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At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Engineering Polyketide Stereocenters with Ketoreductase Domain Exchanges

Polyketide synthases (PKSs) are versatile biosynthetic megasynthases capable of producing a diverse range of natural products with many applications, including in pharmaceuticals. The stereochemical precision of PKSs makes them a powerful tool for engineering tailored, unnatural polyketides; however, modifying the stereocenters of a PKS product while maintaining production levels remains a significant challenge. In this study, we systematically tested and evaluated strategies for ketoreductase (KR) domain exchanges, the domain responsible for setting stereocenters of polyketide products. After first optimizing the method for KR exchanges, we then performed 44 KR domain exchanges on three different PKSs to obtain high production of all four stereoisomers in vivo. By testing both one- and two-module PKS systems, we investigated how downstream modules process intermediates with altered stereochemistry and found that the configuration of the α-substituents was critical for gatekeeping by the ketosynthase (KS). To overcome this constraint, we investigated two different strategies for altering the KS domain, including introducing targeted mutations in the downstream KS, and exploring boundaries in exchanging the entire functional unit from the donor PKS. Both strategies successfully modified the KS stereocontrol with distinct trade-offs; the functional unit exchange resulted in higher titer improvements, though it was more likely to break the entire PKS. This study demonstrates a comprehensive approach to successfully engineering all four stereochemical configurations in multiple PKS systems, advancing our understanding of and ability to rationally modify polyketide stereochemistry through multiple engineering strategies.

Keiser, Leah S. [Joint BioEnergy Institute (JBEI),↗
DOE OSTI2023

Fringing Analysis and Simulation for the Vera C. Rubin Observatory’s Legacy Survey of Space and Time

Abstract The presence of fringing in astronomical Charge-Coupled Device (CCD) images will have an impact on photometric quality and measurements. Yet its impact on the Vera C. Rubin Observatory’s Legacy Survey of Space and Time (LSST) has not been fully studied. We present a detailed study on fringing for CCDs already implemented on the Rubin Observatory LSST Camera’s focal plane. After making physical measurements and knowing the compositions, we developed a model for the e2v CCDs. We present a method to fit for the internal height variation of the epoxy layer within the sensors based on fringing measurements in a laboratory setting. This method is generic enough that it can be easily modified to work for other CCDs. Using the derived fringing model, we successfully reproduce comparable fringing amplitudes that match the observed levels in images taken by existing telescopes with different optical designs. This model is then used to forecast the expected level of fringing in a single LSST y -band sky background exposure with Rubin telescope optics in the presence of a realistic time-varying sky spectrum. The predicted fringing amplitude in LSST images ranges from 0.04% to 0.2% depending on the location of a CCD on the focal plane. We find that the predicted variation in surface brightness caused by fringing in LSST y -band sky background images is about 0.6 μ Jy arcsec − 2 , which is 40 times larger than the current measurement error. We conclude that it is necessary to include fringing correction in the Rubin’s LSST image processing pipeline.

Astronomy & Astrophysics↗
DOE OSTI2017

Recent advances in stellarator optimization

Computational optimization has revolutionized the field of stellarator design. To date, optimizations have focused primarily on optimization of neoclassical confinement and ideal MHD stability, although limited optimization of other parameters has also been performed. Here, we outline a select set of new concepts for stellarator optimization that, when taken as a group, present a significant step forward in the stellarator concept. One of the criticisms that has been leveled at existing methods of design is the complexity of the resultant field coils. Recently, a new coil optimization code—COILOPT++, which uses a spline instead of a Fourier representation of the coils,—was written and included in the STELLOPT suite of codes. The advantage of this method is that it allows the addition of real space constraints on the locations of the coils. The code has been tested by generating coil designs for optimized quasi-axisymmetric stellarator plasma configurations of different aspect ratios. As an initial exercise, a constraint that the windings be vertical was placed on large major radius half of the non-planar coils. Further constraints were also imposed that guaranteed that sector blanket modules could be removed from between the coils, enabling a sector maintenance scheme. Results of this exercise will be presented. New ideas on methods for the optimization of turbulent transport have garnered much attention since these methods have led to design concepts that are calculated to have reduced turbulent heat loss. We have explored possibilities for generating an experimental database to test whether the reduction in transport that is predicted is consistent with experimental observations. Thus, a series of equilibria that can be made in the now latent QUASAR experiment have been identified that will test the predicted transport scalings. Fast particle confinement studies aimed at developing a generalized optimization algorithm are also discussed. A new algorithm developed for the design of the scraper element on W7-X is presented along with ideas for automating the optimization approach.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

