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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

The DESC stellarator code suite. Part 1. Quick and accurate equilibria computations

Three-dimensional equilibrium codes are vital for stellarator design and operation, and high-accuracy equilibria are also necessary for stability studies. This paper details comparisons of two three-dimensional equilibrium codes: VMEC, which uses a steepest-descent algorithm to reach a minimum-energy plasma state, and DESC, which minimizes the magnetohydrodynamic (MHD) force error in real space directly. Accuracy as measured by satisfaction of MHD force balance is presented for each code, along with the computation time. It is shown that DESC is able to achieve more accurate solutions, especially near axis. The importance of higher-accuracy equilibria is shown in DESC's better agreement of stability metrics with asymptotic formulae. DESC's global Fourier–Zernike basis also yields solutions with analytic derivatives explicitly everywhere in the plasma volume, provides improved accuracy in the radial direction versus conventional finite differences and allows for exponential convergence. Further, DESC can compute a solution with the same accuracy as VMEC in order-of-magnitude less time.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

qSIEVE: Efficient qLDPC Memory via Systolic Movement in Atom Arrays

As quantum machines have scaled up in their number of qubits, significant research has turned towards increasing their fidelity with quantum error correction codes. Although promising results have been shown with the surface code, which only requires near-neighbor connections between qubits, the high qubit overhead of such local codes promises to be problematic. Consequently, recent work has explored non-local quantum LDPC (qLDPC) codes, which have good asymptotic encoding rates. Despite theoretical progress, hardware implementations of these codes have been a longstanding challenge. At the experimental level, demonstrations of movement based communication on atom arrays suggest this is a powerful new primitive to achieve non-local connectivity. Leveraging this, we present a protocol for implementing non-local qLDPC codes in hardware. Our protocol, qSIEVE, is a co-design of such codes with movement in atom arrays. qSIEVE defines a restricted family of qLDPC codes that can be implemented efficiently with systolic movement. We then quantify the utility of qSIEVE in the context of a complete fault tolerant architecture. We compare the cost of implementing benchmark programs in a standard, surface code only architecture and a mixed architecture where data is stored in qLDPC memory with qSIEVE and loaded to surface codes for computation.

Quantum error correction↗
DOE OSTI2021

Scalable Comparative Visualization of Ensembles of Call Graphs

Optimizing the performance of large-scale parallel codes is critical for efficient utilization of computing resources. Code developers often explore various execution parameters, such as hardware configurations, system software choices, and application parameters, and are interested in detecting and understanding bottlenecks in different executions. They often collect hierarchical performance profiles represented as call graphs, which combine performance metrics with their execution contexts. The crucial task of exploring multiple call graphs together is tedious and challenging because of the many structural differences in the execution contexts and significant variability in the collected performance metrics (e.g., execution runtime). In this paper, we present Ensemble CallFlow to support the exploration of ensembles of call graphs using new types of visualizations, analysis, graph operations, and features. We introduce ensemble-Sankey , a new visual design that combines the strengths of resource-flow (Sankey) and box-plot visualization techniques. Whereas the resource-flow visualization can easily and intuitively describe the graphical nature of the call graph, the box plots overlaid on the nodes of Sankey convey the performance variability within the ensemble. Our interactive visual interface provides linked views to help explore ensembles of call graphs, e.g., by facilitating the analysis of structural differences, and identifying similar or distinct call graphs. Finally, we demonstrate the effectiveness and usefulness of our design through case studies on large-scale parallel codes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Stochastic GW -GPU: Rapid Quasi-Particle Energies for Molecules beyond 10,000 Atoms

StochasticGW is a code for computing accurate quasi-particle (QP) energies of molecules and material systems in the GW approximation. StochasticGW utilizes the stochastic Resolution of the Identity (sROI) technique to enable a massively parallel implementation with computational costs that scale semilinearly with system size, allowing the method to access systems with tens of thousands of electrons. Here, we introduce a new implementation, StochasticGW-GPU, for which the main bottleneck steps have been ported to GPUs and give substantial performance improvements over previous versions of the code. We showcase the new code by computing band gaps of hydrogenated silicon clusters (Si x H y ) containing up to 10,001 atoms and 35,144 electrons, and we obtain individual QP energies with a statistical precision of better than ±0.03 eV with times-to-solution of less than 1 h.

