-tuned models. The experimental results show that most code models fail to translate CUDA codes to SYCL correctly. However, fine-tuning these models using a small set of CUDA and SYCL kernels can enhance the capabilities of these models in kernel translation. Depending on the sizes of the models, the correctness rate ranges from 19.9% to 81.7% for a test dataset of 62 CUDA kernels.

Jin, Zheming [ORNL] (ORCID:000000027197780X)↗

DOE OSTI2020

CTF Theory Manual (V.4.2)

Coolant-Boiling in Rod Arrays—Two Fluids (COBRA-TF) is a thermal/hydraulic (T/H) simulation code designed for light water reactor (LWR) vessel analysis. It uses a two-fluid, three-field (i.e. fluid film, fluid drops, and vapor) modeling approach. Both sub-channel and 3D Cartesian forms of 9 conservation equations are available for LWR modeling. The code was originally developed by Pacific Northwest Laboratory in 1980 and had been used and modified by several institutions over the last few decades. COBRA-TF also found use at the Pennsylvania State University (PSU) by the Reactor Dynamics and Fuel Modeling Group (RDFMG) and has been improved, updated, and subsequently re-branded as CTF. As part of the improvement process, it was necessary to generate sufficient documentation for the open-source code which had lacked such material upon being adopted by RDFMG. This document serves mainly as a theory manual for CTF, detailing the many two-phase heat transfer, drag, and important accident scenario models contained in the code as well as the numerical solution process utilized. Coding of the models is also discussed, all with consideration for updates that have been made when transitioning from COBRA-TF to CTF. Further documentation outside of this manual is also available at RDFMG which focus on code input deck generation and source code global variable and module listings

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2022

HiPACE++: A portable, 3D quasi-static particle-in-cell code

Modeling plasma accelerators is a computationally challenging task and the quasi-static particle-in-cell algorithm is a method of choice in a wide range of situations. In this work, we present the first performance-portable, quasi-static, three-dimensional particle-in-cell code HiPACE++. By decomposing all the computation of a 3D domain in successive 2D transverse operations and choosing appropriate memory management, HiPACE++ demonstrates orders-of-magnitude speedups on modern scientific GPUs over CPU-only implementations. The 2D transverse operations are performed on a single GPU, avoiding time-consuming communications. The longitudinal parallelization is done through temporal domain decomposition, enabling near-optimal strong scaling from 1 to 512 GPUs. HiPACE++ is a modular, open-source code enabling efficient modeling of plasma accelerators from laptops to state-of-the-art supercomputers.

97 MATHEMATICS AND COMPUTING↗

NASA NTRSDate not supplied

High School Citizen Scientists Use AI/ML to Predict Intra-Ocular Pressure From Gene Expression Data for Spaceflown Mice

Artificial Intelligence (AI) and Machine Learning (ML) have increasingly become pivotal in biological and biomedical research, largely due to the culture of open data sharing and its associated benefits. The methodologies inherent in AI/ML are particularly adept at identifying and forecasting biological phenotypes from the vast amounts of data generated by next-generation sequencing technologies. These techniques offer substantial promise for advancing research in space biosciences and for the development of automated systems for monitoring space health. Nevertheless, there are crucial aspects to consider when training, validating, and testing machine learning models in both biological research and clinical contexts. It is essential that Open Science principles, including data sharing and the availability of open-source code, are complemented by high-quality, publicly accessible training resources. These resources should focus on best practices and include modules based on real-world scientific cases and data to ensure that future AI/ML practitioners gain practical experience with genuine problems. Addressing this knowledge gap, we have designed, developed, and delivered both interactive and self-paced training programs for citizen scientists worldwide, enabling them to utilize AI/ML for space biology research. This initiative was made possible through generous funding from a Transformation to Open Science Training grant. The interactive training sessions, conducted this summer, utilized AI/ML techniques to analyze data from the Open Science Data Repository, specifically targeting the effects of spaceflight on ocular structure and function. The dataset OSD-583, from the Rodent Research 9 mission, provides experimental data detailing the ocular responses of mice subjected to a 35-day spaceflight, compared with ground control counterparts. Using OSD-583 as observational data, our summer training participants applied AI/ML methods to predict intraocular pressure from RNA-seq data and identify the genes most predictive of the observed responses. Further analysis through pathway enrichment and gene set enrichment revealed that these genes are involved in molecular and cellular processes contributing to retinal degeneration.