The AGORA High-resolution Galaxy Simulations Comparison Project. VI. Similarities and Differences in the Circumgalactic Medium

Abstract We analyze the circumgalactic medium (CGM) for eight commonly-used cosmological codes in the AGORA collaboration. The codes are calibrated to use identical initial conditions, cosmology, heating and cooling, and star formation thresholds, but each evolves with its own unique code architecture and stellar feedback implementation. Here, we analyze the results of these simulations in terms of the structure, composition, and phase dynamics of the CGM. We show properties such as metal distribution, ionization levels, and kinematics are effective tracers of the effects of the different code feedback and implementation methods, and as such they can be highly divergent between simulations. This is merely a fiducial set of models, against which we will in the future compare multiple feedback recipes for each code. Nevertheless, we find that the large parameter space these simulations establish can help disentangle the different variables that affect observable quantities in the CGM, e.g., showing that abundances for ions with higher ionization energy are more strongly determined by the simulation’s metallicity, while abundances for ions with lower ionization energy are more strongly determined by the gas density and temperature.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1983

Computation of Jupiter interior models from gravitational inversion theory

Spacecraft measurements of Jupiter have provided the mass, standard pressure level radius, rotation law, internal mass distribution multipole moments, and internal composition and temperature distribution constraints, for the present implementation of a method for deriving planetary interior models that exactly satisfy a set of N gravitational constraints by means of appropriate iteration. The models are not forced to fit the more indirectly derived constraints, which are instead used as conistency checks. In the case of an He mass fraction in the envelope Y of 0.2, the inferred pressure at a mass density of about 0.2 g/cu cm is about a factor of 2 higher than would be indicated by experimental H compression data in the relevant pressure range of 100,000 to one million bar. The inferred pressure distribution is in better agreement with the shock data for a nominal Y value of 0.3 + or - 0.05.

Hubbard, W. B.↗
NASA NTRS1990

Extensions of algebraic image operators: An approach to model-based vision

Researchers extend their previous research on a highly structured and compact algebraic representation of grey-level images which can be viewed as fuzzy sets. Addition and multiplication are defined for the set of all grey-level images, which can then be described as polynomials of two variables. Utilizing this new algebraic structure, researchers devised an innovative, efficient edge detection scheme. An accurate method for deriving gradient component information from this edge detector is presented. Based upon this new edge detection system researchers developed a robust method for linear feature extraction by combining the techniques of a Hough transform and a line follower. The major advantage of this feature extractor is its general, object-independent nature. Target attributes, such as line segment lengths, intersections, angles of intersection, and endpoints are derived by the feature extraction algorithm and employed during model matching. The algebraic operators are global operations which are easily reconfigured to operate on any size or shape region. This provides a natural platform from which to pursue dynamic scene analysis. A method for optimizing the linear feature extractor which capitalizes on the spatially reconfiguration nature of the edge detector/gradient component operator is discussed.

Lerner, Bao-Ting↗
NASA NTRS1991

Implementation of a partitioned algorithm for simulation of large CSI problems

The implementation of a partitioned numerical algorithm for determining the dynamic response of coupled structure/controller/estimator finite-dimensional systems is reviewed. The partitioned approach leads to a set of coupled first and second-order linear differential equations which are numerically integrated with extrapolation and implicit step methods. The present software implementation, ACSIS, utilizes parallel processing techniques at various levels to optimize performance on a shared-memory concurrent/vector processing system. A general procedure for the design of controller and filter gains is also implemented, which utilizes the vibration characteristics of the structure to be solved. Also presented are: example problems; a user's guide to the software; the procedures and algorithm scripts; a stability analysis for the algorithm; and the source code for the parallel implementation.