Thomas, Phillip S. [Lawrence Berkeley National Lab↗
DOE OSTI2014

Computerized detection of breast cancer on automated breast ultrasound imaging of women with dense breasts

Purpose: Develop a computer-aided detection method and investigate its feasibility for detection of breast cancer in automated 3D ultrasound images of women with dense breasts. Methods: The HIPAA compliant study involved a dataset of volumetric ultrasound image data, “views,” acquired with an automated U-Systems Somo•V{sup ®} ABUS system for 185 asymptomatic women with dense breasts (BI-RADS Composition/Density 3 or 4). For each patient, three whole-breast views (3D image volumes) per breast were acquired. A total of 52 patients had breast cancer (61 cancers), diagnosed through any follow-up at most 365 days after the original screening mammogram. Thirty-one of these patients (32 cancers) had a screening-mammogram with a clinically assigned BI-RADS Assessment Category 1 or 2, i.e., were mammographically negative. All software used for analysis was developed in-house and involved 3 steps: (1) detection of initial tumor candidates, (2) characterization of candidates, and (3) elimination of false-positive candidates. Performance was assessed by calculating the cancer detection sensitivity as a function of the number of “marks” (detections) per view. Results: At a single mark per view, i.e., six marks per patient, the median detection sensitivity by cancer was 50.0% (16/32) ± 6% for patients with a screening mammogram-assigned BI-RADS category 1 or 2—similar to radiologists’ performance sensitivity (49.9%) for this dataset from a prior reader study—and 45.9% (28/61) ± 4% for all patients. Conclusions: Promising detection sensitivity was obtained for the computer on a 3D ultrasound dataset of women with dense breasts at a rate of false-positive detections that may be acceptable for clinical implementation.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

An elastography method based on the scanning contact resonance of a piezoelectric cantilever

Purpose: Most tissues may become significantly stiffer than their normal states when there are lesions inside. The tissue's modulus can then act as an identification parameter for clinic diagnosis of tumors or fibrosis, which leads to elastography. This study introduces a novel elastography method that can be used for modulus imaging of superficial organs. Methods: This method is based on the scanning contact-resonance of a unimorph piezoelectric cantilever. The cantilever vibrates in its bending mode with the tip pressed tightly on the sample. The contact resonance frequency of the cantilever-sample system is tracked at each scanning point, from which the sample's modulus can be derived based on a beam dynamic model and a contact mechanics model. Scanning is performed by a three-dimensional motorized stage and the whole system is controlled by a homemade software program based on LabVIEW. Results: Testing onin vitro beef tissues indicates that the fat and the muscle can be easily distinguished using this system, and the accuracy of the modulus measurement can be comparable with that of nanoindentation. Imaging on homemade gelatin phantoms shows that the depth information of the abnormalities can be qualitatively obtained by varying the pressing force. The detection limit of this elastography method is specially examined both experimentally and numerically. Results show that it can detect the typical lesions in superficial organs with the depth of several centimeters. The lateral resolution of this elastography method/system is better than 0.5 mm, and could be further enhanced by using more scanning points. Conclusions: The proposed elastography system can be regarded as a sensitive palpation robot, which may be very promising in early diagnosis of tumors in superficial organs such as breast and thyroid.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Offline multiple adaptive planning strategy for concurrent irradiation of the prostate and pelvic lymph nodes

