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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,441 records · Page 80
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Predicting fracture behavior in single crystal nickel using a coupled crystal plasticity phase field damage approach

Understanding the fracture behavior of single crystal metals is critical for predicting material performance under mechanical loading. Here, in this study, we investigate the fracture characteristics of single crystal nickel tensile bars using a crystal plasticity coupled phase field damage (CP-PFD) model. Experimental tensile tests were conducted on 15 specimens spanning five crystallographic orientations and three thickness variants per orientation. The results revealed two distinct fracture modes: brittle fractures with 45-degree angled surfaces and ductile fractures characterized by significant necking. The CP-PFD model successfully replicated these fracture behaviors, demonstrating strong agreement with experimental observations. The model effectively predicted the strain at which necking and fracture occurred, as well as the orientation-dependent fracture mechanisms. By comparing experimental and simulated fracture surfaces, we establish the CP-PFD model as a robust tool for predicting single crystal behavior and damage evolution. This work provides insight into the microstructural dependence of fracture behavior and establishes a predictive framework for modeling orientation-dependent damage evolution in single-crystal nickel.

Crystal plasticity↗
DOE OSTI2024

Experimental investigation of probabilistic failure of SiC/SiC composite tubes under multiaxial loading

This paper presents an experimental investigation of the failure behavior of SiC fiber-reinforced SiC matrix (SiC/SiC) composite tubes under multiaxial loading. A new testing apparatus is designed to independently apply axial stress and internal pressure to SiC/SiC tubes. Acoustic emission (AE) is used to monitor the damage growth in the specimen. Based on the measured stress–strain response, a strain-based criterion is proposed to determine the proportional limit stress (PLS). The proposed strain-based criterion is compared with the PLS determined by the AE measurement. The PLS is determined for different loading ratios to form a multiaxial failure surface. By testing multiple replicates, the statistical variations of the PLS are determined. In conclusion, based on the experimental results, a mathematical model is developed to characterize the probability distribution of the PLS of SiC/SiC composites under multiaxial loading.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Standards, dissemination, and best practices in systems biology

In this study, the reproducibility of scientific research is crucial to the success of the scientific method. Here, we review the current best practices when publishing mechanistic models in systems biology. We recommend, where possible, to use software engineering strategies such as testing, verification, validation, documentation, versioning, iterative development, and continuous integration. In addition, adhering to the Findable, Accessible, Interoperable, and Reusable modeling principles allows other scientists to collaborate and build off of each other’s work. Existing standards such as Systems Biology Markup Language, CellML, or Simulation Experiment Description Markup Language can greatly improve the likelihood that a published model is reproducible, especially if such models are deposited in well-established model repositories. Where models are published in executable programming languages, the source code and their data should be published as open-source in public code repositories together with any documentation and testing code. For complex models, we recommend container-based solutions where any software dependencies and the run-time context can be easily replicated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Aggregate attack surface management for network discovery of operational technology

Interconnectivity has become a substratum of technology as the benefits of data-driven functionality are being realized in nearly all industries. Increased connectivity of Operational Technology (OT) exacerbates cyber risks because Industrial Control Systems (ICS) are becoming exposed to the Internet. These exposures are often done inadvertently through misconfigurations as additional network devices come online. Attack surface management (ASM) platforms can be used to identify vulnerabilities by performing external network discovery over the Internet using web spiders. These web spiders enable big data analytics of Internet of Things (IoT) devices as identifiable information of Internet-exposed equipment are archived in searchable databases that are made publicly available. There are a multitude of ASM service providers on the market. Here, this study was conducted to evaluate several commonly known tools to determine the aggregate attack surface of control systems. Queries were crafted by targeting commonly known manufacturers and communication protocols found in OT networks. Identified devices were that categorized based on technology types. Each query was replicated between several tools to target identical ICS equipment. Findings in this paper suggested a significant variance in the exposures discovered by each tool, but unique contributions were identified for each tool when a merged attack surface was derived. Therefore, all tools should be used in aggregate.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

A sparse matrix–vector multiplication based algorithm for accurate density matrix computations on systems of millions of atoms

