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DOE OSTI2021

Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14

Abstract The inter-residue contact prediction and deep learning showed the promise to improve the estimation of protein model accuracy (EMA) in the 13th Critical Assessment of Protein Structure Prediction (CASP13). To further leverage the improved inter-residue distance predictions to enhance EMA, during the 2020 CASP14 experiment, we integrated several new inter-residue distance features with the existing model quality assessment features in several deep learning methods to predict the quality of protein structural models. According to the evaluation of performance in selecting the best model from the models of CASP14 targets, our three multi-model predictors of estimating model accuracy (MULTICOM-CONSTRUCT, MULTICOM-AI, and MULTICOM-CLUSTER) achieve the averaged loss of 0.073, 0.079, and 0.081, respectively, in terms of the global distance test score (GDT-TS). The three methods are ranked first, second, and third out of all 68 CASP14 predictors. MULTICOM-DEEP, the single-model predictor of estimating model accuracy (EMA), is ranked within top 10 among all the single-model EMA methods according to GDT-TS score loss. The results demonstrate that inter-residue distance features are valuable inputs for deep learning to predict the quality of protein structural models. However, larger training datasets and better ways of leveraging inter-residue distance information are needed to fully explore its potentials.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Recognition of nonproline N-terminal residues by the Pro/N-degron pathway

Eukaryotic N-degron pathways are proteolytic systems whose unifying feature is their ability to recognize proteins containing N-terminal (Nt) degradation signals called N-degrons, and to target these proteins for degradation by the 26S proteasome or autophagy. GID4, a subunit of the GID ubiquitin ligase, is the main recognition component of the proline (Pro)/N-degron pathway. GID4 targets proteins through their Nt-Pro residue or a Pro at position 2, in the presence of specific downstream sequence motifs. Here we show that human GID4 can also recognize hydrophobic Nt-residues other than Pro. One example is the sequence Nt-IGLW, bearing Nt-Ile. Nt-IGLW binds to wild-type human GID4 with a $K_d$ of 16 μM, whereas the otherwise identical Nt-Pro–bearing sequence PGLW binds to GID4 more tightly, with a $K_d$ of 1.9 μM. Despite this difference in affinities of GID4 for Nt-IGLW vs. Nt-PGLW, we found that the GID4-mediated Pro/N-degron pathway of the yeast Saccharomyces cerevisiae can target an Nt-IGLW–bearing protein for rapid degradation. We solved crystal structures of human GID4 bound to a peptide bearing Nt-Ile or Nt-Val. We also altered specific residues of human GID4 and measured the affinities of resulting mutant GID4s for Nt-IGLW and Nt-PGLW, thereby determining relative contributions of specific GID4 residues to the GID4-mediated recognition of Nt-Pro vs. Nt-residues other than Pro. These and related results advance the understanding of targeting by the Pro/N-degron pathway and greatly expand the substrate recognition range of the GID ubiquitin ligase in both human and yeast cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Photoelectron–residual-ion interaction in angle-resolved streaked shake-up ionization of helium

Streaked photoelectron emission spectra access the correlated dynamics of photoelectrons and residual target electrons with attosecond temporal resolution. Here, we calculated ab initio single-ionization spectra for photoemission from helium atoms by colinearly polarized ultrashort XUV and assisting few-femtosecond IR pulses. Distinguishing direct and shake-up ionization resulting in ground-state and excited (𝑛 = 2, 3) He + residual ions, respectively, we examined the effects of the correlated photoemission dynamics on the photoelectron phase accumulation as a function of the observable photoelectron detection direction and kinetic energy and XUV–IR pulse delay. We tracked the dynamical evolution of the residual ion in relative streaked photo- emission delays and found dominant contributions for shake-up emission from the residual-ion–photoelectron interaction. These are in very good and fair agreement, respectively, for 𝑛 = 2 and 𝑛 = 3 shake-up photoemission along the pulse-polarization directions, with previous experimental and theoretical investigations [Ossiander et al ., Nat. Phys. 13, 280 (2017)] and reveal a strong photoemission-direction dependence for shake-up ionization due to the coupling between the photoelectron and evolving residual-ion charge distribution in the IR-laser field.

