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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Performance Assessment for the E-Area Low-Level Radioactive Waste Disposal Facility at the Savannah River Site: Appendix H

This section provides supporting material for the development of DU-specific final inventory limits for the GW pathways for every generic waste form and SWF parent radionuclide requiring an inventory limit. The final inventory limits are based on nominal PA transport simulations using PORFLOW as reported in Chapter 5. The nominal PA settings represent the compliance case where some modeling parameter settings are defined based on conservative (pessimistically leaning) arguments. In the overall computational approach employed in this PA, a multitiered radionuclide screening process is adopted as discussed in Chapter 2, Section 2.3.7. In the multitiered process, the initial list of 1,252 parent radionuclides is shortened substantially using conservative, but simple, transport models, along with a reasonably low cutoff criterion of 0.1% SOF value. Multidimensional PORFLOW flow and transport modeling is employed for every parent radionuclide that failed the GW screening. The generic waste form limits represent Tier-3 analyses, while Tier-4 analyses are employed for SWF limits, where warranted.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2026

General framework for quantifying dissipation pathways in open quantum systems. III. Off-diagonal subsystem–bath couplings

This paper extends the previously reported theory of dissipation pathways [C. W. Kim and I. Franco, J. Chem. Phys. 160, 214111 (2024)] to incorporate off-diagonal subsystem–bath coupling, which is often required to model molecular systems where the environment directly influences transitions and couplings between subsystem states. We systematically derive master equations for both population transfer and dissipation into individual bath components, for which we also rigorously prove energy conservation and detailed balance. The approach is based on second-order perturbation theory with respect to the subsystem–bath couplings, whose form is not limited to any specific model. The accuracy of the developed method is tested by applying it to diverse model Hamiltonians involving linearly coupled harmonic oscillator baths and comparing the outcomes against the hierarchical equations of motion (HEOM) method. Overall, our method accurately quantifies the contributions of specific bath components to the overall dissipation while significantly reducing the computational cost compared to numerically exact methods such as HEOM, thus offering a path to examine how vibronic interactions steer non-adiabatic processes in realistic chemical systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Impossible symmetries and conformal gravity

We explore the physics of relativistic gapless phases defined by a mixed anomaly between two generalized conserved currents. The gapless modes can be understood as Goldstone modes arising from the nonlinear realization of (generically higher-form) symmetries arising from these currents. In some cases, the anomaly cannot be reproduced by any local and unitary theory, indicating that the corresponding symmetries are impossible, in the sense that they cannot appear in a Lorentzian physical system. We give a general construction and illustrate it with several examples. Most notably, we study conformal gravity from this perspective, describing the higher-form symmetries of the linear theory and showing how it can be understood in terms of anomalies. Along the way we clarify some aspects of electric-magnetic duality in linear conformal gravity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Linking the Salmonella enterica 1,2-Propanediol Utilization Bacterial Microcompartment Shell to the Enzymatic Core via the Shell Protein PduB

Bacterial microcompartments (MCPs) are protein-based organelles that house the enzymatic machinery for metabolism of niche carbon sources, allowing enteric pathogens to outcompete native microbiota during host colonization. While much progress has been made toward understanding MCP biogenesis, questions still remain regarding the mechanism by which core MCP enzymes are enveloped within the MCP protein shell. Here, we explore the hypothesis that the shell protein PduB is responsible for linking the shell of the 1,2-propanediol utilization (Pdu) MCP from Salmonella enterica serovar Typhimurium LT2 to its enzymatic core. Using fluorescent reporters, we demonstrate that all members of the Pdu enzymatic core are encapsulated in Pdu MCPs. We also demonstrate that PduB is critical for linking the entire Pdu enzyme core to the MCP shell. Using MCP purifications, transmission electron microscopy, and fluorescence microscopy, we find that shell assembly can be decoupled from the enzymatic core, as apparently empty MCPs are formed in Salmonella strains lacking PduB. Mutagenesis studies reveal that PduB is incorporated into the Pdu MCP shell via a conserved, lysine-mediated hydrogen bonding mechanism. Finally, growth assays and system-level pathway modeling reveal that unencapsulated pathway performance is strongly impacted by enzyme concentration, highlighting the importance of minimizing polar effects when conducting these functional assays. Together, these results provide insight into the mechanism of enzyme encapsulation within Pdu MCPs and demonstrate that the process of enzyme encapsulation and shell assembly are separate processes in this system, a finding that will aid future efforts to understand MCP biogenesis.