Alvin, Kenneth F.↗
NASA NTRSDate not supplied

Quiet High Speed Fan II (22-inch) Duct Mode Characteristics as Measured by the Rotating Rake Mode Measurement System while Operated in the NASA Glenn 9x15 Low Speed Wind Tunnel

Wind Tunnel test at a tunnel Mach number of 0.10. This was an entry to investigate the effect of “stator clocking” on noise. The fan consisted of a moderately aft swept rotor and an aft swept set of stator vanes. The fan stage consisted of 22 rotor blades, 50 stator vanes, and 10 downstream support struts. A set of stator vanes designed for lower noise was tested as well as a baseline stator vane set. The stator assembly could be rotated several degrees to adjust the clocking angle between the stator vane pack and the strut assembly. All configurations were with a hard wall duct (no acoustic treatment). The NASA Glenn Research Center’s Rotating Rake Mode Measurement System was utilized to obtain a complete map of the acoustic duct modes present in the ducted fan. The system is a radial rake emersed into the duct that continuously rotates about the duct centerline. For the two stator configurations, data were acquired at several different fan speeds which included nominal, approach, cutback, and takeoff conditions. Analysis of the mode power level results at the fan fundamentals showed the improved designed set resulted in lower rotor-stator and rotor-strut interaction acoustic levels for the interaction modes. Varying the angle between the stators and struts was shown to be a viable method to achieve a minimum in rotor-strut interaction mode power level. Multiple-pure-tones generated by the Quiet High Speed Fan II in the inlet were also measured.

Turbofan, Duct Modes↗
NASA NTRSDate not supplied

Quiet High Speed Fan II (22-inch) Duct Mode Characteristics as Measured by the Rotating Rake Mode Measurement System while Operated in the NASA Glenn 9x15 Low Speed Wind Tunnel

Wind Tunnel at a tunnel Mach number of 0.10. This was an entry to investigate the effect of “stator clocking” on noise. The fan consisted of a moderately aft swept rotor and an aft swept set of stator vanes. The fan stage consisted of 22 rotor blades, 50 stator vanes, and 10 downstream support struts. A set of stator vanes designed for lower noise was tested as well as a baseline stator vane set. The stator assembly could be rotated several degrees to adjust the clocking angle between the stator vane pack and the strut assembly. All configurations were with a hard wall duct (no acoustic treatment). The NASA Glenn Research Center’s Rotating Rake Mode Measurement System was utilized to obtain a complete map of the acoustic duct modes present in the ducted fan. The system is a radial rake emersed into the duct that continuously rotates about the duct centerline. For the two stator configurations, data were acquired at several different fan speeds which included nominal, approach, cutback, and takeoff conditions. Analysis of the mode power level results at the fan fundamentals showed the improved designed set resulted in lower rotor-stator and rotor-strut interaction acoustic levels for the interaction modes. Varying the angle between the stators and struts was shown to be a viable method to achieve a minimum in rotor-strut interaction mode power level. Multiple-pure-tones generated by the Quiet High Speed Fan II in the inlet were also measured.

Turbofan, Duct Modes↗
NASA NTRSDate not supplied

Source Diagnostic Fan II (22-Inch) Duct Mode Characteristics as Measured by the Rotating Rake Mode Measurement System while Operated in the NASA Glenn 9x15 Low Speed Wind Tunnel

