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DOE OSTI2020

Accurate Identification of Deamidation and Citrullination from Global Shotgun Proteomics Data Using a Dual-Search Delta Score Strategy

While proteins with deamidated/citrullinated amino acids play critical roles in the pathogenesis of many human diseases, identifying these modifications in complex biological samples has been an ongoing challenge. Herein we present a method to accurately identify these modifications from shotgun proteomics data from a deep proteome profiling study of human pancreatic islets obtained by laser capture microdissection. All MS/MS spectra were searched against database by MSGF+ twice with or without a +0.9840 Da mass shift on amino acids asparagine, glutamine, and arginine (NQR) as a dynamic modification. Consequently, for each spectrum the resulting two peptide-to-spectrum matches (PSM) with their respective MSGF+ scores were used for Delta Score calculation. It was observed that all PSMs with positive Delta Score values were clustered with mass errors around 0 ppm, while PSMs with negative Delta Score values were distributed nearly equally within the defined mass error range (20 ppm) for database searching. To estimate false discovery rate (FDR), a “pseudo-decoy” approach was applied whether datasets were searched against a database with a “real modification” mass shift (+0.9840 Da) and a “mock modification” mass shift (+1.0227 Da). FDR was controlled to ~2% with a Delta Score filter greater than zero. Manual inspection of spectra showed that PSMs with positive Delta Score value contained deamidated/citrullinated fragments in their MS/MS spectra. Finally, the results demonstrated that in-situ deamidated/citrullinated peptides can be accurately identified from shotgun tissue proteomics data by the Dual-search Delta Score Strategy.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1979

Recent theoretical developments and experimental studies pertinent to vortex flow aerodynamics, with a view towards design

Recent progress in a research program directed toward an improved vortex flow technology base was reviewed. Analysis methods for conical flow and analysis and design methods for nonconical flows are presented. Applications are made for a variety of planar, nonplanar, and interferring lifting surfaces. Several methods are shown to provide reasonable estimates of over-all forces and moments for simple wing planforms with the suction analogy method currently offering the most versatility for arbitrary configuration applications. For the prediction of surface loadings the free vortex sheet method being developed by Boeing is shown to have considerable promise and further development of this type of method is encouraged. A data base for ogee strake-wing configurations is summarized with an emphasis on the requirements for maximizing the interference lift. A strake planform design procedure is discussed and a first solution (gothic in planview) is integrated with a wing body. The data show the strake to exhibit expected stable vortex characteristics. It was found that, apart from increasing sweep, conically cambered delta wings developed drag levels approaching that of attached flow with increasing either the lift or the wing camber height, lastly, an approximate vortex flow design method, based on the suction analogy, is outlined and an example is given.

Lamar, J. E.↗

NASA NTRS2003

Blind Leak Detection for Closed Systems

The current inspection technique for locating interstitial leaking in the Space Shuttle Main Engine nozzles is the application of a liquid leak check solution in the openings where the interstitials space between the tubing and the structural jacket vent out the aft end of the nozzle, while its cooling tubes are pressurized to 25 psig with Helium. When a leak is found, it is classified, and if the leak is severe enough the suspect tube is cut open so that a boroscope can be inserted to find the leak point. Since the boroscope can only cover a finite tube length and since it is impossible to identify which tube (to the right or left of the identified interstitial) is leaking, many extra and undesired repairs have been made to fix just one leak. In certain instances when the interstitials are interlinked by poor braze bonding, many interstitials will show indications of leaking from a single source. What is desired is a technique that can identify the leak source so that a single repair can be performed. Dr, Samuel Russell and James Walker, both with NASA/MSFC have developed a thermographic inspection system that addresses a single repair approach. They have teamed with Boeing/Rocketdyne to repackage the inspection processes to be suitable to address full scale Shuttle development and flight hardware and implement the process at NASA centers. The methods and results presented address the thermographic identification of interstitial leaks in the Space Shuttle Main Engine nozzles. A highly sensitive digital infrared camera (capable of detecting a delta temperature difference of 0.025 C) is used to record the cooling effects associated with a leak source, such as a crack or pinhole, hidden within the nozzle wall by observing the inner hot wall surface as the nozzle is pressurized, These images are enhanced by digitally subtracting a thermal reference image taken before pressurization. The method provides a non-intrusive way of locating the tube that is leaking and the exact leak source position to within a very small axial distance. Many of the factors that influence the inspectability of the nozzle are addressed; including pressure rate, peak pressure, gas type, ambient temperature and surface preparation. Other applications for this thermographic inspection system are the Reinforced-Carbon-Carbon (RCC) leading edge of the Space Shuttle orbiter and braze joint integrity.

