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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 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies

The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples. We systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy. A high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Disruption of histone acetylation homeostasis reveals multilayered chromatin regulation for transcriptional resiliency

Background Epigenetic modifications, nucleosome occupancy, and three-dimensional chromatin architecture collectively create a multi-layered, highly interactive regulatory system for controlling genomic functionality. Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states. Therapies focused on epigenetic modulation can alter gene expression to correct dysfunction, though the perpetuation of these states and the relationships among chromatin regulatory layers is not well understood. Results Here, we investigated global and local chromatin structural and functional responses after acute histone deacetylase inhibitor treatment (suberoylanilide hydroxamic acid) in lung cancer cells across time. Treatment substantially increased global histone acetylation resulting in a pervasive but not distinctive signature. The spread of acetylation did not significantly impact global chromatin accessibility, and nucleosome remodeling largely occurred at finer scales in functionally relevant genomic regions. Indeed, both H 3 K 4 trimethylation, a mark of active transcription, and gene expression changes were altered in a controlled locus-specific manner, suggesting aberrant acetylation indirectly leads to balanced and bidirectional gene expression profiles from tighter regulation of other chromatin features. HDACi treatment induced (13%) genomic rearrangement in chromatin compartmentalization and moderate weakening of topologically associating domains. Conclusions Continuous wavelet analysis of these features demonstrates that scale-dependent, locus-specific factors influence the relationship between chromatin architecture and functional output, suggesting that regulation of transcription and nucleosome remodeling is not entirely (nor linearly) dependent upon large scale compartment exchange. Structural and functional responses are most pronounced early after treatment with partial persistence of differential local chromatin features and expression later in time; this highlights the plasticity of chromatin regulation, which may have implications for the efficacy of epigenetic treatments. These results demonstrate the effectiveness of multi-layered regulation of transcription: in resilient systems, disruption of one chromatin feature does not distort the regulation of other features in supporting a transcriptional program that allows for survival.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Adaptive language model training for molecular design

Abstract The vast size of chemical space necessitates computational approaches to automate and accelerate the design of molecular sequences to guide experimental efforts for drug discovery. Genetic algorithms provide a useful framework to incrementally generate molecules by applying mutations to known chemical structures. Recently, masked language models have been applied to automate the mutation process by leveraging large compound libraries to learn commonly occurring chemical sequences (i.e., using tokenization) and predict rearrangements (i.e., using mask prediction). Here, we consider how language models can be adapted to improve molecule generation for different optimization tasks. We use two different generation strategies for comparison, fixed and adaptive. The fixed strategy uses a pre-trained model to generate mutations; the adaptive strategy trains the language model on each new generation of molecules selected for target properties during optimization. Our results show that the adaptive strategy allows the language model to more closely fit the distribution of molecules in the population. Therefore, for enhanced fitness optimization, we suggest the use of the fixed strategy during an initial phase followed by the use of the adaptive strategy. We demonstrate the impact of adaptive training by searching for molecules that optimize both heuristic metrics, drug-likeness and synthesizability, as well as predicted protein binding affinity from a surrogate model. Our results show that the adaptive strategy provides a significant improvement in fitness optimization compared to the fixed pre-trained model, empowering the application of language models to molecular design tasks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Recyclable Cellulose Fiber Reinforced Vitrimer Composite