1, 2-propanediol utilization↗
DOE OSTI2025

A conserved chaperone protein is required for the formation of a noncanonical type VI secretion system spike tip complex

Type VI secretion systems (T6SSs) are dynamic protein nanomachines found in Gram-negative bacteria that deliver toxic effector proteins into target cells in a contact-dependent manner. Prior to secretion, many T6SS effector proteins require chaperones and/or accessory proteins for proper loading onto the structural components of the T6SS apparatus. However, despite their established importance, the precise molecular function of several T6SS accessory protein families remains unclear. In this study, we set out to characterize the DUF2169 family of T6SS accessory proteins. Using gene co-occurrence analyses, we find that DUF2169-encoding genes strictly co-occur with genes encoding T6SS spike complexes formed by valine-glycine repeat protein G (VgrG) and DUF4150 domains. Although structurally similar to Pro-Ala-Ala-Arg (PAAR) domains, “PAAR-like” DUF4150 domains lack PAAR motifs and instead contain a conserved PIPY motif, leading us to designate them PIPY domains. Next, we present both genetic and biochemical evidence that PIPY domains require a cognate DUF2169 protein to form a functional T6SS spike complex with VgrG. This contrasts with canonical PAAR proteins, which bind VgrG on their own to form functional spike complexes. By solving the first crystal structure of a DUF2169 protein, we show that this T6SS accessory protein adopts a novel protein fold. Furthermore, biophysical and structural modeling data suggest that DUF2169 contains a dynamic loop that physically interacts with a hydrophobic patch on the surface of its cognate PIPY domain. Based on these findings, we propose a model whereby DUF2169 proteins function as molecular chaperones that maintain VgrG–PIPY spike complexes in a secretion-competent state prior to their export by the T6SS apparatus.

DUF2169↗
DOE OSTI2024

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection

Abstract Large-genome bacteriophages (jumbo phages) of the proposed family Chimalliviridae assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and DNA-targeting CRISPR-Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here, we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d results in accumulation of phage-encoded mRNAs in the phage nucleus, reduces phage protein production, and compromises virion assembly. Taken together, our data show that the conserved ChmC protein plays crucial roles in the viral life cycle, potentially by facilitating phage mRNA translocation through the nuclear shell to promote protein production and virion development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Probing the high-density nuclear symmetry energy with the Ξ – / Ξ 0 ratio in heavy-ion collisions at s N N ≈ 3 GeV

Recent beam energy scan experiments at the BNL Relativistic Heavy Ion Collider by the STAR Collaboration found that hadronic interactions dominate the collective flow and the proton cumulant ratios are driven by baryon number conservation in a region of high baryon density in √ s NN = 3 GeV Au + Au reactions, indicating that the dense medium formed in such collisions is likely hadronic matter. Within an updated a relativistic transport model with momentum dependent isoscalar and isovector single-nucleon mean-field potentials corresponding to different symmetry energies at suprasaturation densities, the n/p, π – /π + , $K$ $^{0}_{s}$/K + , Σ – /Σ + , and Ξ – /Ξ 0 ratios are studied for central Au + Au collisions at √ s NN = 3 GeV, where the maximum central density reaches about (3.6–4.0) ρ 0 . The doubly strange Ξ – /Ξ 0 ratio is found to have the strongest sensitivity to the variation of high-density nuclear symmetry energy. Furthermore, the Ξ – /Ξ 0 ratio in relativistic heavy-ion reactions at √ s NN~3 GeV may help probe sensitively the poorly known symmetry energy of dense neutron-rich matter critically important for understanding various properties of neutron stars.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Hydrodynamics of higher-rank gauge theories

We extend recent work on hydrodynamics with global multipolar symmetries — known as “fracton hydrodynamics” — to systems in which the multipolar symmetries are gauged. We refer to the latter as “fracton magnetohydrodynamics”, in analogy to conventional magnetohydrodynamics (MHD), which governs systems with gauged charge conservation. We show that fracton MHD arises naturally from higher-rank Maxwell’s equations and in systems with one-form symmetries obeying certain constraints; while we focus on “minimal” higher-rank generalizations of MHD that realize diffusion, our methods may also be used to identify other, more exotic hydrodynamic theories (e.g., with magnetic subdiffusion). In contrast to semi-microscopic derivations of MHD, our approach elucidates the origin of the hydrodynamic modes by identifying the corresponding higher-form symmetries. Being rooted in symmetries, the hydrodynamic modes may persist even when the semi-microscopic equations no longer provide an accurate description of the system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Development of a Novel Bioprocess for Synthesizing and Purifying Adipic Acid

