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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Inhibition of Pyruvate Kinase From Thermoanaerobacterium saccharolyticum by IMP Is Independent of the Extra-C Domain

The pyruvate kinase (PYK) isozyme from Thermoanaerobacterium saccharolyticum (TsPYK) has previously been used in metabolic engineering for improved ethanol production. This isozyme belongs to a subclass of PYK isozymes that include an extra C-domain. Like other isozymes that include this extra C-domain, we found that TsPYK is activated by AMP and ribose-5-phosphate (R5P). Our use of sugar-phosphate analogs generated a surprising result in that IMP and GMP are allosteric inhibitors (rather than activators) of TsPYK. We believe this to be the first report of any PYK isozyme being inhibited by IMP and GMP. A truncated protein that lacks the extra C-domain is also inhibited by IMP. A screen of several other bacterial PYK enzymes (include several that have the extra-C domain) indicates that the inhibition by IMP is specific to only a subset of those isozymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The structural basis for RNA selectivity by the IMP family of RNA-binding proteins

The IGF2 mRNA-binding proteins (ZBP1/IMP1, IMP2, IMP3) are highly conserved post-transcriptional regulators of RNA stability, localization and translation. They play important roles in cell migration, neural development, metabolism and cancer cell survival. The knockout phenotypes of individual IMP proteins suggest that each family member regulates a unique pool of RNAs, yet evidence and an underlying mechanism for this is lacking. Here, we combine systematic evolution of ligands by exponential enrichment (SELEX) and NMR spectroscopy to demonstrate that the major RNA-binding domains of the two most distantly related IMPs (ZBP1 and IMP2) bind to different consensus sequences and regulate targets consistent with their knockout phenotypes and roles in disease. We find that the targeting specificity of each IMP is determined by few amino acids in their variable loops. As variable loops often differ amongst KH domain paralogs, we hypothesize that this is a general mechanism for evolving specificity and regulation of the transcriptome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Role of the Mobile Active Site Flap in IMP Dehydrogenase Inhibitor Binding

Inosine 5′-monophosphate dehydrogenase (IMPDH) is a promising antibiotic target. This enzyme catalyzes the NAD-dependent oxidation of inosine 5′-monophosphate (IMP) to xanthosine 5′-monophosphate (XMP), which is the rate-limiting step in guanine nucleotide biosynthesis. Bacterial IMPDH-specific inhibitors have been developed that bind to the NAD + site. These inhibitors display varied affinities to different bacterial IMPDHs that are not easily rationalized by X-ray crystal structures of enzyme–inhibitor complexes. Inspection of X-ray crystal structures of 25 enzyme–inhibitor complexes, including 10 newly described, suggested that a mobile active site flap may be a structural determinant of inhibitor potency. Saturation transfer difference NMR experiments also suggested that the flap may contact the inhibitors to varying extents in different IMPDHs. Flap residue Leu413 contacted some inhibitors but was not structured in the crystal structures of other inhibitor complexes. The substitution of Leu413 with Phe or Ala in Bacillus anthracis IMPDH had inhibitor-selective effects, suggesting residue 413 could be a structural determinant of affinity. Curiously, the Ala substitution increased the potency of most inhibitors, even those that contacted Leu413 in the crystal structures. Presteady-state and steady-state kinetics experiments showed that the Leu413Ala substitution had comparable effects on inhibitor binding to the noncovalent E·IMP complex and the covalent intermediate E-XMP*, suggesting that the flap had similar interactions in both complexes. These results demonstrate that contacts do not necessarily indicate favorable interactions, and poorly structured mobile regions should not be discounted when assessing binding determinants.

Conformation↗
DOE OSTI2024

Status of Mercury and Imp: Two Monte Carlo Transport Codes Developed Using Shared Infrastructure at Lawrence Livermore National Laboratory

The Monte Carlo Transport Project at Lawrence Livermore National Laboratory develops two Monte Carlo transport codes used in production by a sizable internal user community. Mercury is a Monte Carlo particle transport code used to model the interaction of neutrons, gammas, and light ions with a material. Imp is an implicit Monte Carlo thermal x-ray photon transport code used to model the interaction of x-ray photons with a material. This paper describes the two codes and highlights recent developments.

