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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

The Pseudoenzyme β‐Amylase9 From Arabidopsis Activates α‐Amylase3: A Possible Mechanism to Promote Stress‐Induced Starch Degradation

ABSTRACT Starch accumulation in plants provides carbon for nighttime use, for regrowth after periods of dormancy, and for times of stress. Both ɑ‐ and β‐amylases (AMYs and BAMs, respectively) catalyze starch hydrolysis, but their functional roles are unclear. Moreover, the presence of catalytically inactive amylases that show starch excess phenotypes when deleted presents questions on how starch degradation is regulated. Plants lacking one of these catalytically inactive β‐amylases, BAM9, have enhanced starch accumulation when combined with mutations in BAM1 and BAM3, the primary starch degrading BAMs in response to stress and at night, respectively. BAM9 has been reported to be transcriptionally induced by stress although the mechanism for BAM9 function is unclear. From yeast two‐hybrid experiments, we identified the plastid‐localized AMY3 as a potential interaction partner for BAM9. We found that BAM9 interacted with AMY3 in vitro and that BAM9 enhances AMY3 activity about three‐fold. Modeling of the AMY3‐BAM9 complex predicted a previously undescribed alpha–alpha hairpin in AMY3 that could serve as a potential interaction site. Additionally, AMY3 lacking the alpha–alpha hairpin is unaffected by BAM9. Structural analysis of AMY3 showed that it can form a homodimer in solution and that BAM9 appears to replace one of the AMY3 monomers to form a heterodimer. The presence of both BAM9 and AMY3 in many vascular plant lineages, along with model‐based evidence that they heterodimerize, suggests that the interaction is conserved. Collectively these data suggest that BAM9 is a pseudoamylase that activates AMY3 in response to cellular stress, possibly facilitating stress recovery.

Biochemistry & Molecular Biology↗
DOE OSTI2023

A crucial role for dynamic expression of components encoding the negative arm of the circadian clock

In the Neurospora circadian system, the White Collar Complex (WCC) drives expression of the principal circadian negative arm component frequency ( frq ). FRQ interacts with FRH (FRQ-interacting RNA helicase) and CKI, forming a stable complex that represses its own expression by inhibiting WCC. In this study, a genetic screen identified a gene, designated as brd-8 , that encodes a conserved auxiliary subunit of the NuA4 histone acetylation complex. Loss of brd-8 reduces H4 acetylation and RNA polymerase (Pol) II occupancy at frq and other known circadian genes, and leads to a long circadian period, delayed phase, and defective overt circadian output at some temperatures. In addition to strongly associating with the NuA4 histone acetyltransferase complex, BRD-8 is also found complexed with the transcription elongation regulator BYE-1. Expression of brd-8, bye-1, histone h2a.z , and several NuA4 subunits is controlled by the circadian clock, indicating that the molecular clock both regulates the basic chromatin status and is regulated by changes in chromatin. Taken together, our data identify auxiliary elements of the fungal NuA4 complex having homology to mammalian components, which along with conventional NuA4 subunits, are required for timely and dynamic frq expression and thereby a normal and persistent circadian rhythm.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nonuniqueness of generalized quantum master equations for a single observable

When deriving exact generalized master equations for the evolution of a reduced set of degrees of freedom, one is free to choose what quantities are relevant by specifying projection operators. However, obtaining a reduced description does not always need to be achieved through projections-one can also use conservation laws for this purpose. Such an operation should be considered as distinct from any kind of projection; that is, projection onto a single observable yields a different form of master equation compared to that resulting from a projection followed by the application of a constraint. Here, we give a simple example to show this point and give relationships that the different memory kernels must satisfy to yield the same dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity

HIV-1 reverse transcription initiates at the primer binding site (PBS) in the viral genomic RNA (gRNA). Although the structure of the PBS-segment undergoes substantial rearrangement upon tRNALys3 annealing, the proper folding of the PBS-segment during gRNA packaging is important as it ensures loading of beneficial host factors. DHX9/RNA helicase A (RHA) is recruited to gRNA to enhance the processivity of reverse transcriptase. Because the molecular details of the interactions have yet to be defined, we solved the solution structure of the PBS-segment preferentially bound by RHA. Evidence is provided that PBS-segment adopts a previously undefined adenosine-rich three-way junction structure encompassing the primer activation stem (PAS), tRNA-like element (TLE) and tRNA annealing arm. Disruption of the PBS-segment three-way junction structure diminished reverse transcription products and led to reduced viral infectivity. Because of the existence of the tRNA annealing arm, the TLE and PAS form a bent helical structure that undergoes shape-dependent recognition by RHA double-stranded RNA binding domain 1 (dsRBD1). Mutagenesis and phylogenetic analyses provide evidence for conservation of the PBS-segment three-way junction structure that is preferentially bound by RHA in support of efficient reverse transcription, the hallmark step of HIV-1 replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A new soil mixing layer model for simulating conservative solute loss from initially saturated soil to surface runoff