Oelgoetz, Peter↗

DOE OSTI2023

Calculation of Dynamical Response Functions Using a Bound-State Method

Abstract We investigate a method to extract response functions (dynamical polarisabilities) directly from a bound-state approach applied to calculations of perturbation-induced reactions. The use of a square-integrable basis leads to a response in the form of a sum of $$\delta $$ δ functions. We integrate this over energy and fit a smooth function to the resulting stepwise-continuous one. Its derivative gives the final approximation to the physical response function. We show that the method reproduces analytical results where known, and analyse the details for a variety of models. We apply it to some simple models, using the stochastic variational method as the numerical method. Albeit we find that this approach, and other numerical techniques, have some difficulties with the threshold behavior in coupled-channel problems with multiple thresholds, its stochastic nature allows us to extract robust results even for such cases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Machine Learning-Driven Conservative-to-Primitive Conversion in Hybrid Piecewise Polytropic and Tabulated Equations of State

We present a novel machine learning (ML)-based method to accelerate conservative-to-primitive inversion, focusing on hybrid piecewise polytropic and tabulated equations of state. Traditional root-finding techniques are computationally expensive, particularly for large-scale relativistic hydrodynamics simulations. To address this, we employ feedforward neural networks (NNC2PS and NNC2PL), trained in PyTorch (2.0+) and optimized for GPU inference using NVIDIA TensorRT (8.4.1), achieving significant speedups with minimal accuracy loss. The NNC2PS model achieves 𝐿 1 and 𝐿 ∞ errors of 4.54 × 10 −7 and 3.44 × 10−6, respectively, while the NNC2PL model exhibits even lower error values. TensorRT optimization with mixed-precision deployment substantially accelerates performance compared to traditional root-finding methods. Specifically, the mixed-precision TensorRT engine for NNC2PS achieves inference speeds approximately 400 times faster than a traditional single-threaded CPU implementation for a dataset size of 1,000,000 points. Ideal parallelization across an entire compute node in the Delta supercomputer (dual AMD 64-core 2.45 GHz Milan processors and 8 NVIDIA A100 GPUs with 40 GB HBM2 RAM and NVLink) predicts a 25-fold speedup for TensorRT over an optimally parallelized numerical method when processing 8 million data points. Moreover, the ML method exhibits sub-linear scaling with increasing dataset sizes. We release the scientific software developed, enabling further validation and extension of our findings. By exploiting the underlying symmetries within the equation of state, these findings highlight the potential of ML, combined with GPU optimization and model quantization, to accelerate conservative-to-primitive inversion in relativistic hydrodynamics simulations.

conservative-to-primitive conversion↗

DOE OSTI2026

Surface water nitrogen and sediment potential nitrate reduction rates, nutrient stocks, and stable isotopes from nine wetlands at the Tanglewood Biological Station, Alabama

