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NASA NTRSDate not supplied

Science Workflows using Kamodo

Kamodo is a powerful python software package based on data functionalization. Once a given data set is functionalized, a large variety of capabilities are easily accessible in Kamodo, including unit conversions, custom analysis via function composition, interactive publication quality visualizations, and LaTeX encoding. The entirety of capabilities available in Kamodo are easily applied to both simulated and observed data across the multiple domains of Heliophysics and even in other disciplines. This work includes a variety of science workflows using Kamodo in combination with other resources, including with other python software packages, that expand the utility of Kamodo even further. These workflows include model-data comparisons, ensemble modeling examples, satellite mission planning examples, and other applications, all of which are freely available on CCMC’s Kamodo Github page for the community to adapt to their own uses (https://github.com/nasa/Kamodo). We invite the community to use these workflows and to contribute their own to share.

software↗

NASA NTRSDate not supplied

Science Workflows using Kamodo

python↗

NASA NTRS1990

System identification in the repetition domain

Procedures for system identification using realization theory in conjunction with learning control ideas are developed. The Markov parameters of the system are identified by combining data from repeated experiments. Three approaches are discussed for identification of as many Markov parameters as sample points in the experiment. Making use of all the parameters, realization theory is then employed to determine the system order and to obtain a minimal order representation. The first two approaches are non-recursive, which in the case of noise-free data yields a one step solution. The third approach uses a recursive formulation rendered from adaptive control but modified for successive experiments. A simple example shows the numerical convergence of the identified parameters as a function of the number of experiments. The procedure presented herein is an extension of the existing Eigensystem Realization Algorithm (ERA), which has been successfully applied for system identification of large structures.

Juang, Jer-Nan↗

DOE OSTI2022

A Decision-Making Machine Learning Approach in Hermite Spectral Approximations of Partial Differential Equations

The accuracy and effectiveness of Hermite spectral methods for the numerical discretization of partial differential equations on unbounded domains are strongly affected by the amplitude of the Gaussian weight function employed to describe the approximation space. This is particularly true if the problem is under-resolved, i.e., there are no enough degrees of freedom. The issue becomes even more crucial when the equation under study is time-dependent, forcing in this way the choice of Hermite functions where the corresponding weight depends on time. In order to adapt dynamically the approximation space, it is here proposed an automatic decision-making process that relies on machine learning techniques, such as deep neural networks and support vector machines. The algorithm is numerically tested with success on a simple 1D problem, but the main goal is its exportability in the context of more serious applications. Here we also show at the end an application in the framework of plasma physics.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2012

The Mechanisms for the Onset and Explosive Eruption of Coronal Mass Ejections and Eruptive Flares

We have investigated the onset and acceleration of coronal mass ejections (CMEs) and eruptive flares. To isolate the eruption physics, our study uses the breakout model, which is insensitive to the energy buildup process leading to the eruption. We performed 2.5D simulations with adaptive mesh refinement that achieved the highest overall spatial resolution to date in a CME/eruptive flare simulation. The ultra-high resolution allows us to separate clearly the timing of the various phases of the eruption. Using new computational tools, we have determined the number and evolution of all X- and O-type nulls in the system, thereby tracking both the progress and the products of reconnection throughout the computational domain. Our results show definitively that CME onset is due to the start of fast reconnection at the breakout current sheet. Once this reconnection begins, eruption is inevitable; if this is the only reconnection in the system, however, the eruption will be slow. The explosive CME acceleration is triggered by fast reconnection at the flare current sheet. Our results indicate that the explosive eruption is caused by a resistive instability, not an ideal process. Moreover, both breakout and flare reconnections begin first as a form of weak tearing characterized by a slowly evolving plasmoids, but eventually transition to a fast form with well-defined Alfvenic reconnection jets and rapid flux transfer. This transition to fast reconnection is required for both CME onset and explosive acceleration. We discuss the key implications of our results for CME/flare observations and for theories of magnetic reconnection.