Vitrimer is an innovative class of polymeric materials which demonstrates traditional thermoset-like mechanical and chemical resilience while still being able to flow on demand like a traditional thermoplastic through covalently adaptive dynamic linkages. Herein, high-performance cellulose fiber reinforced vitrimer composites are developed using an epoxy-based vitrimer and natural cellulose paper. The reinforced vitrimer composite was fabricated by impregnating the porous structure of cellulose paper with two curable monomers, followed by in-situ polymerization of the monomers inside the fibrous scaffold. The introduction of hydroxyl group present on the cellulosic framework assisted in a faster topological rearrangement of the crosslinked matrix through transesterification exchange reaction, thus imparting various sought-after properties like shape recovery and recyclability via simple thermal reprocessing. Moreover, the reinforced vitrimer composite exhibits superior tensile properties as high as 90 MPa with 15-25 volume% vitrimer loading due to the interfacial adhesion via ester exchange reaction between the epoxy matrix and functionalities on the cellulosic fibers. Noteworthily, the key ingredients of the resulting composite (i.e., epoxy-based vitrimer and cellulose fibers) can be comfortably recycled without using aggressive chemical treatment, enabling composite to be easily recycled or disposed of at the end of service life and assist in reducing the subsequent manufacturing cost. This study would shed light on the development of a recyclable polymer composite with exceptional mechanical properties while simultaneously demonstrating self-healing and shape memory capabilities.

Rohewal, Sargun Singh↗
DOE OSTI2025

Data for "Viral Delivery of Recombinases Activates Heritable Genetic Switches in Plants"

Viral vectors provide an increasingly versatile platform for transformation-free reagent delivery to plants. RNA viral vectors can be used to induce gene silencing, overexpress proteins, or introduce gene editing reagents; however, they are often constrained by carrying capacity or restricted tropism in germline cells. Site-specific recombinases that catalyze precise genetic rearrangements are powerful tools for genome engineering that vary in size and, potentially, efficacy in plants. In this work, we show that viral vectors based on tobacco rattle virus (TRV) deliver and stably express four recombinases ranging in size from ∼0.6 to ∼1.5 kb and achieve simultaneous marker removal and reporter activation through targeted excision in transgenic Nicotiana benthamiana lines. TRV vectors with Cre, FLP, CinH, and Integrase13 efficiently mediated recombination in infected somatic tissue and led to heritable modifications at high frequency. An excision-activated Ruby reporter enabled simple and high-resolution tracing of infected cell lineages without the need for molecular genotyping. Together, our experiments broaden the scope of viral recombinase delivery and offer insights into infection dynamics that may be useful in developing future viral vectors.

gene editing↗
DOE OSTI2021

Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii

Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and together with deletions that were unassociated with a plasmid insertion, 1470 genes were identified to be affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 253 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4 . The inventory of candidate genes includes 53 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 70 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas , land plants, and/or cyanobacteria; 14 genes encode proteins previously shown to have functions unrelated to photosynthesis. Among the remaining 169 uncharacterized genes, 38 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, will aid in advancing gene discovery and protein functional analysis in photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Stepwise recombination suppression around the mating-type locus in an ascomycete fungus with self-fertile spores

Recombination is often suppressed at sex-determining loci in plants and animals, and at self-incompatibility or mating-type loci in plants and fungi. In fungal ascomycetes, recombination suppression around the mating-type locus is associated with pseudo-homothallism, i.e. the production of self-fertile dikaryotic sexual spores carrying the two opposite mating types. This has been well studied in two species complexes from different families of Sordariales: Podospora anserina and Neurospora tetrasperma. However, it is unclear whether this intriguing association holds in other species. We show here that Schizothecium tetrasporum, a fungus from a third family in the order Sordariales, also produces mostly self-fertile dikaryotic spores carrying the two opposite mating types. This was due to a high frequency of second meiotic division segregation at the mating-type locus, indicating the occurrence of a single and systematic crossing-over event between the mating-type locus and the centromere, as in P. anserina. The mating-type locus has the typical Sordariales organization, plus a MAT1-1-1 pseudogene in the MAT1-2 haplotype. High-quality genome assemblies of opposite mating types and segregation analyses revealed a suppression of recombination in a region of 1.47 Mb around the mating-type locus. We detected three evolutionary strata, indicating a stepwise extension of recombination suppression. The three strata displayed no rearrangement or transposable element accumulation but gene losses and gene disruptions were present, and precisely at the strata margins. Our findings indicate a convergent evolution of self-fertile dikaryotic sexual spores across multiple ascomycete fungi. The particular pattern of meiotic segregation at the mating-type locus was associated with recombination suppression around this locus, that had extended stepwise. This association between pseudo-homothallism and recombination suppression across lineages and the presence of gene disruption at the strata limits are consistent with a recently proposed mechanism of sheltering deleterious alleles to explain stepwise recombination suppression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An intensity-based post-processing tool for 3D instance segmentation of organelles in soft X-ray tomograms