Here we present an efficient sparse matrix–vector (SpMV) based method to compute the density matrix P from a given Hamiltonian in electronic structure computations. Our method is a hybrid approach based on Chebyshev–Jackson approximation theory and matrix purification methods like the second order spectral projection purification (SP2). Recent methods to compute the density matrix scale as O(N) in the number of floating point operations but are accompanied by large memory and communication overhead, and they are based on iterative use of the sparse matrix–matrix multiplication kernel (SpGEMM), which is known to be computationally irregular. In addition to irregularity in the sparse Hamiltonian H, the nonzero structure of intermediate estimates of P depends on products of H and evolves over the course of computation. On the other hand, an expansion of the density matrix P in terms of Chebyshev polynomials is straightforward and SpMV based; however, the resulting density matrix may not satisfy the required constraints exactly. In this paper, we analyze the strengths and weaknesses of the Chebyshev–Jackson polynomials and the second order spectral projection purification (SP2) method, and propose to combine them so that the accurate density matrix can be computed using the SpMV computational kernel only, and without having to store the density matrix P. Our method accomplishes these objectives by using the Chebyshev polynomial estimate as the initial guess for SP2, which is followed by using sparse matrix–vector multiplications (SpMVs) to replicate the behavior of the SP2 algorithm for purification. We demonstrate the method on a tight-binding model system of an oxide material containing more than 3 million atoms. In addition, we also present the predicted behavior of our method when applied to near-metallic Hamiltonians with a wide energy spectrum.

42 ENGINEERING↗
DOE OSTI2025

Particle collisionality in scaled kinetic plasma simulations

Kinetic plasma processes, such as magnetic reconnection, collisionless shocks, and turbulence, are fundamental to the dynamics of astrophysical and laboratory plasmas. Simulating these processes often requires particle-in-cell (PIC) methods, but the computational cost of fully kinetic simulations can necessitate the use of artificial parameters, such as a reduced speed of light and ion-to-electron mass ratio, to decrease expense. While these approximations can preserve overall dynamics under specific conditions, they introduce nontrivial impacts on particle collisionality that are not yet well understood. In this work, we develop a method to scale particle collisionality in simulations employing an artificial speed of light and/or an artificial ion-to-electron mass ratio. By introducing species-dependent scaling factors, we independently adjust inter- and intra-species collision rates to better replicate the collisional properties of the physical system. Our approach maintains the fidelity of electron and ion transport properties while preserving critical relaxation rates, such as energy exchange timescales, within the limits of weakly collisional plasma theory. Furthermore, we demonstrate the accuracy of this scaling method through benchmarking tests against theoretical relaxation rates and connecting to fluid theory, highlighting its ability to retain key transport properties. Existing collisional PIC implementations can be easily modified to include this scaling, which will enable deeper insights into the behavior of marginally collisional plasmas across various contexts.

Totorica, S. R. [Princeton Univ., NJ (United State↗
DOE OSTI2024

Integrated multimodel analysis reveals achievable pathways toward reliable, 100% renewable electricity for Los Angeles

Climate change has prompted many communities to set targets for carbon-free power supplies, but they often lack data-driven strategies to achieve them. We present a comprehensive analysis of an entirely renewable electric power system that can maintain operating reliability and resource adequacy using detailed models of the city of Los Angeles power grid. In consultation with the operating utility, the Los Angeles Department of Water and Power (LADWP), and the local community, we develop four supply scenarios across three demand projections to analyze which types of infrastructure and operational changes would achieve reliable electricity at least cost. We find that a reliable, 100%-renewable power system yielding more than $1 billion annually in health and climate co-benefits is achievable. Solar can supply most future energy needs, while combustion turbines that use renewable, storable carbon-neutral fuels are key to maintaining reliability. This study provides a replicable methodology that other jurisdictions globally can follow.