Pozulp, Michael↗
DOE OSTI2020

In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5’-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Intermediate Molecular Phenotypes to Identify Genetic Markers of Anthracycline-Induced Cardiotoxicity Risk

Cardiotoxicity due to anthracyclines (CDA) affects cancer patients, but we cannot predict who may suffer from this complication. CDA is a complex trait with a polygenic component that is mainly unidentified. We propose that levels of intermediate molecular phenotypes (IMPs) in the myocardium associated with histopathological damage could explain CDA susceptibility, so variants of genes encoding these IMPs could identify patients susceptible to this complication. Thus, a genetically heterogeneous cohort of mice (n = 165) generated by backcrossing were treated with doxorubicin and docetaxel. We quantified heart fibrosis using an Ariol slide scanner and intramyocardial levels of IMPs using multiplex bead arrays and QPCR. We identified quantitative trait loci linked to IMPs (ipQTLs) and cdaQTLs via linkage analysis. In three cancer patient cohorts, CDA was quantified using echocardiography or Cardiac Magnetic Resonance. CDA behaves as a complex trait in the mouse cohort. IMP levels in the myocardium were associated with CDA. ipQTLs integrated into genetic models with cdaQTLs account for more CDA phenotypic variation than that explained by cda-QTLs alone. Allelic forms of genes encoding IMPs associated with CDA in mice, including AKT1, MAPK14, MAPK8, STAT3, CAS3, and TP53, are genetic determinants of CDA in patients. Two genetic risk scores for pediatric patients (n = 71) and women with breast cancer (n = 420) were generated using machine-learning Least Absolute Shrinkage and Selection Operator (LASSO) regression. Thus, IMPs associated with heart damage identify genetic markers of CDA risk, thereby allowing more personalized patient management.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

The Carbon Budget of Land Conversion: Sugarcane Expansion and Implications for a Sustainable Bioenergy Landscape in Southeastern United States

The expansion of sugarcane onto land currently occupied by improved (IMP) and semi-native (SN) pastures will reshape the U.S. bioenergy landscape. We combined biometric, ground-based and eddy covariance methods to investigate the impact of sugarcane expansion across subtropical Florida on the carbon (C) budget over a 3-year rotation. With 2.3- and 5.1-fold increase in productivity over IMP and SN pastures, sugarcane displayed a C use efficiency (CUE; i.e., fraction of gross C uptake allocated to plant growth) of 0.59, well above that of pastures (0.31–0.23). Sugarcane also had greater C allocation to aboveground productivity and hence, harvestable biomass relative to IMP and SN. Cane heterotrophic respiration over the 3-year rotation (903 ± 335 gC m −2 year −1 ) was 1% and 14% higher than IMP and SN pastures, respectively. These soil C losses responded largely to disturbance over the first year after conversion (1510 ± 227 gC m −2 year −1 ) but declined in subsequent years to an average 599 ± 90 gC m −2 year −1 —well below those of IMP (933 ± 140 gC m −2 year −1 ) and SN (759 ± 114 gC m −2 year −1 ) pastures—despite a significant 40%–61% increase in soil C inputs. Soil C inputs, however, shifted from root-dominated in pastures to litter-dominated in sugarcane, with only 5% C allocation to roots. Reduced decomposition rates in sugarcane were likely driven by changes in the recalcitrance and distribution rather than the size of the newly incorporated soil C pool. As a result, we observed a rapid shift in the net ecosystem C balance (NECB) of sugarcane from a large source immediately following conversion to approaching the net C losses of IMP pastures only 2 years after conversion. The environmental cost of converting pasture to sugarcane underscores the importance of implementing management practices to harness the soil C storage potential of sugarcane in advancing a sustainable bioeconomy in Southeastern United States.