Surface water pollution due to solute loss from soil to surface runoff is a serious threat to the environment, and it is of great significance to predict the solute loss. While soil mixing layer theory has been widely used to predict the solute loss, it has been observed that the conventional soil mixing layer models with constant mixing layer depth underestimate solute concentration in surface runoff, and thus underestimate the solute loss after surface runoff starts. This study introduced a new soil mixing layer model with a new concept that the mixing layer depth increases downward with time after surface runoff occurs. This new concept was implemented by adding a mixing front between the soil mixing layer and its underlying soil layer, which is conceptually similar to the wetting front of soil infiltration given by the Green-Ampt equation. This is equivalent to treating the soil mixing layer as a deforming control volume. A mechanistic explanation for the new model was presented. This study also developed a closed form solution of the new model. The new model was evaluated by simulating five laboratory experiments conducted by two groups of researchers. The first two experiments have ponding water, and consider different drainage and runoff conditions at both early and late runoff times. The other three experiments do not have ponding water, and consider different infiltration conditions at the bottom of soil boxes. Simulation results of the five experiments show that the new model resolves the underestimation problem of conventional soil mixing layer models. The new model is subject to a total of six limits such as that the new model only considers conservative solute. Three limits are related to the assumptions used to derive the closed form solution, and they may be alleviated in a future research as briefly discussed at the end of the paper.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Diverse Antibody Responses to Conserved Structural Motifs in Plasmodium falciparum Circumsporozoite Protein

Malaria vaccine candidate RTS,S/AS01 is based on the central and C-terminal regions of the circumsporozoite protein (CSP) of P. falciparum. mAb397 was isolated from a volunteer in an RTS,S/AS01 clinical trial, and it protects mice from infection by malaria sporozoites. However, mAb397 originates from the less commonly used VH3-15 germline gene compared to the VH3-30/33 antibodies generally elicited by RTS,S to the central NANP repeat region of CSP. The crystal structure of mAb397 with an NPNA4 peptide shows that the central NPNA forms a type I β-turn and is the main recognition motif. In most anti-NANP antibodies studied to date, a germline-encoded Trp is used to engage the Pro in NPNA β-turns, but here the Trp interacts with the first Asn. This “conserved” Trp, however, can arise from different germline genes and be located in the heavy or the light chain. Variation in the terminal ψ angles of the NPNA β-turns results in different dispositions of the subsequent NPNA and, hence, different stoichiometries and modes of antibody binding to rsCSP. Diverse protective antibodies against NANP repeats are therefore not limited to a single germline gene response or mode of binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Discovery of an ultraspecific triuret hydrolase (TrtA) establishes the triuret biodegradation pathway

Triuret (carbonyldiurea) is an impurity found in industrial urea fertilizer (<0.1% w/w) that is applied, worldwide, around 300 million pounds each year on agricultural lands. In addition to anthropogenic sources, endogenous triuret has been identified in amoeba and human urine, the latter being diagnostic for hypokalemia. The present study is the first to describe the metabolic breakdown of triuret, which funnels into biuret metabolism. We identified the gene responsible for triuret decomposition ( trtA ) in bacterial genomes, clustered with biuH , which encodes biuret hydrolase and has close protein sequence homology. TrtA is a member of the isochorismatase-like hydrolase (IHL) protein family, similarly to BiuH, and has a catalytic efficiency (k cat/ K M ) of 6 x 10 5 M –1 s –1 , a K M for triuret of 20 μM, and exquisite substrate specificity. Indeed, TrtA has four orders of magnitude less activity with biuret. Crystal structures of TrtA in apo and holo form were solved and compared with the BiuH structure. The high substrate selectivity was found to be conveyed by second shell residues around each active site. Mutagenesis of residues conserved in TrtA to the alternate consensus found in BiuHs revealed residues critical to triuret hydrolase activity but no single mutant evolved more biuret activity, and likely a combination of mutations is required to interconvert between TrtA, BiuH functions. TrtA-mediated triuret metabolism is relatively rare in recorded genomes (1–2%), but is largely found in plant-associated, nodulating, and endophytic bacteria. This study suggests functions for triuret hydrolase in certain eukaryotic intermediary processes and prokaryotic intermediary or biodegradative metabolism.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Explicit structure-preserving geometric particle-in-cell algorithm in curvilinear orthogonal coordinate systems and its applications to whole-device 6D kinetic simulations of tokamak physics