14 SOLAR ENERGY↗
DOE OSTI2022

SPARC: Structural properties associated with residue constraints

SPARC facilitates the generation of plausible hypotheses regarding underlying biochemical mechanisms by structurally characterizing protein sequence constraints. Such constraints appear as residues co-conserved in functionally related subgroups, as subtle pairwise correlations (i.e., direct couplings), and as correlations among these sequence features or with structural features. SPARC performs three types of analyses. First, based on pairwise sequence correlations, it estimates the biological relevance of alternative conformations and of homomeric contacts, as illustrated here for death domains. Second, it estimates the statistical significance of the correspondence between directly coupled residue pairs and interactions at heterodimeric interfaces. Third, given molecular dynamics simulated structures, it characterizes interactions among constrained residues or between such residues and ligands that: (a) are stably maintained during the simulation; (b) undergo correlated formation and/or disruption of interactions with other constrained residues; or (c) switch between alternative interactions. We illustrate this for two homohexameric complexes: the bacterial enhancer binding protein (bEBP) NtrC1, which activates transcription by remodeling RNA polymerase (RNAP) containing σ 54 , and for DnaB helicase, which opens DNA at the bacterial replication fork. Based on the NtrC1 analysis, we hypothesize possible mechanisms for inhibiting ATP hydrolysis until ADP is released from an adjacent subunit and for coupling ATP hydrolysis to restructuring of σ 54 binding loops. Based on the DnaB analysis, we hypothesize that DnaB ‘grabs’ ssDNA by flipping every fourth base and inserting it into cavities between subunits and that flipping of a DnaB-specific glutamine residue triggers ATP hydrolysis.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Numerical investigation of mixing and heat transfer in a 7.9 m JP-8 pool fire

The response of objects engulfed in, and adjacent to, large-scale pool fires is of interest in accident and safety assessments. In this study, Fuego, a low-Mach turbulent reacting flow code was used to study conjugate heat transfer in a 7.9 m diameter JP-8 pool fire. Simulations were designed to replicate past experimental measurements (Blanchat et al., 2006) of incident heat flux to three cylindrical calorimeters in and around the pool fire. Two turbulent combustion models were compared directly - the eddy dissipation concept and a more recently developed unsteady flamelet model. First and second order spatial and temporal discretization schemes were also compared to assess the performance of low-dissipation numerical operators. Heat flux predictions to the transportation size calorimeter outside the fire were within experimental uncertainties. Inside the fire, experimental measurements were higher than predicted values and may have been a consequence of soot deposition and augmented participating media radiation from soot and fuel vapor. Simulation predictions improved in cases where turbulent kinetic energy and mixing were more resolved. This work, and others referenced herein, suggest that spatial resolution on the order of 0.5–1.0 cm may be required to fully resolve fluid instabilities, vortex production between fire plumes and crosswind, soot production, and fuel-air mixing. This presents a substantial computational challenge for safety assessments of engulfed objects in fully turbulent pool fires.

Conjugate heat transfer↗
DOE OSTI2016

The Eukaryotic Replisome Goes Under the Microscope

The machinery at the eukaryotic replication fork has seen many new structural advances using EM and crystallography. Recent structures of eukaryotic replisome components include the Mcm2-7 complex, the CMG helicase, DNA polymerases, a Ctf4 trimer hub and the first look at a core replisome of 20 different proteins containing the helicase, primase, leading polymerase and a lagging strand polymerase. The eukaryotic core replisome shows an unanticipated architecture, with one polymerase sitting above the helicase and the other below. Additionally, structures of Mcm2 bound to an H3/H4 tetramer suggest a direct role of the replisome in handling nucleosomes, which are important to DNA organization and gene regulation. This review provides a summary of some of the many recent advances in the structure of the eukaryotic replisome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Long-term CRISPR locus dynamics and stable host-virus co-existence in subsurface fractured shales

Viruses are the most ubiquitous biological entities on Earth. Even so, elucidating the impact of viruses on microbial communities and associated ecosystem processes often requires identification of unambiguous host-virus linkages-an undeniable challenge in many ecosystems. Subsurface fractured shales present a unique opportunity to first make these strong linkages via spacers in CRISPR-Cas arrays and subsequently reveal complex long-term host-virus dynamics. Here, we sampled two replicated sets of fractured shale wells for nearly 800 days, resulting in 78 metagenomes from temporal sampling of six wells in the Denver-Julesburg Basin (Colorado, USA). At the community level, there was strong evidence for CRISPR-Cas defense systems being used through time and likely in response to viral interactions. Within our host genomes, represented by 202 unique MAGs, we also saw that CRISPR-Cas systems were widely encoded. Together, spacers from host CRISPR loci facilitated 2,110 CRISPR-based viral linkages across 90 host MAGs spanning 25 phyla. We observed less redundancy in host-viral linkages and fewer spacers associated with hosts from the older, more established wells, possibly reflecting enrichment of more beneficial spacers through time. Leveraging temporal patterns of host-virus linkages across differing well ages, we report how host-virus co-existence dynamics develop and converge through time, possibly reflecting selection for viruses that can evade host CRISPR-Cas systems. Together, our findings shed light on the complexities of host-virus interactions as well as long-term dynamics of CRISPR-Cas defense among diverse microbial populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Close encounters: Moving along bumps, breaks, and bubbles on expanded trinucleotide tracts