09 BIOMASS FUELS↗
DOE OSTI2018

Large-scale Meteorological Organization of Extreme Weather Events: Final Technical Report

Although the occurrence of regional extreme weather events (EWEs) such as cold air outbreaks, heat waves, droughts and floods are known to be related to planetary climate modes (PCMs) such as the El-Nino Southern Oscillation or North Atlantic Oscillation, intermediate meteorological patterns (IMPs) such as jet stream blocking, cyclones, and high pressure systems are required to connect PCMs to EWEs. Our project has revealed a physical pathway for the interplay among EWEs, IMPs and PCMs. Under support of this award, we have characterized the behavior of IMPs that cause winter cold air outbreaks, extreme floods and warm season dry spells in the US. This includes formulating meteorological “fingerprints” for easily identifying IMPs. The research performed includes a parallel analysis of how well modern climate models are able to simulate IMP behavior. We have also developed a novel approach for characterizing PCM structures and identifying EWE-LMP-PCM linkages. We discovered that dry spells occurring during spring and summer over the US are affected by changes in the North Pacific Ocean temperature. We further revealed the physical origin of a critical jet stream pattern occurring over the North Pacific Ocean that provides a “bridge” between the water cycles of East Asia and North America, respectively. We developed an advanced diagnostic technique (called piecewise tendency diagnosis or PTD) to understand the physical causes for the IMP formation and EWE-LMP-PCM linkages.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Characterizing the X-Ray Emission of Intermediate-mass Pre-main-sequence Stars

We use X-ray and infrared observations to study the properties of three classes of young stars in the Carina Nebula: intermediate-mass (2–5 M {sub ⊙}) pre-main-sequence stars (IMPS; i.e., intermediate-mass T Tauri stars), late-B and A stars on the zero-age main sequence (AB), and lower-mass T Tauri stars (TTS). We divide our sources among these three subclassifications and further identify disk-bearing young stellar objects versus diskless sources with no detectable infrared (IR) excess emission using IR (1–8 μm) spectral energy distribution modeling. We then perform X-ray spectral fitting to determine the hydrogen-absorbing column density (N {sub H}), absorption-corrected X-ray luminosity (L {sub X}), and coronal plasma temperature (kT) for each source. We find that the X-ray spectra of both IMPS and TTS are characterized by similar kT and N {sub H}, and on average L {sub X}/L {sub bol} ~ 4 × 10{sup -4}. IMPS are systematically more luminous in X-rays (by ~0.3 dex) than all other subclassifications, with median L {sub X} = 2.5 × 10{sup 31} erg s{sup -1}, while AB stars of similar masses have X-ray emission consistent with TTS companions. These lines of evidence converge on a magnetocoronal flaring source for IMPS X-ray emission, a scaled-up version of the TTS emission mechanism. IMPS therefore provide powerful probes of isochronal ages for the first ~10 Myr in the evolution of a massive stellar population, because their intrinsic, coronal X-ray emission decays rapidly after they commence evolving along radiative tracks. We suggest that the most luminous (in both X-rays and IR) IMPS could be used to place empirical constraints on the location of the intermediate-mass stellar birth line.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Finite and infinite matrix product states for Gutzwiller projected mean-field wave functions

Matrix product states (MPS) and “dressed” ground states of quadratic mean fields (e.g., Gutzwiller projected Slater determinants) are both important classes of variational wave functions. This latter class has played important roles in understanding superconductivity and quantum spin liquids. We present a method to obtain both the finite and infinite MPS (iMPS) representation of the ground state of an arbitrary fermionic quadratic mean-field Hamiltonian (which in the simplest case is a Slater determinant and in the most general case is a Pfaffian). We also show how to represent products of such states (e.g., determinants times Pfaffians). From this representation one can project to single occupancy and evaluate the entanglement spectra after Gutzwiller projection. We then obtain the MPS and iMPS representation of Gutzwiller projected mean-field states that arise from the variational slave-fermion approach to the S = 1 bilinear-biquadratic quantum spin chain. To accomplish this, we develop an approach to orthogonalize degenerate iMPS to find all the states in the degenerate ground-state manifold. We find the energies of the MPS and iMPS states match the variational energies closely, indicating the method is accurate and there is minimal loss due to truncation error. We then present an exploration of the entanglement spectra of projected slave-fermion states, exploring their qualitative features and finding good qualitative agreement with the respective exact ground-state spectra found from density matrix renormalization group.