Explicit structure-preserving geometric particle-in-cell (PIC) algorithm in curvilinear orthogonal coordinate systems is developed. The work reported represents a further development of the structure-preserving geometric PIC algorithm achieving the goal of practical applications in magnetic fusion research. The algorithm is constructed by discretizing the field theory for the system of charged particles and electromagnetic field using Whitney forms, discrete exterior calculus, and explicit non-canonical symplectic integration. In addition to the truncated infinitely dimensional symplectic structure, the algorithm preserves exactly many important physical symmetries and conservation laws, such as local energy conservation, gauge symmetry and the corresponding local charge conservation. As a result, the algorithm possesses the long-term accuracy and fidelity required for first-principles-based simulations of the multiscale tokamak physics. The algorithm has been implemented in the SymPIC code, which is designed for high-efficiency massively-parallel PIC simulations in modern clusters. The code has been applied to carry out whole-device 6D kinetic simulation studies of tokamak physics. A self-consistent kinetic steady state for fusion plasma in the tokamak geometry is numerically found with a predominately diagonal and anisotropic pressure tensor. The state also admits a steady-state sub-sonic ion flow in the range of 10 km s -1 , agreeing with experimental observations and analytical calculations Kinetic ballooning instability in the self-consistent kinetic steady state is simulated. It is shown that high-n ballooning modes have larger growth rates than low-n global modes, and in the nonlinear phase the modes saturate approximately in 5 ion transit times at the 2% level by the E × B flow generated by the instability. These results are consistent with early and recent electromagnetic gyrokinetic simulations.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

A Consistent BGK Model with Velocity-Dependent Collision Frequency for Gas Mixtures

Abstract We derive a multi-species BGK model with velocity-dependent collision frequency for a non-reactive, multi-component gas mixture. The model is derived by minimizing a weighted entropy under the constraint that the number of particles of each species, total momentum, and total energy are conserved. We prove that this minimization problem admits a unique solution for very general collision frequencies. Moreover, we prove that the model satisfies an H-Theorem and characterize the form of equilibrium.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Role of underlying surface, rainstorm and antecedent wetness condition on flood responses in small and medium sized watersheds in the Yangtze River Delta region, China

Floods are becoming more frequent and are hard to control due to the shortage of water conservancy projects in small and medium sized basins, especially in developing regions. Understanding the hydrologic responses and estimated flood characteristics to storm events can help to predict flood disasters and form better effective mitigation and adaptation strategies. Here, using observations of several representative watersheds and Artificial Neural Networks (ANN) and Principal Component Regression (PCR) models, we conducted data-driven analyses to examine the flood responding characteristics. We quantified the relative contributions of the influencing factors to the variation of each flood characteristic. Statistical analysis of the observations shows that the drainage area plays a key role in determining the distribution of lag time and peak discharge. Rainstorm variability has direct influence on floods, and typhoon-induced rainstorms with high total rainfall and rainfall intensity generate higher lag time, flood peak, unit discharge and runoff depth, but lower runoff coefficient. The ANN and PCR models accurately predicted the variations of flood features using the driving factors including physical geographical characteristics, rainstorm features, and antecedent condition. Physical geographic characteristics are key influential factors of lag time, flood peak and runoff coefficient, while the rainstorm features control the magnitude of unit discharge and runoff depth. These results indicate that floods are mainly affected by rainstorm features and physical geographic characteristics in the Yangtze River delta, and it might become more damaging with the increasing rainfall extremes and sprawling impervious surfaces in a changing environment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Fractional Quantum Hall Effect in Weyl Semimetals

Weyl semimetal may be thought of as a gapless topological phase protected by the chiral anomaly, where the symmetries involved in the anomaly are the U(1) charge conservation and the crystal translational symmetry. The absence of a band gap in a weakly interacting Weyl semimetal is mandated by the electronic structure topology and is guaranteed as long as the symmetries and the anomaly are intact. The nontrivial topology also manifests in the Fermi arc surface states and topological response, in particular taking the form of an anomalous Hall effect in magnetic Weyl semimetals, whose magnitude is only determined by the location of the Weyl nodes in the Brillouin zone. In this work, we consider the situation when the interactions are not weak and ask whether it is possible to open a gap in a magnetic Weyl semimetal while preserving its nontrivial electronic structure topology along with the translational and the charge conservation symmetries. Surprisingly, the answer turns out to be yes. The resulting topologically ordered state provides a nontrivial realization of the fractional quantum Hall effect in three spatial dimensions in the absence of an external magnetic field, which cannot be viewed as a stack of two dimensional states. Our state contains loop excitations with nontrivial braiding statistics when linked with lattice dislocations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains

Abstract Type IA topoisomerases interact with G-strand and T-strand ssDNA to regulate DNA topology. However, simultaneous binding of two ssDNA segments to a type IA topoisomerase has not been observed previously. We report here the crystal structure of a type IA topoisomerase with ssDNA segments bound in opposite polarity to the N- and C-terminal domains. Titration of small ssDNA oligonucleotides to Mycobacterium smegmatis topoisomerase I with progressive C-terminal deletions showed that the C-terminal region has higher affinity for ssDNA than the N-terminal active site. This allows the C-terminal domains to capture one strand of underwound negatively supercoiled DNA substrate first and position the N-terminal domains to bind and cleave the opposite strand in the relaxation reaction. Efficiency of negative supercoiling relaxation increases with the number of domains that bind ssDNA primarily with conserved aromatic residues and possibly with assistance from polar/basic residues. A comparison of bacterial topoisomerase I structures showed that a conserved transesterification unit (N-terminal toroid structure) for cutting and rejoining of a ssDNA strand can be combined with two different types of C-terminal ssDNA binding domains to form diverse bacterial topoisomerase I enzymes that are highly efficient in their physiological role of preventing excess negative supercoiling in the genome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genomic region associated with run timing has similar haplotypes and phenotypic effects across three lineages of Chinook salmon

Abstract Conserving life‐history variation is a stated goal of many management programs, but the most effective means by which to accomplish this are often far from clear. Early‐ and late‐migrating forms of Chinook salmon ( Oncorhynchus tshawytscha ) face unequal pressure from natural and anthropogenic forces that may alter the impacts of genetic variation underlying heritable migration timing. Genomic regions of chromosome 28 are known to be strongly associated with migration variation in adult Chinook salmon, but it remains unclear whether there is consistent association among diverse lineages and populations in large basins such as the Columbia River. With high‐throughput genotyping (GT‐seq) and phenotyping methods, we examined the association of genetic variation in 28 markers (spanning GREB1L to ROCK1 of chromosome 28) with individual adult migration timing characteristics gleaned from passive integrated transponder recordings of over 5000 Chinook salmon from the three major phylogeographic lineages that inhabit the Columbia River Basin. Despite the strong genetic differences among them in putatively neutral genomic regions, each of the three lineages exhibited very similar genetic variants in the chromosome 28 region that were significantly associated with adult migration timing phenotypes. This is particularly notable for the interior stream‐type lineage, which exhibits an earlier and more constrained freshwater entry than the other lineages. In both interior stream‐type and interior ocean‐type lineages of Chinook salmon, heterozygotes of the most strongly associated linkage groups had largely intermediate migration timing relative to homozygotes, and results indicate codominance or possibly marginal partial dominance of the allele associated with early migration. Our results lend support to utilization of chromosome 28 variation in tracking and predicting run timing in these lineages of Chinook salmon in the Columbia River.

Willis, Stuart C.↗
DOE OSTI2023

Data-driven Whitney forms for structure-preserving control volume analysis

Control volume analysis models physics via the exchange of generalized fluxes between subdomains. Here, we introduce a scientific machine learning framework adopting a partition of unity architecture to identify physically-relevant control volumes, with generalized fluxes between subdomains encoded via Whitney forms. The approach provides a differentiable parameterization of geometry which may be trained in an end-to-end fashion to extract reduced models from full field data while exactly preserving physics. The architecture admits a data-driven finite element exterior calculus allowing discovery of mixed finite element spaces with closed form quadrature rules. An equivalence between Whitney forms and graph networks reveals that the geometric problem of control volume learning is equivalent to an unsupervised graph discovery problem. The framework is developed for manifolds in arbitrary dimension, with examples provided for H(div) problems in $\mathbb{R}$ establishing convergence and structure preservation properties. Finally, we consider a lithium-ion battery problem where we discover a reduced finite element space encoding transport pathways from high-fidelity microstructure resolved simulations. The approach reduces the 5.89M finite element simulation to 136 elements while reproducing pressure to under 0.1% error and preserving conservation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Using Financial Contracts to Facilitate Informal Leases Within a Western United States Water Market Based on Prior Appropriation