Karpen, Judith T.↗

DOE OSTI2025

Summer Internship Report: ARA2 Benchmarking

Over the past decade, the RISC-V Instruction Set Architecture (ISA) has emerged as a significant player in both academic and industrial processor design due to its open-source nature, modular extension system, and versatility across domains ranging from microcontrollers to high-performance computing (HPC). One of its most important recent advancements is the RISC-V Vector Extension (RVV), which enables explicit data-level parallelism through vector registers and vectorized instructions. Unlike traditional SIMD (Single Instruction, Multiple Data) architectures that fix vector lengths at design time, RVV uses the concept of VLEN (vector register length) as a hardware-independent parameter and allows software to adapt dynamically to the available vector width. This flexible approach ensures portability across implementations while enabling scalable performance. The ARA2 core is a parameterizable RISC-V vector processor developed at the Integrated Systems Lab at ETH Zürich and the University of Bologna. Designed as a tightly-coupled accelerator to a scalar RISC-V core, ARA2 implements the RVV 1.0 specification and offers tunable architectural parameters such as the number of vector lanes, VLEN, and cache sizes.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2006

Flexible Generation of Kalman Filter Code

Domain-specific program synthesis can automatically generate high quality code in complex domains from succinct specifications, but the range of programs which can be generated by a given synthesis system is typically narrow. Obtaining code which falls outside this narrow scope necessitates either 1) extension of the code generator, which is usually very expensive, or 2) manual modification of the generated code, which is often difficult and which must be redone whenever changes are made to the program specification. In this paper, we describe adaptations and extensions of the AUTOFILTER Kalman filter synthesis system which greatly extend the range of programs which can be generated. Users augment the input specification with a specification of code fragments and how those fragments should interleave with or replace parts of the synthesized filter. This allows users to generate a much wider range of programs without their needing to modify the synthesis system or edit generated code. We demonstrate the usefulness of the approach by applying it to the synthesis of a complex state estimator which combines code from several Kalman filters with user-specified code. The work described in this paper allows the complex design decisions necessary for real-world applications to be reflected in the synthesized code. When executed on simulated input data, the generated state estimator was found to produce comparable estimates to those produced by a handcoded estimator

Richardson, Julian↗

DOE OSTI2020

Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease

DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific PIKK. Here, we find that DNA-PKcs is widely distributed in invertebrates, fungi, plants, and protists, and that threonines 2609, 2638, and 2647 of the ABCDE cluster of phosphorylation sites are highly conserved amongst most Eukaryotes. Furthermore, we identify highly conserved amino acid sequence motifs and domains that are characteristic of DNA-PKcs relative to other PIKKs. These include residues in the Forehead domain and a novel motif we have termed YRPD, located in an α helix C-terminal to the ABCDE phosphorylation site loop. Combining sequence with biochemistry plus structural data on human DNA-PKcs unveils conserved sequence and conformational features with functional insights and implications. The defined generally progressive DNA-PKcs sequence diversification uncovers conserved functionality supported by Evolutionary Trace analysis, suggesting that for many organisms both functional sites and evolutionary pressures remain identical due to fundamental cell biology. The mining of cancer genomic data and germline mutations causing human inherited disease reveal that robust DNA-PKcs activity in tumors is detrimental to patient survival, whereas germline mutations compromising function are linked to severe immunodeficiency and neuronal degeneration. We anticipate that these collective results will enable ongoing DNA-PKcs functional analyses with biological and medical implications.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1993

Compatibility of information and mode of control: The case for natural control systems

The operation of control systems has been determined largely by mechanical constraints. Compatibility with the characteristics of the operator is a secondary consideration, with the result that control may never be optimal, control workload may interfere with performance of secondary tasks, and learning may be more difficult and protracted than necessary. With the introduction of a computer in the control loop, the mode of operation can be adapted to the operator, rather than vice versa. The concept of natural control is introduced to describe a system that supports control of the information used by the operator in achieving an intended goal. As an example, control of speed during simulated approach to a pad by helicopter pilots is used to contrast path-speed control with direct control of global optical flow-pattern information. Differences are evidenced in the performance domains of control activity, speed, and global optical flow velocity.