Through DOE’s Bioenergy Technologies Office and the Energy Efficiency and Renewable Energy Small Business Voucher (SBV) Pilot, ZymoChem, Inc received support to work with the ABPDU to accelerate the development of a novel adipic acid (AA) bioprocess by evaluating technologies to demonstrate the following: 1) Process development of AA via ZymoChem’s carbon-conserving (C 2 ) pathway in 2L bioreactors, using industrial feedstocks, and as a salt with hexamethylenediamine (HMDA), i.e., the industrially desired form of AA as AA-HMDA is the precursor for nylon 6,6 synthesis. 2) Pilot scale aerobic fermentation at the 300 L scale (stage 1) followed by a high cell density (HCD) anaerobic resting cell biotransformation (RCB) at the 50 L scale (stage 2). 3) Demonstration of a viable recovery process at the 50 L scale for purifying the product (i.e., AA-HMDA salt) and deliver multiple kg-quantity batches of purified product for further testing.

09 BIOMASS FUELS↗
DOE OSTI2022

Post-closure Nuclear Criticality Safety Evaluations for Disposition of Criticality Control Overpacks at the Waste Isolation Pilot Plant

The Waste Isolation Pilot Plant (WIPP) is a geological repository in southern New Mexico that provides for disposal of transuranic (TRU) wastes from atomic energy defense activities. The Sandia National Laboratories (Sandia) Report, Consideration of Nuclear Criticality When Disposing of Transuranic Waste at the Waste Isolation Pilot Plant, addresses nuclear criticality safety based on the projected inventory characteristics for the initial compliance certification application of WIPP in 1996. As the inventory, waste forms, and disposal package designs change, revised or new analyses are necessary to demonstrate acceptability for these configurations within the WIPP safety basis and compliance with 10,000-year post-closure standards of the US Environmental Protection Agency (EPA). Saylor and Scaglione evaluated criticality control overpacks (CCOs) in 2017 based on conservative assumptions for post-closure repository structural conditions with resulting effects on containers and container spacing, The Saylor and Scaglione evaluation of CCOs addressed a single waste configuration that represents the Surplus Plutonium Disposition Program’s dilute and dispose waste form and composition. This initial CCO study demonstrated that 50 grams of boron carbide (B 4 C) per CCO is sufficient to ensure post-closure criticality safety based on a well-mixed waste composition, and Oak Ridge National Laboratory (ORNL) subsequently determined that this amount of B 4 C does not require constraints on moisture or plastic present as moderator. The Saylor and Scaglione analysis conservatively assumes repository room closure that eliminates all space between fissile gram equivalent (FGE) 239 Pu masses. The close-packed array was selected based on limited availability of repository salt creep modeling results at that time. In 2019, Brickner provided additional evaluations for pipe overpack containers (POCs), building on the conservative basis provided by Saylor and Scaglione. Brickner’s 2019 analysis made use of new geomechanical data for post-closure spacing that rely on advances in repository modeling as documented in the work by Reedlunn and Bean. This current CCO evaluation for generic waste materials expands on earlier work performed at ORNL and includes evaluation of CCOs across a much broader range of possible waste compositions and geometries. This evaluation is intended to provide input for the required feature, event and process (FEP) screening to determine if post-closure criticality must be included as an event in the 10,000-year regulatory evaluation. As such, the approach to modeling post-closure criticality presented in this report has been coordinated with the Sandia team responsible for FEP screening. The resulting analysis supports disposition of fissile materials in the CCO containing up to 380 FGE 239 Pu and expands conditions acceptable for disposal of fissile material in CCOs. This evaluation builds on the methodology of Saylor and Scaglione and Brickner, using the most recently available geomechanical data for CCO spacing under salt creep compaction scenarios provided by Reedlunn and Bean. The broad range of fissile material configurations analyzed in this report are intended to account for configurations that may occur during the post-closure disposal time period, and it also includes waste configurations that are not physically possible to support analysis of conditions that influence neutron fluence.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

Structure of the D1-Val185Asn mutated photosystem II complex with slow O–O bond formation reveals changes in the Cl1 water channel