Stark effect↗

DOE OSTI2022

Residual mean field model of valence quarks in the nucleon

Abstract We develop a non-perturbative model for valence parton distribution functions (PDFs) based on the mean field interactions of valence quarks in the nucleonic interior. The main motivation for the model is to obtain a mean field description of the valence quarks as a baseline to study the short range quark–quark interactions that generate the high x tail of PDFs. The model is based on the separation of the valence three-quark cluster and residual system in the nucleon. Then the nucleon structure function is calculated within the effective light-front diagrammatic approach introducing nonperturbative light-front valence quark and residual wave functions. Within the model a new relation is obtained between the position, $$x_p$$ x p , of the peak of $$xq_V(x)$$ x q V ( x ) distribution of the valence quark and the effective mass of the residual system, $$m_R$$ m R , in the form: $$x_{p} \approx {1\over 4} (1-{m_R\over m_N})$$ x p ≈ 1 4 ( 1 - m R m N ) at starting $$Q^2$$ Q 2 . This relation explains the difference in the peak positions for d- and u-quarks through the expected difference of residual masses for valence d- and u-quark distributions. The parameters of the model are fixed by fitting the calculated valence quark distributions to the phenomenological PDFs. This allowed us to estimate the overall mean field contribution in baryonic and momentum sum rules for valence d- and u-quarks. Finally, the evaluated parameters of the non-perturbative wave functions of valence 3q-cluster and residual system can be used in calculation of other quantities such as nucleon form factors, generalized partonic and transverse momentum distributions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Determination of Stress-Free Lattice Spacing (D₀) for Residual Stress Relaxation Measurement in Ni-based Superalloys by Neutron Diffraction

The residual stress and its relaxation in critical engineering components are key to structural materials reliability. The determination of residual stress in bulk engineering structures like Ni-based superalloys can be conducted by measuring the lattice strain with penetrating neutron diffraction. The state-of-the-art engineering diffraction beamline VULCAN at the Oak Ridge National Laboratory (ORNL) Spallation Neutron Source (SNS) provides the critical capability to evaluate the residual strain/stress relaxation in engineering component thanks to the high flux and event data features. By the means of residual stress/strain calculation, it is critical to accurately determine the stress-free lattice spacing d₀, which can be altered by the change of chemistry, unrelieved stress, and measurement scheme. Here we reported d₀ determination for determining residual stress relaxation and distribution in Alloy 718 superalloys after different quenching treatments. Selection of locations for d₀ measurement was discussed by considering the neutron path, attenuation and sample alignment. A dynamic d₀ that resulted from atom diffusion and chemistry change was estimated as function of time for the in-situ relaxation characterization. It demonstrated how the dynamic d₀ values may influence on the strain calculation in different thermally treated samples. The results highlight the importance of dynamic d₀ for in-situ relaxation involving chemical changes and provide guidance to the dynamic d₀ measurement and simulation.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Total Residual Radiation Source Term Produced by the Hiroshima Detonation

Residual radiation from a nuclear detonation consists of fission products and activation products produced by the excess neutrons released during the explosion. The ability to accurately predict nuclear fallout begins with a calculation of the residual radiation source term. The intent of this paper is to define the residual radiation source term for the Hiroshima detonation. The calculation was performed using the Livermore Weapon Activation Code (LWAC), which is a simplified three-region model that estimates the residual radiation associated with the fission products, the unburnt fuel, and activation products produced in the weapon components, the surrounding air, and the ground in the vicinity of ground zero. For the Hiroshima detonation, ~1200 radionuclides were produced. A time-dependent solution for the total activity of each of the major residual radiation source terms is provided in the Appendices. In addition, the timedependent exposure rates produced by the activation rings are included in the report.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2024

Quantification of Residual Water in Spent Fuel Dry Storage Canisters Using Mass Spectrometry

