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DOE OSTI2024

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration

Abstract Motivation Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools. Results This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics. Availability and implementation ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.

Lai, Jhih-Siang (ORCID:0000000156775890)↗

DOE OSTI2021

Investigation of the background in coherent J/ψ production at the EIC

Understanding various fundamental properties of nucleons and nuclei is among the most important scientific goals at the upcoming Electron-Ion Collider (EIC). With the unprecedented opportunity provided by the next-generation machine, the EIC might provide definitive answers to many standing puzzles and open questions in modern nuclear physics. We investigate one of the golden measurements proposed at the EIC, which is to obtain the spatial gluon density distribution within a lead (Pb) nucleus. The proposed experimental process is the exclusive J/ψ vector-meson production off the Pb nucleus: e + Pb → e' + J/ψ + Pb'. The Fourier transformation of the momentum transfer |t| distribution of the coherent diffraction is the transverse gluon spatial distribution. In order to measure it, the experiment has to overcome an overwhelmingly large background arising from the incoherent diffractive production, where the nucleus Pb' mostly breaks up into fragments of particles in the far-forward direction close to the hadron-going beam rapidity. We systematically study the rejection of incoherent J/ψ production by vetoing products from these nuclear breakups—protons, neutrons, and photons—which is based on the BeAGLE event generator and the most up-to-date EIC Far-forward Interaction Region design. The achieved vetoing efficiency, the ratio between the numbers of vetoed events and total incoherent events, ranges from about 80% to 99% depending on |t|. Assuming a 5% smearing applied to the reconstructed |t| resolution in the Sar t re model, this vetoing efficiency can suppress the incoherent background to at least the first minimum of the coherent |t| distribution. Experimental and accelerator machine challenges as well as potential improvements are discussed herein.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Threshold photoproduction of η c and η b using holographic QCD

We discuss the possibility that threshold photoproduction of η c , b may be sensitive to the pseudovector 1 + − glueball exchange. We use the holographic construction to identify the pseudovector glueball with the Kalb-Ramond field, minimally coupled to bulk Dirac fermions. We derive the holographic C-odd form factor and its respective charge radius. Using the pertinent Witten diagrams, we derive and analyze the differential photoproduction cross section for η c , b in the threshold regime, including the interference from the dual bulk photon exchange with manifest vector dominance. The possibility of measuring this process at current and future electron facilities is discussed. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

DOE OSTI2024

A Geodatabase Designed to Inform and Support Safe CO2 Transport-Route Planning

The National Energy Technology Laboratory developed the Carbon Capture and Storage (CCS) Pipeline Route Planning Database to inform safe and sustainable CO2 transport planning in support of decarbonization efforts. This comprehensive Esri Geodatabase contains over 90 GBs of data and 60+ spatial layers representing key considerations including natural hazards, infrastructure, energy, and social justice. Leveraging ArcGIS Pro, nationwide raster, and vector datasets containing millions of features were processed to be easily digestible for users and complex modeling software.

Romeo, Lucy↗

DOE OSTI2025

Energy-enhanced dimension eight SMEFT effects in VBF Higgs production

We study Higgs boson production via vector boson fusion at the LHC, focusing on the process pp → H + jj and capturing the leading energy-enhanced contributions within the Standard Model Effective Field Theory (SMEFT) up to order 1/Λ$^{4}$. Employing energy-scaling arguments, we predict the magnitude of each higher-dimensional operator’s contribution. Utilizing the geometric formulation of SMEFT, our analysis incorporates dimension-eight operators not previously considered. We find that the kinematics of vector boson fusion — characterized by two highly forward jets — tend to suppress contributions from higher-dimensional operators, requiring a lower scale Λ for SMEFT effects to become observable. This suggests that the SMEFT remains valid for lower Λ than expected. Combined with the fact that LEP constrains the dimension-six operators with the most considerable impact on vector boson fusion, a regime exists where dimension-eight operators can have significant effects. In many cases, these dimension-eight operators also influence associated production processes like pp → HV(jj), though differences in analysis cuts and kinematics mean this is not always the case. Our findings provide insights that could refine the search for SMEFT signals in collider experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Nuclear Power Fault Diagnostics and Preventative Maintenance Optimization NPIC presentation