Owen, Dean H.↗

NASA NTRSDate not supplied

Assessment of Quantum ML Applicability for Climate Actions: Comparison of the Variational Quantum Classifier and the Quantum Support Vector Classifier with Classical ML Models

Climate change refers to significant and long-term alterations in the Earth’s climate patterns, typically resulting from human activities that increase greenhouse gas emissions. Addressing climate change is not merely an option but a necessity, demanding creative solutions and efforts from individuals, researchers, communities, and governments. Despite the capabilities of machine learning (ML) with data-driven solutions promising to combat climate change-related problems, they face challenges stemming from traditional computational methods and prolonged training times, impeding their practical utility. Recent strides in quantum computing have permeated diverse domains, spanning from manufacturing engineering and pharmaceutical discovery to the latest frontier of detecting climate anomalies. With the potential to substantially reduce time and computational complexity, quantum computing shows promise in addressing climate change impacts. Its distinctive features will enable the concurrent exploration of expansive solution spaces, making it well-suited for analyzing extensive climate datasets, simulating intricate climate models, optimizing resource allocation, and discerning patterns in climate data for mitigation and adaptation endeavors. This study explores the potential of using Quantum machine learning (QML) techniques on climate and weather data obtained from NASA Giovannis. We used two QML algorithms, the Quantum Support Vector Classifier (QSVC) and the Variational Quantum Classifier (VQC) models, using the IBM Qiskit ML 0.7.2 ecosystem. We used an actual 127-Qubit IBM Quantum Computer (IBM 127-qubit Eagle) in this study. The methodology and results sections describe the experiences gained from applying and evaluating quantum ML results on climate and weather data obtained from NASA satellites as a novel practical application of quantum computing.

Earth Observational Data↗

NASA NTRS1991

Integrated adaptive filtering and design for control experiments of flexible structures

A novel method is presented of identifying a state space model and a state estimator for linear stochastic systems from input and output data. The method is primarily based on the relations between the state space model and the finite difference model for linear stochastic systems derived through projection filters. It is proven that least squares identification of a finite difference model converges to the model derived from the projection filters. System pulse response samples are computed from the coefficients of the finite difference model. In estimating the corresponding state estimator gain, a z-domain method is used. First the deterministic component of the output is subtracted out, and then the state estimator gain is obtained by whitening the remaining signal. Experimental example is used to illustrate the feasibility of the method.

Huang, Jen-Kuang↗

DOE OSTI2025

The mevalonate pathway of isoprenoid biosynthesis supports metabolic flexibility in Mycobacterium marinum

ABSTRACT Isoprenoids are a diverse class of natural products that are essential in all domains of life. Most bacteria synthesize isoprenoids through either the methylerythritol phosphate (MEP) pathway or the mevalonate (MEV) pathway, while a small subset encodes both pathways, including the pathogen Mycobacterium marinum (Mm). It is unclear whether the MEV pathway is functional in Mm, or why Mm encodes seemingly redundant metabolic pathways. Here, we show that the MEP pathway is essential in Mm, while the MEV pathway is dispensable in culture, with the ΔMEV mutant having no growth defect in axenic culture but a competitive growth defect compared to WT Mm. We found that the MEV pathway does not play a role in ex vivo or in vivo acute infection but does play a role in survival of peroxide stress. Metabolite profiling revealed that modulation of the MEV pathway causes compensatory changes in the concentration of MEP intermediates DOXP and CDP-ME, suggesting that the MEV pathway is functional and that the pathways interact at the metabolic level. Finally, the MEV pathway is upregulated early in the shift down to hypoxia, suggesting that it may provide metabolic flexibility to this bacterium. Interestingly, we found that our complemented strains, which vary in copy number of the polyprenyl synthetase idsB2 , responded differently to peroxide and UV stresses, suggesting a role for this gene as a determinant of downstream prenyl phosphate metabolism. Together, these findings suggest that MEV may serve as an anaplerotic pathway to make isoprenoids under stress conditions. IMPORTANCE Organisms from all domains of life utilize isoprenoids to carry out thousands of critical and auxiliary cellular processes, including signaling, maintaining membrane integrity, stress response, and host-pathogen interactions. The common precursor of all isoprenoids is synthesized via one of two biosynthetic pathways. Importantly, some bacteria encode both pathways, including M. marinum . We found that only one pathway is essential in M. marinum , while the nonessential pathway may confer metabolic flexibility to help the bacterium better adapt to various environmental conditions. We also found that the polyprenyl synthetase IdsB2 plays an important role in driving such phenotypes. Further, we demonstrate metabolic interplay between both functional pathways. These insights represent the first characterization of isoprenoid biosynthesis in dual pathway-encoding mycobacteria.