The purpose of this report is to document updates on the apparatus to simulate commercial vacuum drying procedures at the Nuclear Energy Work Complex at Sandia National Laboratories. Validation of the extent of water removal in a dry spent nuclear fuel storage system based on drying procedures used at nuclear power plants is needed to close existing technical gaps. Operational conditions leading to incomplete drying may have potential impacts on the fuel, cladding, and other components in the system during subsequent storage and disposal, such as fuel degradation; cladding corrosion, embrittlement, or breaching; and the creation of a flammable environment via radiolysis of water. A general lack of data suitable for model validation of commercial nuclear canister drying processes necessitates well-designed investigations of drying process efficacy and water retention. Scaled tests that incorporate relevant physics and well-controlled boundary conditions are essential to provide insight and guidance to the simulation of prototypic systems undergoing drying processes. This report documents details on the quantification of residual water in the Advanced Drying Cycle Simulator (ADCS), an apparatus built to simulate commercial drying procedures and quantify the amount of residual water remaining in a pressurized water reactor (PWR) fuel assembly after drying. The ADCS was constructed with a prototypic 17×17 PWR fuel skeleton and waterproof heater rods to simulate decay heat. The ADCS is outfitted with thermocouples to measure the thermal response of the ADCS to simulated decay heats and internal helium fill pressures relevant to commercial drying procedures. The ADCS is also instrumented with pressure transducers to measure the pressures and vacuum levels observed during simulated commercial drying. The most unique instrumentation used for quantifying residual water in the ADCS is a Hiden Analytical HPR-30 mass spectrometer (MS), which measures gas compositions of the ADCS internal free volume, based on partial pressures calculated from relative proportions of gas molecules detected by the MS. This report details the methodology used to implement MS measurements in quantifying residual water in the ADCS. This methodology includes the calibration of the HPR-30 MS to a Buck Research Instruments CR-4 chilled mirror hygrometer, which itself is calibrated to a NIST-traceable standard. Data collected by both the MS and the chilled mirror hygrometer from water/helium mixtures ranging from 150 to 500,000 ppmv water in helium were used to generate calibration curves, establishing a source of verification of MS measured water contents. Details regarding water content measurement uncertainties are included in this report, defining the accuracy and verifiability of the HPR-30 MS in measuring residual water content in simulated dry storage canister environments.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Biomass Resources and Emission Reduction Potential of Agricultural and Livestock Residues in Mainland China from 2013 to 2022

Controlling carbon emissions is a global goal, and China is actively implementing carbon reduction measures. As a major agricultural nation, China has considerable potential for developing agricultural residues as renewable and environmentally friendly biomass energy. In this study, we obtained data on crop yields, crop-to-grain ratios, and livestock excretion coefficients to calculate the biomass resources of agricultural and livestock residues in Chinese provinces from 2013 to 2022. Crop residue biomass resources showed a distribution pattern with higher levels in the north than in the south and the east than in the west. Henan and Heilongjiang provinces consistently had the highest resource levels, exceeding 35 million tons annually for 10 years. The biomass resources from livestock residues were relatively abundant in Sichuan, Henan, Yunnan, Shandong, Hunan, and Inner Mongolia. Inner Mongolia, Sichuan, Shandong, and Henan had the greatest potential for CO2 emission reductions, primarily located in regions abundant in biomass resources and with high traditional energy consumption levels. ArcGIS was used to apply natural break classification to categorize the potential for emission reductions from agricultural and livestock residues across China from 2013 to 2022 into five classes. Based on factors such as crop planting area and livestock numbers, the spatiotemporal distribution of factors influencing the quantity of biomass resources was examined using Geographically and Temporally Weighted Regression. A tailored and integrated approach should be used for biomass, and the development of biomass energy should be promoted through policy support and technological innovation.

Environmental Sciences & Ecology↗

DOE OSTI2022

Chemical Cartography with APOGEE: Mapping Disk Populations with a 2-process Model and Residual Abundances

We apply a novel statistical analysis to measurements of 16 elemental abundances in 34,410 Milky Way disk stars from the final data release (DR17) of APOGEE-2. Building on recent work, we fit median abundance ratio trends [X/Mg] versus [Mg/H] with a 2-process model, which decomposes abundance patterns into a "prompt" component tracing core-collapse supernovae and a "delayed" component tracing Type Ia supernovae. For each sample star, we fit the amplitudes of these two components, then compute the residuals Δ[X/H] from this two-parameter fit. The rms residuals range from ~0.01–0.03 dex for the most precisely measured APOGEE abundances to ~0.1 dex for Na, V, and Ce. The correlations of residuals reveal a complex underlying structure, including a correlated element group comprised of Ca, Na, Al, K, Cr, and Ce and a separate group comprised of Ni, V, Mn, and Co. Selecting stars poorly fit by the 2-process model reveals a rich variety of physical outliers and sometimes subtle measurement errors. Residual abundances allow for the comparison of populations controlled for differences in metallicity and [α/Fe]. Relative to the main disk (R = 3–13 kpc), we find nearly identical abundance patterns in the outer disk (R = 15–17 kpc), 0.05–0.2 dex depressions of multiple elements in LMC and Gaia Sausage/Enceladus stars, and wild deviations (0.4–1 dex) of multiple elements in ω Cen. The residual abundance analysis opens new opportunities for discovering chemically distinctive stars and stellar populations, for empirically constraining nucleosynthetic yields, and for testing chemical evolution models that include stochasticity in the production and redistribution of elements.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1973

Residual stress alleviation of aircraft metal structures reinforced with filamentary composites

Methods to eliminate or reduce residual stresses in aircraft metal structures reinforced by filamentary composites are discussed. Residual stress level reductions were achieved by modifying the manufacturing procedures used during adhesive bonding. The residual stress alleviation techniques involved various forms of mechanical constraint which were applied to the components during bonding. Nine methods were evaluated, covering a wide range in complexity. All methods investigated during the program affected the residual stress level. In general, residual stresses were reduced by 70 percent or more from the stress level produced by conventional adhesive bonding procedures.