1-dimensional spin chains↗
DOE OSTI2020

A Novel Architecture for Attack-Resilient Wide-Area Protection and Control System in Smart Grid

Wide-area protection and control (WAPAC) systems are widely applied in the energy management system (EMS) that rely on a wide-area communication network to maintain system stability, security, and reliability. As technology and grid infrastructure evolve to develop more advanced WAPAC applications, however, so do the attack surfaces in the grid infrastructure. This paper presents an attack-resilient system (ARS) for the WAPAC cybersecurity by seamlessly integrating the network intrusion detection system (NIDS) with intrusion mitigation and prevention system (IMPS). In particular, the proposed NIDS utilizes signature and behavior-based rules to detect attack reconnaissance, communication failure, and data integrity attacks. Further, the proposed IMPS applies state transition-based mitigation and prevention strategies to quickly restore the normal grid operation after cyberattacks. As a proof of concept, we validate the proposed generic architecture of ARS by performing experimental case study for wide-area protection scheme (WAPS), one of the critical WAPAC applications, and evaluate the proposed NIDS and IMPS components of ARS in a cyber-physical testbed environment. Our experimental results reveal a promising performance in detecting and mitigating different classes of cyberattacks while supporting an alert visualization dashboard to provide an accurate situational awareness in real-time.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2026

Impacts of Pasture Conversion to Sugarcane on Water Fluxes and Water Use Efficiency in the Southeastern US

The expansion of sugarcane (cane), a high-yielding perennial crop, will likely reshape the bioenergy landscape in the Southeastern US. However, its ecohydrological implications, particularly following conversion from grazed pastures, a dominant land use in the region, remain highly uncertain. We investigated the impact of cane expansion on evapotranspiration (ET) and its partitioning, and the mechanisms influencing both ET components and water use efficiency (WUE) across multiple scales and growth cycles in subtropical Florida. We combined eddy covariance, biometric measurements, and process-based stomatal conductance (g s ) models. ET was 1.7% lower in cane than in improved pasture (IMP) but exceeded that in semi-native pasture (SN) by 21%. Transpiration (T) followed a similar pattern, consistent with lower g s in cane relative to IMP. Cane had more conservative water use and greater sensitivity of g s to vapor pressure deficit (VPD) compared to IMP pasture, suggesting cane may be more tolerant of increasing atmospheric water demand. In contrast, SN showed lower g s and weaker stomatal sensitivity to VPD compared to cane, resulting in lower T. In cane, stomatal regulation and T varied across growth cycles, with stomata becoming less water conservative as stands matured, highlighting the importance of incorporating stand age-dependent stomatal regulation into hydrological models. Evaporation (E) was higher in cane than pastures (19%–26%), partially offsetting WUE gains. Cane exhibited higher intrinsic WUE (GPP/g s ; Gross Primary Productivity), ecosystem WUE (GPP/ET), and harvest WUE (harvest/ET) than both pasture types. Large-scale pasture-to-cane conversion could produce widely contrasting hydrological outcomes. The net regional impact will depend on the proportion of each pasture type converted and on cane's high g s sensitivity to VPD, which triggers tight stomatal regulation and conservative water use, both of which will become increasingly consequential under intensifying atmospheric water demand.

bioenergy↗
DOE OSTI2019

Designing Flexibility into the Authorized Radioactive Contents of the 9982 Shipping Package (Midterm Report)