James Casaletto↗

DOE OSTI2023

High-order finite element method for atomic structure calculations

We introduce featom, an open source code that implements a high-order finite element solver for the radial Schrödinger, Dirac, and Kohn-Sham equations. The formulation accommodates various mesh types, such as uniform or exponential, and the convergence can be systematically controlled by increasing the number and/or polynomial order of the finite element basis functions. The Dirac equation is solved using a squared Hamiltonian approach to eliminate spurious states. Here, to address the slow convergence of the $κ=±1$ states due to divergent derivatives at the origin, we incorporate known asymptotic forms into the solutions. We achieve a high level of accuracy (10 -8 Hartree) for total energies and eigenvalues of heavy atoms such as uranium in both Schrödinger and Dirac Kohn-Sham solutions. We provide detailed convergence studies and computational parameters required to attain commonly required accuracies. Finally, we compare our results with known analytic results as well as the results of other methods. In particular, we calculate benchmark results for atomic numbers (Z) from 1 to 92, verifying current benchmarks. We demonstrate significant speedup compared to the state-of-the-art shooting solver dftatom. An efficient, modular Fortran 2008 implementation, is provided under an open source, permissive license, including examples and tests, wherein particular emphasis is placed on the independence (no global variables), reusability, and generality of the individual routines.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Combustion of petroleum-based transportation fuels and their blends with biofuels: a new approach for developing surrogates and understanding the effects of blending

Accurate and versatile reaction mechanisms are necessary to simulate combustion of transportation fuels blended with biofuels for improving fuel efficiency, reducing fuel consumption and mitigating the formation and emissions of combustion products harmful to the atmosphere. This project involved a combined effort of simulation and experimentation of liquid fuel burning using a combustion configuration amenable to numerical modeling with a level of detail not previously achieved for blends of biofuels with gasoline certification and surrogate fuels. The configuration of an isolated droplet burning under conditions where gas transport arises solely from fuel evaporation was selected as the platform for experiments and numerical modeling. The spherical symmetry and one-dimensional gas transport that results enabled simulating the droplet burning process with an precedented level of detail. Processes associated with unsteady gas and liquid transport, formation of particulate and gaseous products, radiation, multicomponent phase equilibrium at the droplet surface and moving boundary effects from droplet evaporation, were incorporated in a single numerical framework. The numerical model was based on the open source code OPENSmoke++ (OS) adapted to incorporate the effects noted above. In addition to simulation, an experimental design was developed for the isolated droplet configuration to acquire the data needed for validating the numerical model. Several broad accomplishments of the project were the following: demonstrating generally excellent agreement between measured and simulated combustion parameters for the fuel blends examined that included mixtures of heptane and isobutanol as a model system, and surrogates comprised of up to seven miscible components mixed with ethanol or isobutanol as representative biofuel additives; using a new approach to validate reaction mechanisms of biofuel blends which incorporated fuel evaporation into the process along with developing an experimental design for acquiring data to compare with simulations; and showing that a wealth of information could be obtained on the combustion physics of biofuels from experiments requiring volumes on the order of only nanoliters at a time thus opening the way to evaluating biofuels synthesized by new processes early in development.

02 PETROLEUM↗

NASA NTRS2019

Integration of MAC/GMC into CalculiX, an Open Source Finite Element Code

An analysis framework is presented that makes available multiscale analysis of composite structures using the open-source FEA solver package CalculiX CrunchiX (CCX). At the center of this framework is the coupling of the Finite Element Analysis - Micromechanics Analysis Code (FEAMAC) library from NASA's Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) to allow micromechanics analysis. The results show that the proposed coupling can be used with appropriate care for multiscale FEA simulations of composite materials. The largest error reported in this validation was in a four-point bend test specimen with an error of less than 1% difference in the maximum deflection of the beam.

Yapor Genao, Francisco A.↗