Kelly, J. B.↗

NASA NTRS1980

Smoke characteristics of distillate and residual fuel burning in gas turbine combustors

During the development of a rich-lean staged dry low NOx combustor, the conventional trend of increasing smoke with increasing operating equivalence ratio was found when tests were run with distillate fuel (% H = 13.0). However, when tests were run with residual fuel (% H = 11.4), the trend was reversed. In addition, when the same combustor was run with blends of distillate fuel and residual fuel, a drastic improvement of smoke was observed when only 6 percent of residual fuel was mixed with distillate fuel, and for any blending of more than 10 percent of residual fuel the combustor was practically smoke free. A chemical analysis of fuel samples revealed an appreciable amount of trace metals in the residual fuel, giving rise to the suspicion that the smoke reduction may have been due in part to these trace metals. Of these elements found, vanadium is believed to be the most likely to cause smoke reduction because of its relatively high concentration.

Liu, T. M.↗

NASA NTRS1982

Gravity and geoid anomalies of the Philippine Sea: Evidence on the depth of compensation for the negative residual water depth anomaly

A negative free-air gravity anomaly which occurs in the central part of the Philippine Sea was examined to determine the distribution and nature of possible regional mass excesses or deficiencies. Geoid anomalies from GEOS-3 observation were positive. A negative residual geoid anomaly consistent with the area of negative free-air gravity anomalies were found. Theoretical gravity-topography and geoid-topography admittance functions indicated that high density mantle at about 60 km dept could account for the magnitudes of the gravity and residual geoid anomaly and the 1 km residual water depth anomaly in the Philippine Sea. The negative residual depth anomaly may be compensated for by excess density in the uppermost mantle, but the residual geoid and regional free-air gravity anomalies and a slow surface wave velocity structure might result from low-density warm upper mantle material lying beneath the zone of high-density uppermost mantle. From a horizontal disk approximation, the depth of the low-density warm mantle was estimated to be on the order of 200 km.

Bowin, C.↗

NASA NTRS1989

Effects of fatigue and environment on residual strengths of center-cracked graphite/epoxy buffer strip panels

The effects of fatigue, moisture conditioning, and heating on the residual tension strengths of center-cracked graphite/epoxy buffer strip panels were evaluated using specimens made with T300/5208 graphite epoxy in a 16-ply quasi-isotropic layup, with two different buffer strip materials, Kevlar-49 or S-glass. It was found that, for panels subjected to fatigue loading, the residual strengths were not significantly affected by the fatigue loading, the number of repetitions of the loading spectrum, or the maximum strain level. The moisture conditioning reduced the residual strengths of the S-glass buffer strip panels by 10 to 15 percent below the ambient results, but increased the residual strengths of the Kevlar-49 buffer strip panels slightly. For both buffer strip materials, the heat increased the residual strengths of the buffer strip panels slightly over the ambient results.

Bigelow, Catherine A.↗

NASA NTRS1989

X-ray diffraction measurements of residual stresses in SiC/Ti composites

Residual stresses are developed in metal matrix composites during consolidation because of the difference in the coefficient of thermal expansion of the fiber and matrix constituents. X-ray diffraction techniques were used to measure tensile residual stresses in the matrix component of two different titanium alloy composites reinforced with continuous silicon carbide fibers. The titanium alloy matrices were a beta-stabilized alloy Ti-15V-3Al-3Cr-3Sn, and an ordered multiphase (alpha + beta) alloy, Ti-14Al-21Nb. Residual tensile stresses as high as 62 percent of the yield of Ti-15V-3Al-3Cr-3Sn and 70 percent of the yield of Ti-14Al-21Nb were measured in the longitudinal direction on unidirectionally reinforced composites. By measuring residual stresses in four different composite lay-ups, the composite lay-up was determined to have a significant effect on the residual stress state near the surface.