This dataset supports a broader study investigating wetland hydrologic and biogeochemical responses to inundation disturbances. Bimonthly surface water and sediment sampling events were conducted at nine wetland sites situated within the Tanglewood Biological Station in Alabama from April 2023 to February 2024. The contents included in the data package include surface water nitrogen (nitrogen oxides and ammonium) and sediment potential nitrate reduction rates (measured as potential denitrification and dissimilatory nitrate reduction to ammonium processing), nutrient stocks (total carbon, total nitrogen, and organic matter), and stable isotopes (carbon and nitrogen). Water level data related to each wetland location can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/2530253 (Kirker et al., 2024) and related water geochemistry data can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/3001967 (Forbes et al., 2025). In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) file-level metadata; (2) data dictionary; (3) field metadata and international generic sample numbers (IGSNs); (4) readme; (5) the field protocol; and (6) a subfolder with sample data. The sample data subfolder contains (1) sediment potential denitrification rate, (2) sediment potential dissimilatory nitrate reduction to ammonium (DNRA) rate, (3) sediment total carbon and nitrogen content, (4) sediment stable isotopes (delta nitrogen-15 and delta carbon-13), (5) sediment percent organic matter, (6) surface water nitrous oxides, (7) surface water ammonium, and (8) methods codes. All files are .csv or .pdf.

Ammonium↗

NASA NTRS1992

A low-speed wind tunnel study of vortex interaction control techniques on a chine-forebody/delta-wing configuration

A low speed wind tunnel evaluation was conducted of passive and active techniques proposed as a means to impede the interaction of forebody chine and delta wing vortices, when such interaction leads to undesirable aerodynamic characteristics particularly in the post stall regime. The passive method was based on physically disconnecting the chine/wing junction; the active technique employed deflection of inboard leading edge flaps. In either case, the intent was to forcibly shed the chine vortices before they encountered the downwash of wing vortices. Flow visualizations, wing pressures, and six component force/moment measurements confirmed the benefits of forced vortex de-coupling at post stall angles of attack and in sideslip, viz., alleviation of post stall zero beta asymmetry, lateral instability and twin tail buffet, with insignificant loss of maximum lift.

Rao, Dhanvada M.↗

NASA NTRS1992

A low-speed wind tunnel study of vortex interaction control techniques on a chine-forebody/delta-wing configuration

Rao, Dhanvada M.↗

NASA NTRS1992

Calculations of separated vortex flows at low speed for low-aspect-ratio wings

An implicit finite-difference scheme has been developed for solving three-dimensional incompressible Navier-Stokes equations. Computations for complicated vortical flows past several sharp- and round-edged delta and double-delta wings at high angles of attack and sideslip are discussed. Computed results demonstrate the effectiveness of the present method and show good agreement with experimental data.

Liu, C. H.↗

NASA NTRS2004

Curved-Focal-Plane Arrays Using Deformed-Membrane Photodetectors

A versatile and simple approach to the design and fabrication of curved-focal-plane arrays of silicon-based photodetectors is being developed. This approach is an alternative to the one described in "Curved Focal-Plane Arrays Using Back- Illuminated High-Purity Photodetectors" (NPO-30566), NASA Tech Briefs, Vol. 27, No. 10 (October 2003), page 10a. As in the cited prior article, the basic idea is to improve the performance of an imaging instrument and simplify the optics needed to obtain a given level of performance by making an image sensor (in this case, an array of photodetectors) conform to a curved focal surface, instead of designing the optics to project an image onto a flat focal surface. There is biological precedent for curved-focal-surface designs: retinas - the image sensors in eyes - conform to the naturally curved focal surfaces of eye lenses. The present approach is applicable to both front-side- and back-side-illuminated, membrane photodetector arrays and is being demonstrated on charge-coupled devices (CCDs). The very-large scale integrated (VLSI) circuitry of such a CCD or other array is fabricated on the front side of a silicon substrate, then the CCD substrate is attached temporarily to a second substrate for mechanical support, then material is removed from the back to obtain the CCD membrane, which typically has a thickness between 10 and 20 m. In the case of a CCD designed to operate in back-surface illumination, delta doping can be performed after thinning to enhance the sensitivity. This approach is independent of the design and method of fabrication of the front-side VLSI circuitry and does not involve any processing of a curved silicon substrate. In this approach, a third substrate would be prepared by polishing one of its surfaces to a required focal-surface curvature. A CCD membrane fabricated as described above would be pressed against, deformed into conformity with, and bonded to, the curved surface. The technique used to press and bond the CCD membrane would depend on the nature of the supporting material (see figure). For example, if the third substrate were made of quartz frit, the substrate would be prepared by suffusing it with epoxy. Then one would take advantage of the porosity of the frit by applying a partial vacuum to the opposite surface of the frit, causing atmospheric pressure to push the CCD membrane against the curved surface. The curing of the epoxy would bond the CCD membrane to the curved surface. Alternatively, if the third substrate were made of a nonporous material, the curved substrate surface would be prepared by coating it with a wax or an uncured epoxy. The CCD membrane would be pressed against the coated, curved surface by use of a suitably pressurized balloon. The CCD membrane would then become bonded to the curved surface by curing of the epoxy or freezing of the wax.