Investigating the 3D structures and rearrangements of organelles within a single cell is critical for better characterizing cellular function. Imaging approaches such as soft X-ray tomography have been widely applied to reveal a complex subcellular organization involving multiple inter-organelle interactions. However, 3D segmentation of organelle instances has been challenging despite its importance in organelle characterization. Here we propose an intensity-based post-processing tool to identify and separate organelle instances. Our tool separates sphere-like (insulin vesicle) and columnar-shaped organelle instances (mitochondrion) based on the intensity of raw tomograms, semantic segmentation masks, and organelle morphology. We validate our tool using synthetic tomograms of organelles and experimental tomograms of pancreatic β -cells to separate insulin vesicle and mitochondria instances. As compared to the commonly used connected regions labeling, watershed, and watershed + Gaussian filter methods, our tool results in improved accuracy in identifying organelles in the synthetic tomograms and an improved description of organelle structures in β -cell tomograms. In addition, under different experimental treatment conditions, significant changes in volumes and intensities of both insulin vesicle and mitochondrion are observed in our instance results, revealing their potential roles in maintaining normal β -cell function. Our tool is expected to be applicable for improving the instance segmentation of other images obtained from different cell types using multiple imaging modalities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Exploring the fragmentation efficiency of proteins analyzed by MALDI-TOF-TOF tandem mass spectrometry using computational and statistical analyses

Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) is a rapid technique for identifying intact proteins from unfractionated mixtures by top-down proteomic analysis. MS/MS allows isolation of specific intact protein ions prior to fragmentation, allowing fragment ion attribution to a specific precursor ion. However, the fragmentation efficiency of mature, intact protein ions by MS/MS post-source decay (PSD) varies widely, and the biochemical and structural factors of the protein that contribute to it are poorly understood. With the advent of protein structure prediction algorithms such as Alphafold2, we have wider access to protein structures for which no crystal structure exists. In this work, we use a statistical approach to explore the properties of bacterial proteins that can affect their gas phase dissociation via PSD. We extract various protein properties from Alphafold2 predictions and analyze their effect on fragmentation efficiency. Our results show that the fragmentation efficiency from cleavage of the polypeptide backbone on the C-terminal side of glutamic acid (E) and asparagine (N) residues were nearly equal. In addition, we found that the rearrangement and cleavage on the C-terminal side of aspartic acid (D) residues that result from the aspartic acid effect (AAE) were higher than for E- and N-residues. From residue interaction network analysis, we identified several local centrality measures and discussed their implications regarding the AAE. We also confirmed the selective cleavage of the backbone at D-proline bonds in proteins and further extend it to N-proline bonds. Finally, we note an enhancement of the AAE mechanism when the residue on the C-terminal side of D-, E- and N-residues is glycine. To the best of our knowledge, this is the first report of this phenomenon. Our study demonstrates the value of using statistical analyses of protein sequences and their predicted structures to better understand the fragmentation of the intact protein ions in the gas phase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Cooperation between somatic mutation and germline-encoded residues enables antibody recognition of HIV-1 envelope glycans