The nuclear industry is beginning to see reactors shut down—even after their operating licenses have been extended—because they are not economically competitive with other energy sources. These early closures happen primarily due to economic reasons, despite excellent safety records. Therefore, it is imperative to reduce costs in order to prevent these early closures. One of the contributors to these economic reasons is the large operations and maintenance costs. This paper showcases recent research on advanced fault diagnostics techniques and preventative maintenance optimization (PMO) for reducing NPP maintenance costs. Specifically, it focuses on the feedwater and condensate system (FWCS) for both pressurized- and boiling-water reactor (BWR) systems. The computerized maintenance management system (CMMS), which contains the plant’s digital record of all corrective maintenance (CM) and preventative maintenance (PM) work orders, provided the ground truth for locating potential faults and labeling the process data as either healthy or faulted. Various feature extraction techniques were used to further differentiate the faulted data from the healthy data. Through a cross-validation procedure, support vectors machines were used to label other test sets of process data as either healthy or faulted. With relatively few faults identified in the BWR system, the potential for PMO opens up, since an unnecessary amount of PM leads to inflated maintenance costs. The steps for PMO are summarized, from component health determinations to recommendations for action. An example of PMO assessment is presented for condensate pumps, condensate booster pumps, and the respective motors that drive them.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Nuclear Power Fault Diagnostics and Preventative Maintenance Optimization

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2019

Machine learning applied to wind turbine blades impact detection

The significant development of wind power generation worldwide brings, together with environmental benefits, wildlife concerns, especially for volant species vulnerability to interactions with wind energy facilities. For surveying such events, an automatic system for continuous monitoring of blade collisions is critical. An onboard multi-senor system capable of providing real-time collision detection using integrated vibration sensors is developed and successfully tested. However, to detect low signal-to-noise ratio impact can be challenging; hence, an advanced impact detection method has been developed and presented in this article. A robust automated detection algorithm based on support vector machine is proposed. After a preliminary signal pre-processing, geometric features specifically selected for their sensitivity to impact signals are extracted from raw vibration signal and energy distribution graph. The predictive model is formulated by training conventional support vector machine using extracted features for impact identification. Finally, the performance of the predictive model is evaluated by accuracy, precision, and recall. Results indicate a linear regression relationship between signal-to-noise ratio and model overall performance. Here, the proposed method is much reliable on higher signal-to-noise ratio (SNR≥6), but it shows to be ineffective at lower signal-to-noise ratio (SNR<2).

17 WIND ENERGY↗

DOE OSTI2022

Automated Process Planning for Embossing and Functionally Grading Materials via Site-Specific Control in Large-Format Metal-Based Additive Manufacturing

The potential for site-specific, process-parameter control is an attribute of additive manufacturing (AM) that makes it highly attractive as a manufacturing process. The research interest in the functionally grading material properties of numerous AM processes has been high for years. However, one of the issues that slows developmental progress in this area is process planning. It is not uncommon for manual programming methods and bespoke solutions to be utilized for site-specific control efforts. This article presents the development of slicing software that contains a fully automated process planning approach for enabling through-thickness, process-parameter control for a range of AM processes. The technique includes the use of parent and child geometries for controlling the locations of site-specific parameters, which are overlayed onto unmodified toolpaths, i.e., a vector-based planning approach is used in which additional information, such as melt pool size for large-scale metal AM processes, is assigned to the vectors. This technique has the potential for macro- and micro-structural modifications to printed objects. A proof-of-principle experiment is highlighted in which this technique was used to generate dynamic bead geometries that were deposited to induce a novel surface embossing effect, and additional software examples are presented that highlight software support for more complex objects.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Dispersible Colloid Facilitated Release of Organic Carbon From Two Contrasting Riparian Sediments

In aqueous systems, including groundwater, nano-colloids (1–100 nm diameter) and small colloids (<450 nm diameter) provide a vast store of surfaces to which organic carbon (OC) can sorb, precluding its normal bioavailability. Because nanomaterials are ubiquitous and abundant throughout Earth systems, it is reasonable that they would play a significant role in biogeochemical cycles. As such, mineral nano-colloids (MNC) and small colloids, formed through mineral weathering and precipitation processes, are both an unaccounted-for reservoir and unquantified vector for transport of OC and nutrients and contaminants within watersheds. Water extractions and leaching experiments were conducted under (1) aerobic (ambient) and (2) anaerobic (environmental chamber) conditions for each of two contrasting riparian sediments from (1) Columbia River, Washington and (2) Tims Branch, South Carolina. Water dispersible colloid-adsorbed OC was as high as 48% of OC for Tims Branch anaerobic batch water extraction and as low as 0% for Columbia River aerobic batch water extractions. Anaerobic leaching from column experiments yielded higher colloid and OC release rates. Transmission electron microscopy with electron dispersive spectroscopy mapping revealed organic carbon associated with aggregations of nano-particulate silicate minerals and Mossbauer identified nano-particulate goethite. This exploratory study demonstrates that mineral facilitated release of OC in riparian sediments is both significant and variable between locations.