Qabar, Christine M. [Department of Plant and Micro↗

DOE OSTI2021

Design and analysis of a wake model for spatially heterogeneous flow

Abstract. Methods of turbine wake modeling are being developed to more accurately account for spatially variant atmospheric conditions within wind farms. Most current wake modeling utilities are designed to apply a uniform flow field to the entire domain of a wind farm. When this method is used, the accuracy of power prediction and wind farm controls can be compromised depending on the flow-field characteristics of a particular area. In an effort to improve strategies of wind farm wake modeling and power prediction, FLOw Redirection and Induction in Steady State (FLORIS) was developed to implement sophisticated methods of atmospheric characterization and power output calculation. In this paper, we describe an adapted FLORIS model that features spatial heterogeneity in flow-field characterization. This model approximates an observed flow field by interpolating from a set of atmospheric measurements that represent local weather conditions. The objective of this method is to capture heterogeneous atmospheric effects caused by site-specific terrain features, without explicitly modeling the geometry of the wind farm terrain. The implemented adaptations were validated by comparing the simulated power predictions generated from FLORIS to the actual recorded wind farm output from the supervisory control and data acquisition (SCADA) recordings and large eddy simulations (LESs). When comparing the performance of the proposed heterogeneous model to homogeneous FLORIS simulations, the results show a 14.6 % decrease for mean absolute error (MAE) in wind farm power output predictions for cases using wind farm SCADA data and a 18.9 % decrease in LES case studies. The results of these studies also indicate that the efficacy of the proposed modeling techniques may vary with differing site-specific operational conditions. This work quantifies the accuracy of wind plant power predictions under heterogeneous flow conditions and establishes best practices for atmospheric surveying for wake modeling.

17 WIND ENERGY↗

NASA NTRS1991

Design alternatives for process group membership and multicast

Process groups are a natural tool for distributed programming, and are increasingly important in distributed computing environments. However, there is little agreement on the most appropriate semantics for process group membership and group communication. These issues are of special importance in the Isis system, a toolkit for distributed programming. Isis supports several styles of process group, and a collection of group communication protocols spanning a range of atomicity and ordering properties. This flexibility makes Isis adaptable to a variety of applications, but is also a source of complexity that limits performance. This paper reports on a new architecture that arose from an effort to simplify Isis process group semantics. Our findings include a refined notion of how the clients of a group should be treated, what the properties of a multicast primitive should be when systems contain large numbers of overlapping groups, and a new construct called the casuality domain. As an illustration, we apply the architecture to the problem of converting processes into fault-tolerant process groups in a manner that is 'transparent' to other processes in the system.