Viral glycoproteins are a primary target for host antibody responses. However, glycans on viral glycoproteins can hinder antibody recognition since they are self glycans derived from the host biosynthesis pathway. During natural HIV-1 infection, neutralizing antibodies are made against glycans on HIV-1 envelope glycoprotein (Env). However, such antibodies are rarely elicited with vaccination. Previously, the vaccine-induced, macaque antibody DH501 was isolated and shown to bind to high mannose glycans on HIV-1 Env. Understanding how DH501 underwent affinity maturation to recognize glycans could inform vaccine induction of HIV-1 glycan antibodies. Here, we show that DH501 Env glycan reactivity is mediated by both germline-encoded residues that contact glycans, and somatic mutations that increase antibody paratope flexibility. Only somatic mutations in the heavy chain were required for glycan reactivity. The paratope conformation was fragile as single mutations within the immunoglobulin fold or complementarity determining regions were sufficient for eliminating antibody function. Taken together, the initial germline V H DJ H rearrangement generated contact residues capable of binding glycans, and somatic mutations were required to form a flexible paratope with a cavity conducive to HIV-1 envelope glycan binding. The requirement for the presence of most somatic mutations across the heavy chain variable region provides one explanation for the difficulty in inducing anti-Env glycan antibodies with HIV-1 Env vaccination.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Two human antibodies to a meningococcal serogroup B vaccine antigen enhance binding of complement Factor H by stabilizing the Factor H binding site

Microbial pathogens bind host complement regulatory proteins to evade the immune system. The bacterial pathogen Neisseria meningitidis, or meningococcus, binds several complement regulators, including human Factor H (FH). FH binding protein (FHbp) is a component of two licensed meningococcal vaccines and in mice FHbp elicits antibodies that inhibit binding of FH to FHbp, which defeat the bacterial evasion mechanism. However, humans vaccinated with FHbp develop antibodies that enhance binding of FH to the bacteria, which could limit the effectiveness of the vaccines. In the present study, we show that two vaccine-elicited antibody fragments (Fabs) isolated from different human subjects increase binding of complement FH to meningococcal FHbp by ELISA. The two Fabs have different effects on the kinetics of FH binding to immobilized FHbp as measured by surface plasmon resonance. The 1.7- and 2.0-Å resolution X-ray crystal structures of the Fabs in complexes with FHbp illustrate that the two Fabs bind to similar epitopes on the amino-terminal domain of FHbp, adjacent to the FH binding site. Superposition models of ternary complexes of each Fab with FHbp and FH show that there is likely minimal contact between the Fabs and FH. Collectively, the structures reveal that the Fabs enhance binding of FH to FHbp by altering the conformations and mobilities of two loops adjacent to the FH binding site of FHbp. In addition, the 1.5 Å-resolution structure of one of the isolated Fabs defines the structural rearrangements associated with binding to FHbp. The FH-enhancing human Fabs, which are mirrored in the human polyclonal antibody responses, have important implications for tuning the effectiveness of FHbp-based vaccines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Atomic-level mechanisms of short-circuit diffusion in materials

This paper reviews the recent progress in understanding the atomic mechanisms of short-circuit diffusion along materials interfaces, such as grain and interphase boundaries, as well as lattice and interfacial dislocations/disconnections. Recent atomistic computer simulations have shown that short-circuit diffusion is dominated by collective atomic rearrangements in the form of strings and rings of mobile atoms. The process is dynamically heterogeneous in space and time and has many features in common with atomic dynamics in supercooled glass-forming liquids. We discuss examples of grain boundary, interphase boundary, and dislocation diffusion in metals and alloys, including the solute effect on the diffusion rates and mechanisms. Interphase boundaries are exemplified by Al–Si interfaces with diverse orientation relationships and atomic structures. The hierarchy of short-circuit diffusion paths in materials is reviewed by comparing the rates of grain boundary, interphase boundary, and dislocation diffusion. Future directions in the field of short-circuit diffusion in defect core regions are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Atomic electron tomography in three and four dimensions

Atomic electron tomography (AET) has become a powerful tool for atomic-scale structural characterization in three and four dimensions. It provides the ability to correlate structures and properties of materials at the single-atom level. With recent advances in data acquisition methods, iterative three-dimensional (3D) reconstruction algorithms, and post-processing methods, AET can now determine 3D atomic coordinates and chemical species with sub-Angstrom precision, and reveal their atomic-scale time evolution during dynamical processes. In this work, we review the recent experimental and algorithmic developments of AET and highlight several groundbreaking experiments, which include pinpointing the 3D atom positions and chemical order/disorder in technologically relevant materials and capturing how atoms rearrange during early nucleation at four-dimensional atomic resolution.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2024