Rod, Kenton A.↗

DOE OSTI2026

On the formation of swelling and related flaws in laser powder bed fusion

Process monitoring in laser powder bed fusion additive manufacturing can provide insights into stochastic anomalies, melt pool and plume dynamics, and part quality. Swelling, a build anomaly where overbuilt material protrudes through the powder layer after recoating, is readily detectable in post-recoat visible light images of the powder bed. Here, this work identifies several of the underlying mechanisms driving swelling formation by analyzing the influence of processing parameters, laser scan paths, and build plate locations on the presence of swelling detected in situ. Swelling near the edge of the part and swelling in the internal region of the part are shown to correlate with different process conditions. Edge and internal swelling may be driven by different phenomena, with edge swelling predominately occurring on the edge of a part facing the laser module and correlated to clusters of near-surface voids (detected with X-ray computed tomography). A larger spot size, higher laser power, and lower scan velocity also increased the presence of edge swelling. Laser spot size and scan path influenced internal swelling, which occurred preferentially with a larger spot size and in regions with large melt pools, caused by localized heat accumulation due to non-optimal processing parameters or scan path strategies. For coupons processed with a slicer-defined maximum scan vector length, swelling seldom occurred at internal vector-stripe boundaries. These results provide a mechanistic understanding of how swelling can be linked to material flaws, insight into how some instances of swelling can be avoided, and evidence supporting the use of swelling as an in situ indicator for quality assurance and part qualification.

Anomaly↗

DOE OSTI2026

Precision measurements of Higgs hadronic decay modes at the FCC-ee

The expected precision at the FCC-ee on the product $σ$ x $\mathcal{B} \large{(}H → b\bar{b}, c\bar{c}, s\bar{s}, gg\large{)}$ of Higgs boson production cross sections times branching ratios of hadronic decays is presented. This study provides the first comprehensive determination of all major hadronic Higgs decay modes in a combined fit at future $e^+e^−$ colliders, using both Higgs-strahlung $(ZH)$ and Vector boson fusion $(v\bar{v}H)$ production processes, with a full treatment of interference effects in the $v\bar{v}jj$ final state. It assumes four identical IDEA detectors collecting $e^+e^−$ collisions at $\sqrt{s}$ = 240 and 365 GeV. The combination of all channels across both energies, with full covariance between production and decay modes, yields a production cross-section times branching-ratio precision at the percent to per-mil level for the dominant hadronic final states $(b\bar{b}, c\bar{c}, gg)$. These results provide a comprehensive input to the determination of Higgs coupling projections at the FCC-ee, and they establish for the first time sensitivity to the rare decay $H → s\bar{s}$, demonstrating that FCC-ee has the potential to provide evidence of the strange-quark Yukawa coupling.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Online multimedia retrieval on CPU–GPU platforms with adaptive work partition

Nearest neighbors search is a core operation found in several online multimedia services. These services have to handle very large databases, while, at the same time, they must minimize the query response times observed by users. This is specially complex because those services deal with fluctuating query workloads (rates). Consequently, they must adapt at run-time to minimize the response times as the load varies. In this paper, we address the aforementioned challenges with a distributed memory parallelization of the product quantization nearest neighbor search, also known as IVFADC, for hybrid CPU–GPU machines. Overall, our parallel IVFADC implements an out-of-GPU memory execution scheme to use the GPU for databases in which the index does not fit in its memory, which is crucial for searching in very large databases. The careful use of CPU and GPU with work stealing led to an average response time reduction of 2.4 as compared to using the GPU only. Also, our approach to adapt the system to fluctuating loads, called Dynamic Query Processing Policy (DQPP), attained a response time reduction of up to 5 vs. the best static (BS) policy for moderate loads. The system has attained high query processing rates and near-linear scalability in all experiments. We have evaluated our system on a machine with up to 256 NVIDIA V100 GPUs processing a database of 256 billion SIFT features vectors.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Measurements of the Branching Fraction, Polarization, and C P Asymmetry for the Decay B 0 → ω ω