Expansion of simple triplet repeats (TNR) underlies greater than 30 severe degenerative diseases. There is a good understanding of the major pathways generating an expansion, and the associated polymerases that operate during gap filling synthesis at these “difficult to copy” sequences. However, the mechanism by which a TNR is repaired depends on the type of lesion, the structural features imposed by the lesion, the assembled replication/repair complex, and the polymerase that encounters it. The relationships among these parameters are exceptionally complex and how they direct pathway choice is poorly understood. In this review, we consider the properties of polymerases, and how encounters with GC-rich or abnormal structures might influence polymerase choice and the success of replication and repair. Insights over the last three years have highlighted new mechanisms that provide interesting choices to consider in protecting genome stability.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Synergistic effects of H3 and H4 nucleosome tails on structure and dynamics of a lesion-containing DNA: Binding of a displaced lesion partner base to the H3 tail for GG-NER recognition

How DNA lesions in nucleosomes are recognized for global genome nucleotide excision repair (GG-NER) remains poorly understood, and the roles that histone tails may play remains to be established. Histone H3 and H4 N-terminal tails are of particular interest as their acetylation states are important in regulating nucleosomal functions in transcription, replication and repair. In particular the H3 tail has been the focus of recent attention as a site for the interaction with XPC, the GG-NER lesion recognition factor. Here we have investigated how the structure and dynamics of the DNA lesion cis-B[a]P-dG, derived from the environmental carcinogen benzo[a]pyrene (B[a]P), is impacted by the presence of flanking H3 and H4 tails. This lesion is well-repaired by GG-NER, and adopts a base-displaced/intercalated conformation in which the lesion partner C is displaced into the major groove. We used molecular dynamics simulations to obtain structural and dynamic characterizations for this lesion positioned in nucleosomal DNA so that it is bracketed by the H3 and H4 tails. The H4 tail was studied in unacetylated and acetylated states, while the H3 tail was unacetylated, its state when it binds XPC (Kakumu, Nakanishi et al., 2017). Our results reveal that upon acetylation, the H4 tail is released from the DNA surface; the H3 tail then forms a pocket that induces flipping and capture of the displaced lesion partner base C. This reveals synergistic effects of the behavior of the two tails. We hypothesize that the dual capability of the H3 tail to sense the displaced lesion partner base and to bind XPC could foster recognition of this lesion by XPC for initiation of GG-NER in nucleosomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

A Specific Mutational Signature Associated with DNA 8-Oxoguanine Persistence in MUTYH-defective Colorectal Cancer

8-Oxoguanine, a common mutagenic DNA lesion, generates G:C > T:A transversions via mispairing with adenine during DNA replication. When operating normally, the MUTYH DNA glycosylase prevents 8-oxoguanine-related mutagenesis by excising the incorporated adenine. Biallelic MUTYH mutations impair this enzymatic function and are associated with colorectal cancer (CRC) in MUTYH-Associated Polyposis (MAP) syndrome. Here in this paper, we perform whole-exome sequencing that reveals a modest mutator phenotype in MAP CRCs compared to sporadic CRC stem cell lines or bulk tumours. The excess G:C > T:A transversion mutations in MAP CRCs exhibits a novel mutational signature, termed Signature 36, with a strong sequence dependence. The MUTYH mutational signature reflecting persistent 8-oxoG:A mismatches occurs frequently in the APC, KRAS, PIK3CA, FAT4, TP53, FAT1, AMER1, KDM6A, SMAD4 and SMAD2 genes that are associated with CRC. In conclusion, the occurrence of Signature 36 in other types of human cancer indicates that DNA 8-oxoguanine-related mutations might contribute to the development of cancer in other organs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