Nikzad, Shouleh↗

NASA NTRS2011

Electrodynamic Tethers for Novel LEO Missions

The exponential increase of launch system size - and cost - with deltaV makes missions requiring large total impulse cost prohibitive. Northrop Grumman and partners have matured a fundamentally different method for generating propulsion using electrodynamic tethers (EDTs) that escapes the limitations of the rocket equation. With essentially unlimited delta V, we can perform new classes of missions that are currently unaffordable or unfeasible.

Kantner, Michael↗

NASA NTRS1999

Hardware and Methods of the Optical End-to-End Test of the Far Ultraviolet Spectroscopic Explorer (FUSE)

The Far Ultraviolet Spectroscopic Explorer (FUSE), currently being tested and scheduled for a 1999 launch, is an astrophysics satellite designed to provide high spectral resolving power (Lambda/(Delta)Lambda = 24,000-30,000) over the interval 90.5-118.7 nm. The FUSE optical path consists of four co-aligned, normal incidence, off-axis parabolic, primary mirrors which illuminate separate Rowland circle spectrograph channels equipped with holographic gratings and delay line microchannel plate detectors. We describe the hardware and methods used for the optical end-to-end test of the FUSE instrument during satellite integration and test. Cost and schedule constraints forced us to devise a simplified version of the planned optical test which occurred in parallel with satellite thermal-vacuum testing. The optical test employed a collimator assembly which consisted of four co-aligned, 15" Cassegrain telescopes which were positioned above the FUSE instrument, providing a collimated beam for each optical channel. A windowed UV light source, remotely adjustable in three axes, was mounted at the focal plane of each collimator. Problems with the UV light sources, including high F-number and window failures, were the only major difficulties encountered during the test. The test succeeded in uncovering a significant problem with the secondary structure used for the instrument closeout cavity and, furthermore, showed that the mechanical solution was successful. The hardware was also used extensively for simulations of science observations, providing both UV light for spectra and visible light for the fine error sensor camera.

Conard, Steven J.↗

NASA NTRS1992

A comparison of lidar inversion methods for cirrus applications

Several methods for inverting the lidar equation are suggested as means to derive the cirrus optical properties (beta backscatter, alpha extinction coefficients, and delta optical depth) at one wavelength. The lidar equation can be inverted in a linear or logarithmic form; either solution assumes a linear relationship: beta = kappa(alpha), where kappa is the lidar ratio. A number of problems prevent us from calculating alpha (or beta) with a good accuracy. Some of these are as follows: (1) the multiple scattering effect (most authors neglect it); (2) an absolute calibration of the lidar system (difficult and sometimes not possible); (3) lack of accuracy on the lidar ratio k (taken as constant, but in fact it varies with range and cloud species); and (4) the determination of boundary condition for logarithmic solution which depends on signal to noise ration (SNR) at cloud top. An inversion in a linear form needs an absolute calibration of the system. In practice one uses molecular backscattering below the cloud to calibrate the system. This method is not permanent because the lower atmosphere turbidity is variable. For a logarithmic solution, a reference extinction coefficient (alpha(sub f)) at cloud top is required. Several methods to determine alpha(sub f) were suggested. We tested these methods at low SNR. This led us to propose two new methods referenced as S1 and S2.