Multiscale approaches for optimizing the impact of strain on Na-ion battery cycle life

Abstract The high costs and geopolitical challenges inherent to the lithium-ion (Li-ion) battery supply chain have driven a rising interest in the development of sodium-ion (Na-ion) batteries as a potential alternative. Unfortunately, the larger ionic radius of Na limits the reversibility of cycling because of the extensive atomic rearrangements that accompany Na-ion insertion, which in turn limit diffusion and charging speed, and lead to rapid degradation of the electrodes. The Center for Strain Optimization for Renewable Energy (STORE) was established to address these challenges and develop new electrode materials for Na-ion cells. This article discusses the current state-of-the-art materials used in Na-ion cells and several directions that STORE believes are critical to understand and control the structural and volumetric changes during the reversible (de)insertion of large cations. Graphical abstract Highlights Understanding the fundamental way materials respond to localized strains at the atomic length-scale is a critical first step in the development of highly reversible, long cycle life, Na-ion insertion hosts. This perspective explores a variety of methods that can be employed to mitigate the detrimental effects of large strain. The insights gained from these investigations should help lay the foundation for the creation of more economical and sustainable batteries that could have immediate impact on global energy infrastructure. Discussion Although there is near universal agreement that electrochemical energy storage must be an integral part of a green-energy future, there is less agreement about how to reduce the cost of energy storage. Replacing high-cost lithium-ion cells with lower-cost sodium-ion batteries is one option frequently considered in future energy models, but the details of what can be achieve with optimized sodium cell performance remains unclear. Here we posit that developing methods to mitigating strain on the electrode particle length scale is a key factor for achieving long-cycle-life sodium-ion batteries. Mitigating strain on the atomic scale suppress electrode-level volume change. Allowing for fast cycling in materials without the problems of electrode cracking or delamination. We further posit that understanding volume change in sodium-ion electrodes at a fundamental level will lead to the designing new sodium-ion electrode materials that will allow for efficient, stable, lower-cost energy storage.

Brady, Michael J.↗
DOE OSTI2020

Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio

The cellular response to ionizing radiation continues to be of significant research interest in cancer radiotherapy, and DNA is recognized as the critical target for most of the biologic effects of radiation. Incident particles can cause initial DNA damages through physical and chemical interactions within a short time scale. Initial DNA damages can undergo repair via different pathways available at different stages of the cell cycle. The misrepair of DNA damage results in genomic rearrangement and causes mutations and chromosome aberrations, which are drivers of cell death. This work presents an integrated study of simulating cell response after proton irradiation with energies of 0.5–500 MeV (LET of 60–0.2 keV/µm). A model of a whole nucleus with fractal DNA geometry was implemented in TOPAS-nBio for initial DNA damage simulations. The default physics and chemistry models in TOPAS-nBio were used to describe interactions of primary particles, secondary particles, and radiolysis products within the nucleus. The initial DNA double-strand break (DSB) yield was found to increase from 6.5 DSB/Gy/Gbp at low-linear energy transfer (LET) of 0.2 keV/µm to 21.2 DSB/Gy/Gbp at high LET of 60 keV/µm. A mechanistic repair model was applied to predict the characteristics of DNA damage repair and dose response of chromosome aberrations. It was found that more than 95% of the DSBs are repaired within the first 24 h and the misrepaired DSB fraction increases rapidly with LET and reaches 15.8% at 60 keV/µm with an estimated chromosome aberration detection threshold of 3 Mbp. The dicentric and acentric fragment yields and the dose response of micronuclei formation after proton irradiation were calculated and compared with experimental results.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