A 22-inch scale model of the Honeywell Quiet High Speed Fan II was tested in the NASA Glenn 9- by 15-foot Low Speed Wind Tunnel at a tunnel Mach number of 0.10. This was an entry to investigate the effect of “stator clocking” on noise. The fan consisted of a moderately aft swept rotor, and an aft swept set of stator vanes. The fan stage consisted of 22 rotor blades, 50 stator vanes, and 10 downstream support struts. A set of stator vanes designed for lower noise was tested as well as a baseline stator vane set. The stator assembly could be rotated several degrees to adjust the clocking angle between the stator vane pack and the strut assembly. All configurations were with a hard wall duct (no acoustic treatment). The NASA Glenn Research Center’s Rotating Rake Mode Measurement System was utilized to obtain a complete map of the acoustic duct modes present in the ducted fan. The system is a radial rake emersed into the duct that continuously rotates about the duct centerline. For the two stator configurations, data were acquired at several different fan speeds which included nominal, approach, cutback, and takeoff conditions. Analysis of the mode power level results at the fan fundamentals showed the improved designed set resulted in lower rotor-stator and rotor-strut interaction acoustic levels for the interaction modes. Varying the angle between the stators and struts was shown to be a viable method to achieve a minimum in rotor-strut interaction mode power level. Multiple-pure-tones generated by the Quiet High Speed Fan II in the inlet were also measured.

Fan Noise↗
DOE OSTI2021

Lagrangian–Eulerian multidensity topology optimization with the material point method

Abstract In this paper, a hybrid Lagrangian–Eulerian topology optimization (LETO) method is proposed to solve the elastic force equilibrium with the Material Point Method (MPM). LETO transfers density information from freely movable Lagrangian carrier particles to a fixed set of Eulerian quadrature points. This transfer is based on a smooth radial kernel involved in the compliance objective to avoid the artificial checkerboard pattern. The quadrature points act as MPM particles embedded in a lower‐resolution grid and enable a subcell multidensity resolution of intricate structures with a reduced computational cost. A quadrature‐level connectivity graph‐based method is adopted to avoid the artificial checkerboard issues commonly existing in multiresolution topology optimization methods. Numerical experiments are provided to demonstrate the efficacy of the proposed approach.

Li, Yue↗
DOE OSTI2026

Concordant Mode Approach (CMA): Vibrational Analysis of New and Upgraded Intermolecular Benchmarks for Noncovalent Bonding

The Concordant Mode Approach (CMA) is a novel method that offers tremendous potential for increasing the system size and the level of theory attainable in quantum chemical computations of molecular vibrational frequencies. To investigate the extension of CMA to intermolecular vibrations, computations with coupled cluster singles and doubles with perturbative triples theory [CCSD(T)] using two augmented correlation-consistent polarized-valence triple-ζ basis sets (aug-cc-pVTZ or h-aug-ccpVTZ) were performed on 17 prototypical loosely bound complexes of hydrogen-bonded, dispersion, and mixed character. These Level A results provide new and upgraded benchmarks for noncovalent bonding and a severe test for CMA vibrational analyses. The Level A target frequencies were recovered remarkably well using second-order Møller−Plesset perturbation theory (MP2) with h-aug-cc-pVTZ for generating the underlying (Level B) normal modes of the CMA scheme. Employing this Level B within the lowest-rung CMA-0A method reproduces the 435 benchmark frequencies with a mean absolute error (MAE) of 0.23 cm −1 and a corresponding standard deviation (σ) of 0.84 cm −1 ; strikingly, the corresponding subset of 106 interfragment frequencies exhibits MAE = 0.34 cm −1 and σ = 0.90 cm −1 . Subsequent application of the higher-rung CMA-2A scheme eliminates all outliers and reduces the overall MAE to a minuscule 0.08 cm −1 with the inclusion of only 3.0% of the off-diagonal couplings not accounted for by CMA-0A. Accordingly, the highly efficient CMA methodology proves to be robust even for vibrations on flat potential energy surfaces.