Elouragini, Salem↗

DOE OSTI2020

Affine Approximation of Parametrized Kernels and Model Order Reduction for Nonlocal and Fractional Laplace Models

In this work, we consider parametrized problems driven by spatially nonlocal integral operators with parameter-dependent kernels. In particular, kernels with varying nonlocal interaction radius $\delta > 0$ and fractional Laplace kernels, parametrized by the fractional power $s\in(0,1)$, are studied. Furthermore, in order to provide an efficient and reliable approximation of the solution for different values of the parameters, we develop the reduced basis method as a parametric model order reduction approach. Major difficulties arise since the kernels are not affine in the parameters, singular, and discontinuous. Moreover, the spatial regularity of the solutions depends on the varying fractional power $s$. To address this, we derive regularity and differentiability results with respect to $\delta$ and $s$, which are of independent interest for other applications such as optimization and parameter identification. We then use these results to construct affine approximations of the kernels by local polynomials. Finally, we certify the method by providing reliable a posteriori error estimators, which account for all approximation errors, and support the theoretical findings by numerical experiments.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1981

Effect of leading-edge vortex flaps on aerodynamic performance of delta wings

The effect of leading-edge vortex flaps on the aerodynamic characteristics of highly swept-back wings is analytically investigated, using the free vortex sheet method. The method, based on a three-dimensional inviscid flow model, is an advanced panel type employing quadratic doublet distributions to represent the wing surface, rolled-up vortex sheet and wake and is capable of computing forces, moments and surface pressures.

Reddy, C. S.↗

NASA NTRS1995

A study of the vortex flow over 76/40-deg double-delta wing

A low-speed wind-tunnel study of the flow about a 76/40-deg double-delta wing is described for angles of attack ranging from -10 to 25 deg and Reynolds numbers ranging from 0.5 to 1.5 Million. The study was conducted to provide data for the purpose of understanding the vortical flow behavior and for validating Computational Fluid Dynamics methods. Flow visualization tests have provided insight into the effect of the angle of attack and Reynolds number of the vortex-dominated flow both on and off of the surface of the double-delta wing. Upper surface pressure recordings from pressure orifices and Pressure Sensitive Paint have provided data on the pressures induced by the vortices. Flowfield surveys were carried out at an angle of attack of 10 deg by using a thin 5-hole probe. Numerical solutions of the compressible thin-layer Navier-Stokes equations were conducted and compared to the experimental data.

Verhaagen, N. G.↗

DOE OSTI2021

Measurements of multiplicity fluctuations of identified hadrons in inelastic proton–proton interactions at the CERN Super Proton Synchrotron

Measurements of multiplicity fluctuations of identified hadrons produced in inelastic p+p interactions at 31, 40, 80, and 158 $\text {Ge}\text {V}/c$ beam momentum are presented. Three different measures of multiplicity fluctuations are used: the scaled variance $\omega $ and strongly intensive measures $\Sigma $ and $\Delta $. These fluctuation measures involve second and first moments of joint multiplicity distributions. Data analysis is preformed using the Identity method which corrects for incomplete particle identification. Strongly intensive quantities are calculated in order to allow for a direct comparison to corresponding results on nucleus–nucleus collisions. The results for different hadron types are shown as a function of collision energy. A comparison with predictions of string-resonance Monte-Carlo models: Epos, Smash and Venus, is also presented.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1975

Development and demonstration of a flutter-suppression system using active controls

The application of active control technology to suppress flutter was demonstrated successfully in the transonic dynamics tunnel with a delta-wing model. The model was a simplified version of a proposed supersonic transport wing design. An active flutter suppression method based on an aerodynamic energy criterion was verified by using three different control laws. The first two control laws utilized both leading-edge and trailing-edge active control surfaces, whereas the third control law required only a single trailing-edge active control surface. At a Mach number of 0.9 the experimental results demonstrated increases in the flutter dynamic pressure from 12.5 percent to 30 percent with active controls. Analytical methods were developed to predict both open-loop and closed-loop stability, and the results agreed reasonably well with the experimental results.

Sandford, M. C.↗