The ability to reallocate water to higher-value uses during drought is an increasingly important “soft-path” tool for managing water resources in an uncertain future. In most of the Western United States, state-level water market institutions that enable reallocation also impose substantial transaction costs on market participants related to regulatory approval and litigation. These transaction costs can be prohibitive for many participants in terms of both costs and lengthy approval periods, limiting transfers and reducing allocation efficiency, particularly during drought crises periods. This manuscript describes a mechanism to reduce transaction costs by adapting an existing form of informal leases to facilitate quicker and less expensive transfers among market participants. Instead of navigating the formal approval process to lease a water right, informal leases are financial contracts for conservation that enable more junior holders of existing rights to divert water during drought, thereby allowing the formal transfer approval process to be bypassed. The informal leasing approach is tested in the Upper Colorado River Basin, where drought and institutional barriers to transfers lead to frequent shortages for urban rights holders along Colorado's Front Range. Informal leases are facilitated via option contracts that include adaptive triggers and that define volumes of additional, compensatory, releases designed to mitigate impacts to instream flows and third parties. Results suggest that more rapid reallocation of water via informal leases could have resulted in up to $222 million in additional benefits for urban rights holders during the historical period 1950–2013.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

Conformational heterogeneity in the dGsw purine riboswitch: role of Mg²⁺ and 2’-dG in aptamer folding

Recent advancements in RNA structural biology have focused on unraveling the complexities of non-coding mRNA elements like riboswitches. These cis-acting regulatory regions undergo structural changes in response to specific cellular metabolites, leading to up or downregulation of downstream genes. The purine riboswitch family regulates many prokaryotic genes involved in purine degradation and biosynthesis. They feature an aptamer domain organized around a 3-way helical junction, where ligand encapsulation occurs at the junctional core. In our study, we chemically probed the aptamer domain of the 2’-dG-sensing purine riboswitch from Mesoplasma florum (dGsw) under various solution conditions to understand how Mg²⁺ and 2’-dG influence riboswitch folding. Here, we find that efficient 2’-dG binding strongly depends on Mg²⁺, indicating that Mg²⁺ is essential for priming dGsw for ligand interactions. We identified a previously undescribed sequence in the 5’ tail of dGsw that is complementary to a conserved helix. The inclusion of this region in a construct led to intramolecular competition between the alternate helix, Palt, and P1. Mutational analysis confirmed that 5’ flanking end of the aptamer domain forms an alternate helix in the absence of ligand. Molecular dynamics simulations revealed that this alternative conformation is stable. This helix may, therefore, facilitate the formation of an anti-terminator helix by opening the 3-way junction surrounding the 2’-dG binding site. Our study further establishes the importance of a closed terminal P1 helix conformation for metabolite binding and suggests that the delicate interplay between P1 and Palt may fine-tune downstream gene regulation. These insights offer a new perspective on riboswitch structure and enhance our understanding of the role that a conformational ensemble plays in riboswitch activity and regulation.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Computational fluid dynamic modeling to determine the indoor environment of an electron-ion collider service building

The design for the Electron-Ion Collider (EIC) calls for several service buildings that house various power supplies and control electronics for the collider ring itself. In order to operate within specified conditions, the ambient air entering the power supplies needs to be within a certain temperature range while dissipating the heat from losses. Proper cooling is therefore a necessity in the service buildings to ensure that every aspect of the EIC works as intended. Since the EIC is in the design stage, we are evaluating the indoor environment of the service building using the current design specifications. We have researched multiple forms of literature and performed the necessary calculations to compile a list of boundary conditions that accurately represent the situation at hand. We are using computational fluid dynamics modeling to solve the conservation equations for mass, momentum, and energy (Navier-Stokes). This allows us to perform a finite element analysis which will give us the flow distribution in the room as well as temperature profiles throughout the building. We have obtained a simulation result giving us the temperature profiles for the building and it shows that the placement of the racks and supply vents are essential to obtaining an even temperature distribution. This model will provide a basis for design decisions which will affect the overall cooling of the service building without extending the schedule and avoiding a costly reworking of the cooling system.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Recommended Representative Isotopic Compositions for Potential VTR Pu Supplies

This document recommends isotopic compositions to represent selected Pu supplies that might be made available for use in VTR driver fuel. These compositions are intended to be conservative representations suitable for determination of environmental impacts associated with use of the selected Pu supplies, but not upper bounds of all possible compositions. The selected Pu supplies under consideration are themselves representations of a more complicated set of possibilities, defined in a manner to allow efficient but conservative analysis of impacts. The source definitions to be considered are as follows: 1) Foreign sources of reactor-grade plutonium. This material would be provided as polished material in an oxide form and is assumed to be transported from Europe (France or England); 2) Domestic, non-weapon sources of plutonium such as unused FFTF fuel, Hanford metal (stored at SRS), and various oxides; 3) Domestic sources of weapons-grade plutonium, including metal from dismantled pits and otherwise excess to stockpile needs.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