We present a comprehensive study of B 0 → ω ω decays using 772 × 10 6 B B ¯ pairs collected with the Belle detector at the KEKB e + e − collider. This process is a suppressed charmless decay into two vector mesons and can exhibit interesting polarization and C P violation. The decay is observed for the first time with a significance of 7.9 standard deviations. We measure a branching fraction B = ( 1.53 ± 0.29 ± 0.17 ) × 10 − 6 , a fraction of longitudinal polarization f L = 0.87 ± 0.13 ± 0.13 , and a time-integrated C P asymmetry A C P = − 0.44 ± 0.43 ± 0.11 , where the first uncertainties listed are statistical and the second are systematic. This is the first observation of B 0 → ω ω and the first measurements of f L and A C P for this decay. Published by the American Physical Society 2024

Physics↗

DOE OSTI2018

Polarimetric Interferometric SAR Change Detection Discrimination

A coherent change detection (CCD) image, computed from a geometrically matched, temporally separated pair of complex-valued synthetic aperture radar (SAR) image sets, conveys the pixel-level equivalence between the two observations. Low-coherence values in a CCD image are typically due to either some physical change in the corresponding pixels or a low signal-to-noise observation. A CCD image does not directly convey the nature of the change that occurred to cause low coherence. In this paper, we introduce a mathematical framework for discriminating between different types of change within a CCD image. We utilize the extra degrees of freedom and information from polarimetric interferometric SAR (PolInSAR) data and PolInSAR processing techniques to define a 29-dimensional feature vector that contains information capable of discriminating between different types of change in a scene. We also propose two change-type discrimination functions that can be trained with feature vector training data and demonstrate change-type discrimination on an example image set for three different types of change. In conclusion, we also describe and characterize the performance of the two proposed change-type discrimination functions by way of receiver operating characteristic curves, confusion matrices, and pass matrices.

58 GEOSCIENCES↗

DOE OSTI2020

Deciphering the mechanism of near-threshold $$J/\psi $$ photoproduction

Abstract The photoproduction of the $$J/\psi $$ J / ψ off the proton is believed to deepen our understanding of various physics issues. On the one hand, it is proposed to provide access to the origin of the proton mass, based on the QCD multipole expansion. On the other hand, it can be employed in a study of pentaquark states. The process is usually assumed to proceed through vector-meson dominance, that is the photon couples to a $$J/\psi $$ J / ψ which rescatters with the proton to give the $$J/\psi p$$ J / ψ p final state. In this paper, we provide a compelling hint for and propose measurements necessary to confirm a novel production mechanism via the $$\varLambda _c \bar{D}^{(*)}$$ Λ c D ¯ ( ∗ ) intermediate states. In particular, there must be cusp structures at the $$\varLambda _c \bar{D}^{(*)}$$ Λ c D ¯ ( ∗ ) thresholds in the energy dependence of the $$J/\psi $$ J / ψ photoproduction cross section. The same mechanism also implies the $$J/\psi $$ J / ψ -nucleon scattering lengths of order 1 mfm. Given this, one expects only a minor contribution of charm quarks to the nucleon mass.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

A Study of Performance Portability of Low-bit Fused Matrix-Vector Multiplication Kernels in SYCL

Understanding the causes of performance gaps between a portable programming model and a vendor-specific programming model is important for improving performance portability. This paper studies performance portability of low-bit fused general matrix-vector multiplication kernels in SYCL on vendors’ graphics processing units (GPUs). This work introduces the use case, explains the kernel implementations in detail, evaluates the performance of the CUDA, HIP, and SYCL kernels on datacenter, desktop, and laptop GPUs, and investigates the causes of performance gaps. The results show that loop unrolling, kernel dispatch overhead, and sum reduction contribute to the gaps.

Jin, Zheming [ORNL] (ORCID:000000027197780X)↗

DOE OSTI2019

Probing the Tri-Linear Higgs Self-Coupling

This poster explores my activities during the 2019 CCI program at Fermi National Accelerator Laboratory (Fermilab) and how they contribute to one of the ongoing projects being worked on by many employees and physicists at the LPC (LHC Physics Center). This project uses CMS (Compact Muon Solenoid) simulation samples to study the feasibility of probing tri-linear Higgs-self coupling in a process where a single Higgs is produced in vector boson scattering associated with two additional protons, i.e. , where the W bosons decay leptonically and the Higgs decays to bb. The leptons are required to have the same charge in order to suppress other standard model backgrounds. Any deviations of the Higgs-self coupling from the value predicted by the Standard Model (SM) could be indications of Beyond the Standard Model (BSM) physics. These indications would come from the observed value of an anomalous coupling, and its effects on SM values.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