Brown, K. M.↗

NASA NTRS1992

Scanning electron microscope/energy dispersive x ray analysis of impact residues on LDEF tray clamps

To better understand the nature of particulates in low-Earth orbit (LEO), and their effects on spacecraft hardware, we are analyzing residues found in impacts on the Long Duration Exposure Facility (LDEF) tray clamps. LDEF experiment trays were held in place by 6 to 8 chromic-anodized aluminum (6061-T6) clamps that were fastened to the spacecraft frame using three stainless steel hex bolts. Each clamp exposed an area of approximately 58 sq cm (4.8 cm x 12.7 cm x .45 cm, minus the bolt coverage). Some 337 out of 774 LDEF tray clamps were archived at JSC and are available through the Meteoroid & Debris Special Investigation Group (M&D SIG). Optical scanning of clamps, starting with Bay/Row A01 and working toward H25, is being conducted at JSC to locate and document impacts as small as 40 microns. These impacts are then inspected by Scanning Electron Microscopy/Energy Dispersive X-ray Analysis (SEM/EDXA) to select those features which contain appreciable impact residue material. Based upon the composition of projectile remnants, and using criteria developed at JSC, we have made a preliminary discrimination between micrometeoroid and space debris residue-containing impact features. Presently, 13 impacts containing significant amounts of unmelted and semi-melted micrometeoritic residues were forwarded to Centre National d'Etudes Spatiales (CNES) in France. At the CNES facilities, the upgraded impacts were analyzed using a JEOL T330A SEM equipped with a NORAN Instruments, Voyager X-ray Analyzer. All residues were quantitatively characterized by composition (including oxygen and carbon) to help understand interplanetary dust as possibly being derived from comets and asteroids.

Bernhard, Ronald P.↗

NASA NTRS1995

Analytical electron microscopy of LDEF impactor residues

The LDEF contained 57 individual experiment trays or tray portions specifically designed to characterize critical aspects of meteoroid and debris environment in low-Earth orbit (LEO). However, it was realized from the beginning that the most efficient use of the satellite would be to characterize impact features from the entire surface of the LDEF. With this in mind particular interest has focused on common materials facing in all 26 LDEF facing directions; among the most important of these materials has been the tray clamps. Therefore, in an effort to better understand the nature and flux of particulates in LEO, and their effects on spacecraft hardware, we are analyzing residues found in impact features on LDEF tray clamp surfaces. This paper summarizes all data from 79 clamps located on Bay A & B of the LDEF. We also describe current efforts to characterize impactor residues recovered from the impact craters, and we have found that a low, but significant, fraction of these residues have survived in a largely unmelted state. These residues can be characterized sufficiently to permit resolution of the impactor origin. We have concentrated on the residue from chondritic interplanetary dust particles (micrometeoroids), as these represent the harshest test of our analytical capabilities.

Bernhard, Ronald P.↗

NASA NTRS1992

Compressive residual strength of graphite/epoxy laminates after impact

The issue of damage tolerance after impact, in terms of the compressive residual strength, was experimentally examined in graphite/epoxy laminates using Hercules AS4/3501-6 in a (+ or - 45/0)(sub 2S) configuration. Three different impactor masses were used at various velocities and the resultant damage measured via a number of nondestructive and destructive techniques. Specimens were then tested to failure under uniaxial compression. The results clearly show that a minimum compressive residual strength exists which is below the open hole strength for a hole of the same diameter as the impactor. Increases in velocity beyond the point of minimum strength cause a difference in the damage produced and cause a resultant increase in the compressive residual strength which asymptotes to the open hole strength value. Furthermore, the results show that this minimum compressive residual strength value is independent of the impactor mass used and is only dependent upon the damage present in the impacted specimen which is the same for the three impactor mass cases. A full 3-D representation of the damage is obtained through the various techniques. Only this 3-D representation can properly characterize the damage state that causes the resultant residual strength. Assessment of the state-of-the-art in predictive analysis capabilities shows a need to further develop techniques based on the 3-D damage state that exists. In addition, the need for damage 'metrics' is clearly indicated.

Guy, Teresa A.↗

NASA NTRS1996

Conditional Entropy-Constrained Residual VQ with Application to Image Coding

This paper introduces an extension of entropy-constrained residual vector quantization (VQ) where intervector dependencies are exploited. The method, which we call conditional entropy-constrained residual VQ, employs a high-order entropy conditioning strategy that captures local information in the neighboring vectors. When applied to coding images, the proposed method is shown to achieve better rate-distortion performance than that of entropy-constrained residual vector quantization with less computational complexity and lower memory requirements. Moreover, it can be designed to support progressive transmission in a natural way. It is also shown to outperform some of the best predictive and finite-state VQ techniques reported in the literature. This is due partly to the joint optimization between the residual vector quantizer and a high-order conditional entropy coder as well as the efficiency of the multistage residual VQ structure and the dynamic nature of the prediction.

Kossentini, Faouzi↗