A Critical Role of Zinc Importer AdcABC in Group A Streptococcus -Host Interactions During Infection and Its Implications for Vaccine Development

Bacterial pathogens must overcome host immune mechanisms to acquire micronutrients for successful replication and infection. Streptococcus pyogenes, also known as group A streptococcus (GAS), is a human pathogen that causes a variety of clinical manifestations, and disease prevention is hampered by lack of a human GAS vaccine. Herein, we report that the mammalian host recruits calprotectin (CP) to GAS infection sites and retards bacterial growth by zinc limitation. However, a GAS-encoded zinc importer and a nuanced zinc sensor aid bacterial defense against CP-mediated growth inhibition and contribute to GAS virulence. Immunization of mice with the extracellular component of the zinc importer confers protection against systemic GAS challenge. Together, we identified a key early stage host-GAS interaction and translated that knowledge into a novel vaccine strategy against GAS infection. Furthermore, we provided evidence that a similar struggle for zinc may occur during other streptococcal infections, which raises the possibility of a broad-spectrum prophylactic strategy against multiple streptococcal pathogens.

GAS vaccine↗
DOE OSTI2019

Deep latency: A new insight into a functional HIV cure

Latent HIV reservoir is the main obstacle that prevents a cure for HIV-1 (HIV). While antiretroviral therapy is effective in controlling viral replication, it cannot eliminate latent HIV reservoirs in patients. Several strategies have been proposed to combat HIV latency, including bone marrow transplantation to replace blood cells with CCR5-mutated stem cells, gene editing to disrupt the HIV genome, and “Shock and Kill” to reactivate latent HIV followed by an immune clearance. However, high risks and limitations to scale-up in clinics, off-target effects in human genomes or failure to reduce reservoir sizes in patients hampered our current efforts to achieve an HIV cure. This necessitates alternative strategies to control the latent HIV reservoirs. This review will discuss an emerging strategy aimed to deeply silence HIV reservoirs, the development of this concept, its potential and caveats for HIV remission/cure, and prospective directions for silencing the latent HIV, thereby preventing viruses from rebound.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Comparison of structurally diverse simulation models for prediction of epidemic outcomes caused by a long-distance dispersed pathogen

Long-distance dispersal (LDD) pathogens pose substantial challenges for epidemic control due to their ability to generate new infection foci at great distances. While various modeling approaches have been developed to understand and manage such outbreaks, little work has compared how models of different structures behave under shared conditions. Here, in this study, we compare four structurally distinct epidemiological models — EPIMUL, GEMF, PoPS, and Warwick — each adapted to simulate the spread of wheat stripe rust (WSR), a wind-dispersed LDD pathogen, under identical epidemiological parameters and dispersal kernel. Using data from a controlled field experiment, we evaluate the ability of each model to replicate disease prevalence under nine intervention scenarios that vary in timing and culling area. While the models differ substantially in design — ranging from spatial grid-based to network-based and raster-based frameworks — the shared dispersal kernel allowed for close alignment in their predictions. All models accurately captured general epidemic trends, particularly the strong effect of early intervention on disease suppression. We qualitatively compared their behavioral responses across scenarios and also evaluated an ensemble prediction by averaging across model outputs. Our findings highlight how integrating shared epidemiological components into distinct modeling frameworks can improve consistency and accuracy, while reinforcing the importance of early culling in managing LDD pathogen outbreaks.

Dispersal kernel↗
DOE OSTI2016

Design, synthesis, and evaluation of a novel series of macrocyclic inhibitors of norovirus 3CL protease

Norovirus infections have a major impact on public health worldwide, yet there is a current dearth of norovirus-specific therapeutics and prophylactics. Furthermore, this report describes the discovery of a novel class of macrocyclic inhibitors of norovirus 3C-like protease, a cysteine protease that is essential for virus replication. SAR, structural, and biochemical studies were carried out to ascertain the effect of structure on pharmacological activity and permeability. Insights gained from these studies have laid a solid foundation for capitalizing on the therapeutic potential of the series of inhibitors described herein.

3CLprotease↗