Aromatic compounds↗
DOE OSTI2025

Understanding neutron capture processes in uranium deposits using combined U-Sm-Nd isotopic compositions

Valuable insights into the history and evolution of a geologic deposit can be found by investigating neutron capture reactions. Thermal neutron capture reactions occur within both the samarium (Sm) and the uranium (U) systems, where 149 Sm and 235 U can capture neutrons to become 150 Sm and 236 U, respectively. Although largely unexplored, paired measurements of 150 Sm and 236 U could be important for understanding neutron capture effects within uranium ore bodies, and such measurements are potentially useful in nuclear forensics for assessing a material's provenance or mineral exploration. In this work, we refined measurement procedures of Sm isotope compositions utilizing MC-ICPMS. While geologic reference materials were found to have indistinguishable Sm isotope compositions, we found significant isotope variations consistent with nuclear field shift among synthetic Sm standards. Here, this observation highlights that future high-precision Sm isotope investigations need to carefully evaluate synthetic standard(s) against geologic reference materials until an unfractionated and agreed-upon standard is identified. Here, we applied this method to a set of nine uranium ores from the South Australian Beverley North uranium deposits. Although 236 U excesses had been previously reported for these U ores, we found no measurable isotopic shifts in 149 Sm- 150 Sm at the current level of precision (±5 parts per million). One possible explanation for this disparity in the observed neutron capture signatures between U and Sm is that the source(s) of the U and Sm in these ores may be decoupled. This is consistent with the finding that these ores have variable 143 Nd/ 144 Nd, thus demonstrating that diverse sources were involved in the formation of the Beverley North deposits. Alternatively, this deposit may be too young (<50Ma) to have accumulated measurable neutron capture effects in Sm to be detected with the methods employed here.

Mineral exploration↗
NASA NTRS1977

Nickel cadmium cell designs negative to positive material ratio and precharge levels

A review is made of the factors affecting the choices of negative-to-positive materials ratio and negative precharge in nickel-cadmium cells. The effects of these variables on performance are given, and the different methods for setting precharge are evaluated. The effects of special operating requirements on the design are also discussed.

Gross, S.↗
DOE OSTI2022

Electronic structure of intrinsic defects in c -gallium nitride: Density functional theory study without the jellium approximation

Here, we report the first nonjellium, systematic, density functional theory (DFT) study of intrinsic and extrinsic defects and defect levels in zinc-blende (cubic) gallium nitride. We use the local moment counter charge (LMCC) method, the standard Perdew-Becke-Ernzerhoff (PBE) exchange-correlation potential, and two pseudopotentials, where the Ga 3$\textit{d}$ orbitals are either in the core ($d^0$) or explicitly in the valence set ($d^{10}$). We studied 64, 216, 512, and 1000 atom supercells, and demonstrated convergence to the infinite limit, crucial for delineating deep from shallow states near band edges, and for demonstrating the elimination of finite cell-size errors. Contrary to common claims, we find that exact exchange is not required to obtain defect levels across the experimental band gap. As was true in silicon, silicon carbide, and gallium arsenide, the extremal LMCC defect levels of the aggregate of defects yield an effective LMCC defect band gap that is within 10% of the experimental gap (3.3 eV) for both pseudopotentials. We demonstrate that the gallium vacancy is more complicated than previously reported. There is dramatic metastability–a nearest-neighbor nitrogen atom shifts into the gallium site, forming an antisite, nitrogen vacancy pair, which is more stable than the simple vacancy for positive charge states. Our assessment of the $d^0$ and $d^{10}$ pseudopotentials yields minimal differences in defect structures and defect levels. The better agreement of the $d^0$ lattice constant with experiment suggests that the more computationally economical $d^0$ pseudopotentials are sufficient to achieve the fidelity possible within the physical accuracy of DFT, and thereby enable calculations in larger supercells necessary to demonstrate convergence with respect to finite size supercell errors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Greenhouse gas emissions reduction strategies that maximize portfolio-wide life cycle cost reduction, resilience, and environmental justice benefits