With regards to the planned contents for the 9982, three sets of radionuclides have been analyzed. A set of percentages by weight for plutonium from 3013 canisters, training sources sent in 9977’s, and americium standards from 9978’s were used as the bases for realistic contents that could be shipped in a 9982 package. Using the tables and limits located in G-BDR-A-00001 Rev. E, the calculations began by determining the mass limits for the radionuclides in each source. These mass limits were then used alongside the mass of the radionuclides in the sum-of-the-fractions methodology present in the content description. If this summation is less than or equal to one, the contents are allowed for shipment in the 9982. For the aforementioned sets, the listed radionuclides could be shipped as-is; however, the goal of the calculations is to determine the maximum content mass allowed. To do so, the percentages of weight were used to find where the summations would equal one rather than simply satisfy the inequality. By solving for the content mass when the inequality equals one, the maximum content mass is calculated, which can then be multiplied by each percent weight to get each radionuclide’s mass. The MCNP input files have also been compared to find differences between the oxide and metals forms of the radionuclides. While there are several differences present that make sense, such as oxides have more mass and a lower density due to the presence of oxygen in the oxide forms, there are other differences that are possibly unintentional. With the input files for the metals, both with and without a shielding pig, neutrons are being used in the photon models, seen by “imp:n” being present within the file instead of “imp:p”, where “imp” stands for the importance of a region for either neutrons or photons. Effectively, this results in the dose due to photons being modelled with neutrons instead, potentially resulting in the calculated dose rates being incorrect. As MCNP is proprietary, I do not have access to it here and must consult with the person handling the shielding calculations to discuss what these differences may affect and how to change them. If he remains out of the office or if fixing these files takes longer than expected, the final report may focus more on the contents while discussing these differences; however, it could potentially lack discussion on finalizing the planned contents due to the mass limits still needing to be calculated.

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

Spatial mapping of the localized corrosion behavior of a magnesium alloy AZ31B tungsten inert gas weld

Sections of a magnesium alloy, AZ31B, joined with tungsten inert gas (TIG) welding, were examined with scanning electrochemical microscopy (SECM) and scanning Kelvin probe force microscopy (SKPFM) to investigate corrosion mechanisms by correlating observed corrosion behavior with weld-affected microstructural variations. Insight into the changing nature of the galvanic couples between weld zones and at localized microgalvanic sites were investigated using SECM and SKPFM to map both electrochemically active regions and Volta potential differences across the weld-affected zones. The formation of an Al-Zn solidification network in the fusion zone (FZ) at and near the TIG weld epicenter differs from the outer heat-affected zone (HAZ), where intermetallic particles (IMPs) are the notable secondary phase from the magnesium matrix. These microstructures were mapped with SKPFM before and after brief exposure to a salt solution, revealing micro-galvanic couples as the main driving force to corrosion initiation and propagation within each zone. The IMPs and Al-Zn solidification network act as strong cathodes and govern the corrosion processes. The galvanic coupling and evolution of the intrinsic corrosion behavior between the weld zones is explained by monitoring the hydrogen evolution reaction (HER) with SECM over time. Anodically induced cathodic activation is confirmed for this welded material, as micro-galvanic couples between microstructural features are found to transition over time to broad electrochemically active areas within the weld-affected zones, resulting in polarity reversal as time of exposure proceeds.

Anodically induced cathodic activation↗
DOE OSTI2022

Integration of software tools for integrative modeling of biomolecular systems

Integrative modeling computes a model based on varied types of input information, be it from experiments or prior models. Often, a type of input information will be best handled by a specific modeling software package. In such a case, we desire to integrate our integrative modeling software package, Integrative Modeling Platform (IMP), with software specialized to the computational demands of the modeling problem at hand. After several attempts, however, we have concluded that even in collaboration with the software's developers, integration is either impractical or impossible. The reasons for the intractability of integration include software incompatibilities, differing modeling logic, the costs of collaboration, and academic incentives. In the integrative modeling software ecosystem, several large modeling packages exist with often redundant tools. So we reason, therefore, that the other development groups have similarly concluded that the benefit of integration does not justify the cost. As a result, modelers are often restricted to the set of tools within a single software package. The inability to integrate tools from distinct software negatively impacts the quality of the models and the efficiency of the modeling. As the complexity of modeling problems grows, we seek to galvanize developers and modelers to consider the long-term benefit that software interoperability yields. In this article, we formulate a demonstrative set of software standards for implementing a model search using tools from independent software packages and discuss our efforts to integrate IMP and the crystallography suite Phenix within the Bayesian modeling framework.

59 BASIC BIOLOGICAL SCIENCES↗