Birman, Kenneth P.↗

DOE OSTI2023

A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass

Abstract Switchgrass, a forage and bioenergy crop, occurs as two main ecotypes with different but overlapping ranges of adaptation. The two ecotypes differ in a range of characteristics, including flowering time. Flowering time determines the duration of vegetative development and therefore biomass accumulation, a key trait in bioenergy crops. No causal variants for flowering time differences between switchgrass ecotypes have, as yet, been identified. In this study, we mapped a robust flowering time quantitative trait locus (QTL) on chromosome 4K in a biparental F2 population and characterized the flowering-associated transcription factor gene PvHd1, an ortholog of CONSTANS in Arabidopsis and Heading date 1 in rice, as the underlying causal gene. Protein modeling predicted that a serine to glycine substitution at position 35 (p.S35G) in B-Box domain 1 greatly altered the global structure of the PvHd1 protein. The predicted variation in protein compactness was supported in vitro by a 4 °C shift in denaturation temperature. Overexpressing the PvHd1-p.35S allele in a late-flowering CONSTANS-null Arabidopsis mutant rescued earlier flowering, whereas PvHd1-p.35G had a reduced ability to promote flowering, demonstrating that the structural variation led to functional divergence. Our findings provide us with a tool to manipulate the timing of floral transition in switchgrass cultivars and, potentially, expand their cultivation range.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Customizable adaptive regularization techniques for B-spline modeling

B-spline models are a powerful way to represent scientific data sets with a functional approximation. However, these models can suffer from spurious oscillations when the data to be approximated are not uniformly distributed. Model regularization (i.e., smoothing) has traditionally been used to minimize these oscillations; unfortunately, it is sometimes impossible to sufficiently remove unwanted artifacts without smoothing away key features of the data set. In this article, we present a method of model regularization that preserves significant features of a data set while minimizing artificial oscillations. Our method varies the strength of a smoothing parameter throughout the domain automatically, removing artifacts in poorly-constrained regions while leaving other regions unchanged. Further, the proposed method selectively incorporates regularization terms based on first and second derivatives to maintain model accuracy while minimizing numerical artifacts. The behavior of our method is validated on a collection of two- and three-dimensional data sets produced by scientific simulations. In addition, a key tuning parameter is highlighted and the effects of this parameter are presented in detail. This paper is an extension of our previous conference paper at the 2022 International Conference on Computational Science (ICCS) (Lenz et al., 2022).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Analyzing historical snow trends in interior Alaska

Study region The Chena River watershed in Interior Alaska, USA Study focus This study examines 40 years (water years 1982–2021) of snowpack characteristics to consider its hydrological implications in the 5350 km² Chena River basin. Using observations and a fine-scale physics model, we analyzed trends of snow water equivalent (SWE), snow onset and disappearance, and snow cover duration (SCD). New hydrological insights for the region Results indicate a decline in SWE across the modeled domain, averaging a decrease of 3 mm per decade, with larger decreases (up to 10 mm per decade) at lower elevations. While domain-averaged SWE trends were not statistically significant, observed SCD showed statistically significant decreases: −5.2, −5.0, and −4.4 days per decade at Teuchet Creek, Fairbanks F.O., and Little Chena Ridge, respectively. Notably, observations at SNOTEL stations and modeling revealed no statistically significant change in domain-averaged Rain-on-Snow (ROS) events over the 40-year period, contrasting some regional future estimates of increased ROS frequency. Peak streamflow did not consistently correlate with peak SWE levels, suggesting that other environmental factors such as ROS events and rapid temperature increases (e.g., a 10°C spike observed in 1992) are key drivers of hydrological outcomes. These findings improve understanding of complex subarctic hydrological processes impacting permafrost and highlight the need for adaptive water resource management to mitigate multi-factor risks like flooding and wildfire, requiring proactive planning.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Decoding the protein–ligand interactions using parallel graph neural networks

Abstract Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures: $$\hbox {GNN}_{\mathrm{F}}$$ GNN F is the base implementation that employs distinct featurization to enhance domain-awareness, while $$\hbox {GNN}_{\mathrm{P}}$$ GNN P is a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and 0.958 for $$\hbox {GNN}_{\mathrm{P}}$$ GNN P for predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 with $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and $$\hbox {GNN}_{\mathrm{P}}$$ GNN P , respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of $$\hbox {GNN}_{\mathrm{P}}$$ GNN P on SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.

59 BASIC BIOLOGICAL SCIENCES↗