While strategies to achieve net-zero emissions at an individual site are well understood, new analysis methods are required for organizations seeking to achieve net-zero across multiple facilities, each with concurrent priority goals. At a portfolio level, distinct locations present varied challenges that cannot be addressed through singular solutions, and competing goals can take precedence with the assumption that net-zero emissions strategies deter from energy resilience and cost savings, therefore negatively impacting nearby communities. This study tests these assumptions by analyzing 16 diverse sites (varying in size, climate, and energy use) to identify strategies that reduce emissions and assess the impact these strategies have on life cycle costs, resilience, and communities with environmental justice concerns. Methods were developed to approximate missing information essential to net-zero evaluation. Established methods were augmented to evaluate life cycle costs, resilience, and environmental justice impacts across a set of strategies and accommodate the multi-criteria analyses. Potential benefits from identified strategies were quantified using site characteristics and a set of corresponding metrics. The net-zero analysis found that 11 sites could use on-site strategies to eliminate all but 2% of emissions generated. The remaining emissions can be offset, for instance through sequestration, executed at the portfolio scale. On-site carbon-free energy was found to reduce 51% of emissions across all sites; efficiency reduced 19% of emissions; sequestration 16%; procured carbon-free energy 15%; fuel switching 1.6%; and fleet electrification 1.3%. Building electrification, however, increased emissions by 4.4%. Different strategies also provide cost, resilience, and/or environmental justice benefits—the degree to which varies with individual site conditions. The findings indicate an advantage to considering the strategies as a comprehensive set, which leads to co-benefits, both in the ability to achieve net-zero goals and in advancing other goals. The results present the case for comprehensive advanced planning at the portfolio level to prioritize investments that will balance the minimization of emissions and life cycle cost with the maximization of resilience and environmental justice benefits. The novel methods for evaluation and integration, valuation of benefits, and consideration at the portfolio scale allow organizations to select investments that simultaneously address multiple key priorities.

Net-Zero Emissions↗
DOE OSTI2019

Theoretical level energies and transition data for ion W{sup 28+}

The ab initio quasirelativistic approach was used to derive transition data for Pd-like tungsten W{sup 28+} ion. This approach was developed specifically for the calculation of spectral parameters for highly charged ions. The relativistic effects were taken into account in the Breit–Pauli approximation. The configuration interaction method was applied to include electron correlation effects. The ground configuration 4p{sup 6}4d{sup 10} and the lowest excited 4p{sup 6}4d{sup 9}4f were considered. The calculations for W{sup 28+} were performed with different sets of interacting configurations in order to evaluate reliability and accuracy of produced results. Level energies, radiative lifetimes τ, Landé g-factors were determined for the excited configuration 4p{sup 6}4d{sup 9}4f of W{sup 28+} levels. The radiative transition wavelengths λ and emission transition probabilities A for the electric and magnetic transitions of various multipole order (up to E5 and M4) among the levels of these two configurations were produced. The uncertainties of computed spectroscopic parameters were evaluated.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data

Operon prediction in prokaryotes is critical not only for understanding the regulation of endogenous gene expression, but also for exogenous targeting of genes using newly developed tools such as CRISPR-based gene modulation. A number of methods have used transcriptomics data to predict operons, based on the premise that contiguous genes in an operon will be expressed at similar levels. While promising results have been observed using these methods, most of them do not address uncertainty caused by technical variability between experiments, which is especially relevant when the amount of data available is small. In addition, many existing methods do not provide the flexibility to determine the stringency with which genes should be evaluated for being in an operon pair. We present OperonSEQer, a set of machine learning algorithms that uses the statistic and p-value from a non-parametric analysis of variance test (Kruskal-Wallis) to determine the likelihood that two adjacent genes are expressed from the same RNA molecule. We implement a voting system to allow users to choose the stringency of operon calls depending on whether your priority is high recall or high specificity. In addition, we provide the code so that users can retrain the algorithm and re-establish hyperparameters based on any data they choose, allowing for this method to be expanded as additional data is generated. We show that our approach detects operon pairs that are missed by current methods by comparing our predictions to publicly available long-read sequencing data. OperonSEQer therefore improves on existing methods in terms of accuracy, flexibility, and adaptability.

59 BASIC BIOLOGICAL SCIENCES↗