During photosynthesis, the photosystem II (PSII) enzyme catalyzes the light-driven oxidation of water, fueling life on Earth by storing light energy and releasing O 2 as a byproduct. Determining the molecular mechanism for this water oxidation reaction has been of significant interest for the development of synthetic catalysts, but many details remain elusive. One of the open questions is how protons are strategically removed from the active site, a Mn 4 CaO 5 cluster called the oxygen-evolving complex (OEC), during the reaction cycle via conserved water channels, and how proton transfer contributes to O–O bond formation energetics. Site-directed mutagenesis studies have investigated the role of conserved amino acid side chains in facilitating proton transfer. One of the most influential mutations is the Val185Asn substitution on the D1 subunit, which substantially slows O 2 release kinetics without abolishing catalytic activity. Forming a molecular understanding of how this mutation affects the active site will provide insight into the water oxidation reaction mechanism. Here, we investigated the structural basis of the Val185Asn substitution by determining a 1.99 Å-resolution cryo-EM structure. We observed that Asn185 orients away from the OEC and donates a H-bond to Cl1, a conserved chloride ion. We furthermore observed an alternative D2-Glu312-facing conformation of the D2-Lys317 side chain in the Cl1 water channel, a conformation that is consistent with recent models for proton transfer. These changes also produce perturbations to the hydrogen-bonding network. Overall, these finding provide insight into proton transfer in the Cl1 channel and its effect on the water oxidation reaction mechanism.

cryo-EM↗
DOE OSTI2021

Broadly cross-reactive human antibodies that inhibit genogroup I and II noroviruses

The rational development of norovirus vaccine candidates requires a deep understanding of the antigenic diversity and mechanisms of neutralization of the virus. Here, we isolate and characterize a panel of broadly cross-reactive naturally occurring human monoclonal IgMs, IgAs and IgGs reactive with human norovirus (HuNoV) genogroup I or II (GI or GII). We note three binding patterns and identify monoclonal antibodies (mAbs) that neutralize at least one GI or GII HuNoV strain when using a histo-blood group antigen (HBGA) blocking assay. The HBGA blocking assay and a virus neutralization assay using human intestinal enteroids reveal that the GII-specific mAb NORO-320, mediates HBGA blocking and neutralization of multiple GII genotypes. The Fab form of NORO-320 neutralizes GII.4 infection more potently than the mAb, however, does not block HBGA binding. The crystal structure of NORO-320 Fab in complex with GII.4 P-domain shows that the antibody recognizes a highly conserved region in the P-domain distant from the HBGA binding site. Dynamic light scattering analysis of GII.4 virus-like particles with mAb NORO-320 shows severe aggregation, suggesting neutralization is by steric hindrance caused by multivalent cross-linking. Aggregation was not observed with the Fab form of NORO-320, suggesting that this clone also has additional inhibitory features.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Non-local model for surface tension in fluid-fluid simulations

We propose a non-local model for surface tension obtained in the form of an integral of a molecular-force-like function with support 3.5e added to the Navier-Stokes momentum conservation equation. We demonstrate analytically and numerically that with the non-local model interfaces with a radius of curvature larger than the support length behave macroscopically and microscopically, otherwise. For static droplets, the pressure difference Pe,in - Pe,out satisfies the Young-Laplace law for droplet radius greater than 3.5e and other- wise deviates from the Young-Laplace law. The latter indicates that the surface tension in the proposed model decreases with decreasing radius of curvature, which agrees with molecular dynamics and experimental studies of nanodroplets. Using the non-local model we perform numerical simulations of droplets under dynamic conditions, including a rising droplet, a droplet in shear flow, and two colliding droplets in shear flow, and compare results with a standard Navier-Stokes model subject to the Young-Laplace boundary condition at the fluid-fluid interface implemented via the Conservative Level Set (CLS) method. We find good agreement with existing numerical methods and analytical results for a rising macroscopic droplet and a droplet in a shear flow. For colliding droplets in shear flow, the non- local model converges (with respect to the grid size) to the correct behavior, including sliding, coalescence, and merging and breaking of two droplets depending on the capillary number. In contrast, we find that the results of the CLS model are highly grid-size dependent.