Hydration-driven stabilization and volume collapse of grain boundaries in Mg2SiO4 forsterite predicted by first-principles simulations

Grain boundaries in mantle minerals are of critical importance to geophysical and geochemical processes of the Earth’s interior. One of the fundamental issues is to understand how the water (H 2 O) component influences the properties of grain boundaries in silicate materials. Here, we report the results of the structure and stability of several tilt grain boundaries in Mg 2 SiO 4 forsterite over the pressure range 0 to 15 GPa using density functional theory-based first-principles simulations. Here, the results suggest greater energetic stability and hydration-driven volume collapse (negative excess volume) at zero pressure for the majority of hydrous grain boundaries relative to the anhydrous (dry) ones. All the hydrous grain boundaries become increasingly favorable at elevated pressures as the calculated hydration enthalpy systematically decreases with increasing pressure. The hydrous components at the interfacial regions are predominantly in the hydroxyl form and, to a lesser extent, in the molecular H 2 O form. Their calculated ratio ranges from 1.6 to 8.7 among the different grain boundary configurations. Our structural analysis also reveals that the hydroxyls are bound to either both Mg and Si or to Mg only. In comparison, the molecular species are bound only to Mg sites. Besides direct oxygen-hydrogen bonding, intermolecular hydrogen bonding becomes important with compression. On the basis of our results, we suggest that local atomic rearrangements caused by dissociative adsorption of water facilitate efficient compaction of the boundary interfaces, which, in turn, results in greater relative stability of hydrous grain boundaries. This means that water prefers to be incorporated within the grain boundaries over the bulk of silicate materials.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2019

Initial Simulations of Empty Room Collapse and Reconsolidation at the Waste Isolation Pilot Plant

The Waste Isolation Pilot Plant (WIPP) is a geologic repository for defense-related nuclear waste. If left undisturbed, the virtually impermeable rock salt surrounding the repository will isolate the nuclear waste from the biosphere. If humans accidentally intrude into the repository in the future, then the likelihood of a radionuclide release to the biosphere will depend significantly on the porosity and permeability of the repository itself. Room ceilings and walls at the WIPP tend to collapse over time, causing rubble piles to form on floors of empty rooms. The surrounding rock formation will gradually compact these rubble piles until they eventually become solid salt, but the length of time for a rubble pile to reach a certain porosity and permeability is unknown. This report details the first efforts to build models to predict the porosity and permeability evolution of an empty room as it closes. Conventional geomechanical numerical methods would struggle to model empty room collapse and rubble pile consolidation, so three different meshless methods, the Immersed Isogeometric Analysis Meshfree, Reproducing Kernel Particle Method (RKPM), and the Conformal Reproducing Kernel method, were assessed. First, the meshless methods and the finite element method each simulated gradual room closure, without ceiling or wall collapse. All three methods produced equivalent room closure predictions with comparable computational speed. Second, the Immersed Isogeometric Analysis Meshfree method and RKPM simulated two-dimensional empty room collapse and rubble pile consolidation. Both methods successfully simulated large viscoplastic deformations, fracture, and rubble pile rearrangement to produce qualitatively realistic results. In addition to geomechanical simulations, the flow channels in damaged salt and crushed salt were measured using micro-computed tomography, and input into a computational fluid dynamics simulation to predict the salt's permeability. Although room for improvement exists, the current simulation approaches appear promising.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Boson Fermion Nuclei Energy Levels In The Third Period Of The Periodic Table Of Elements (Monograph No.5)

The boson fermion nucleus (BFN) energy level is shown for sodium, magnesium, aluminum, silicon, phosphorus, sulphur, chlorine, and argon. The BFN energy levels are compared to the energy levels in the shell nuclear model. Individual nucleon fermions in the BFN make minor contributions to the nucleus energy level. Nucleons rearrange into boson structures during stellar nucleosynthesis and condense into the lowest-level energy state. Deconstruction of the BFN structure and conversion to a shell or liquid-drop model brings about a higher energy state. This is not favored in nature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