Howard, Amanda A.↗
DOE OSTI2023

Tad and toxin-coregulated pilus structures reveal unexpected diversity in bacterial type IV pili

<Type IV pili (T4P) are ubiquitous in both bacteria and archaea. They are polymers of the major pilin protein, which has an extended and protruding N-terminal helix, α1, and a globular C-terminal domain. Cryo-EM structures have revealed key differences between the bacterial and archaeal T4P in their C-terminal domain structure and in the packing and continuity of α1. This segment forms a continuous α-helix in archaeal T4P but is partially melted in all published bacterial T4P structures due to a conserved helix breaking proline at position 22. The tad (tight adhesion) T4P are found in both bacteria and archaea and are thought to have been acquired by bacteria through horizontal transfer from archaea. Tad pilins are unique among the T4 pilins, being only 40 to 60 residues in length and entirely lacking a C-terminal domain. They also lack the Pro22 found in all high-resolution bacterial T4P structures. We show using cryo-EM that the bacterial tad pilus from Caulobacter crescentus is composed of continuous helical subunits that, like the archaeal pilins, lack the melted portion seen in other bacterial T4P and share the packing arrangement of the archaeal T4P. We further show that a bacterial T4P, the Vibrio cholerae toxin coregulated pilus, which lacks Pro22 but is not in the tad family, has a continuous N-terminal α-helix, yet its α1 s are arranged similar to those in other bacterial T4P. Our results highlight the role of Pro22 in helix melting and support an evolutionary relationship between tad and archaeal T4P.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

fortfmt-fix

SF-25-126 **fortfmt‑fix** is a small, deterministic codemod that rewrites these descriptors to explicit, standard‑conforming forms (e.g., `I12`, `F25.16`), enabling clean builds on modern compilers without vendor‑specific options. The tool is designed to be idempotent and conservative, preserving semantics while reducing maintenance burden in research codebases.

Bross, David [Argonne National Laboratory (ANL), A↗
DOE OSTI2021

Computing water flow through complex landscapes – Part 3: Fill–Spill–Merge: flow routing in depression hierarchies

Abstract. Depressions – inwardly draining regions – are common to many landscapes. When there is sufficient moisture, depressions take the form of lakes and wetlands; otherwise, they may be dry. Hydrological flow models used in geomorphology, hydrology, planetary science, soil and water conservation, and other fields often eliminate depressions through filling or breaching; however, this can produce unrealistic results. Models that retain depressions, on the other hand, are often undesirably expensive to run. In previous work we began to address this by developing a depression hierarchy data structure to capture the full topographic complexity of depressions in a region. Here, we extend this work by presenting the Fill–Spill–Merge algorithm that utilizes our depression hierarchy data structure to rapidly process and distribute runoff. Runoff fills depressions, which then overflow and spill into their neighbors. If both a depression and its neighbor fill, they merge. We provide a detailed explanation of the algorithm and results from two sample study areas. In these case studies, the algorithm runs 90–2600 times faster (with a reduction in compute time of 2000–63 000 times) than the commonly used Jacobi iteration and produces a more accurate output. Complete, well-commented, open-source code with 97 % test coverage is available on GitHub and Zenodo.

58 GEOSCIENCES↗
DOE OSTI2022

Stable binding to phosphatidylserine-containing membranes requires conserved arginine residues in tandem C domains of blood coagulation factor VIII

At sites of vascular damage, factor VIII (fVIII) is proteolytically activated by thrombin and binds to activated platelet surfaces with activated factor IX (fIXa) to form the intrinsic “tenase” complex. Previous structural and mutational studies of fVIII have identified the C1 and C2 domains in binding to negatively charged membrane surfaces through β-hairpin loops with solvent-exposed hydrophobic residues and a ring of positively charged basic residues. Several hemophilia A-associated mutations within the C domains are suggested to disrupt lipid binding, preventing formation of the intrinsic tenase complex. In this study, we devised a novel platform for generating recombinant C1, C2, and C1C2 domain constructs and performed mutagenesis of several charged residues proximal to the putative membrane binding region of each C domain. Binding measurements between phosphatidylserine (PS)-containing lipid membrane surfaces and fVIII C domains demonstrated an ionic strength dependence on membrane binding affinity. Mutations to basic residues adjacent to the surface-exposed hydrophobic regions of C1 and C2 differentially disrupted membrane binding, with abrogation of binding occurring for mutations to conserved arginine residues in the C1 (R2163) and C2 (R2320) domains. Lastly, we determined the X-ray crystal structure of the porcine fVIII C2 domain bound to o-phospho-L-serine, the polar headgroup of PS, which binds to a basic cleft and makes charge-charge contact with R2320. We conclude that basic clefts in the fVIII C domains bind to PS-containing membranes through conserved arginine residues via a C domain modularity, where each C domain possesses modest electrostatic-dependent affinity and tandem C domains are required for high affinity binding.

59 BASIC BIOLOGICAL SCIENCES↗