Purpose: Concurrent irradiation of the prostate and pelvic lymph nodes (PLNs) can be challenging due to the independent motion of the two target volumes. To address this challenge, the authors have proposed a strategy referred to as Multiple Adaptive Planning (MAP). To minimize the number of MAP plans, the authors’ previous work only considered the prostate motion in one major direction. After analyzing the pattern of the prostate motion, the authors investigated a practical number of intensity-modulated radiotherapy (IMRT) plans needed to accommodate the prostate motion in two major directions simultaneously. Methods: Six patients, who received concurrent irradiation of the prostate and PLNs, were selected for this study. Nine MAP-IMRT plans were created for each patient with nine prostate contours that represented the prostate at nine locations with respect to the PLNs, including the original prostate contour and eight contours shifted either 5 mm in a single anterior-posterior (A-P), or superior-inferior (S-I) direction, or 5 mm in both A-P and S-I directions simultaneously. From archived megavoltage cone beam CT (MV-CBCT) and a dual imaging registration, 17 MV-CBCTs from 33 available MV-CBCT from these patients showed large prostate displacements (>3 mm in any direction) with respect to the pelvic bones. For each of these 17 fractions, one of nine MAP-IMRT plans was retrospectively selected and applied to the MV-CBCT for dose calculation. For comparison, a simulated isocenter-shifting plan and a reoptimized plan were also created for each of these 17 fractions. The doses to 95% (D95) of the prostate and PLNs, and the doses to 5% (D5) of the rectum and bladder were calculated and analyzed. Results: For the prostate, D95 > 97% of the prescription dose was observed in 16, 16, and 17 of 17 fractions for the MAP, isocenter-shifted, and reoptimized plans, respectively. For PLNs, D95 > 97% of the prescription doses was observed in 10, 3, and 17 of 17 fractions for the three types of verification plans, respectively. The D5 (mean ± SD) of the rectum was 45.78 ± 5.75, 45.44 ± 4.64, and 44.64 ± 2.71 Gy, and the D5 (mean ± SD) of the bladder was 45.18 ± 2.70, 46.91 ± 3.04, and 45.67 ± 3.61 Gy for three types of verification plans, respectively. Conclusions: The MAP strategy with nine IMRT plans to accommodate the prostate motions in two major directions achieved good dose coverage to the prostate and PLNs. The MAP approach can be immediately used in clinical practice without requiring extra hardware and software.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2017

Investigation of the n =1 resistive wall modes in the ITER high-mode confinement

The n = 1 resistive wall mode (RWM) stability of ITER high-mode confinement is investigated with bootstrap current included for equilibrium, together with the rotation and diamagnetic drift effects for stability. Here, n is the toroidal mode number. We use the CORSICA code for computing the free boundary equilibrium and AEGIS code for stability. We find that the inclusion of bootstrap current for equilibrium is critical. It can reduce the local magnetic shear in the pedestal, so that the infernal mode branches can develop. Consequently, the n = 1 modes become unstable without a stabilizing wall at a considerably lower beta limit, driven by the steep pressure gradient in the pedestal. Typical values of the wall position stabilize the ideal mode, but give rise to the 'pedestal' resistive wall modes. We find that the rotation can contribute a stabilizing effect on RWMs and the diamagnetic drift effects can further improve the stability in the co-current rotation case. But, generally speaking, the rotation stabilization effects are not as effective as the case without including the bootstrap current effects on equilibrium. We also find that the diamagnetic drift effects are actually destabilizing when there is a counter-current rotation.

Zheng, L. J.↗
DOE OSTI2014

A real-time applicator position monitoring system for gynecologic intracavitary brachytherapy

Purpose: To develop a real-time applicator position monitoring system (RAPS) for intracavitary brachytherapy using an infrared camera and reflective markers. Methods: 3D image-guided brachytherapy requires high accuracy of applicator localization; however, applicator displacement can happen during patient transfer for imaging and treatment delivery. No continuous applicator position monitoring system is currently available. The RAPS system was developed for real-time applicator position monitoring without additional radiation dose to patients. It includes an infrared camera, reflective markers, an infrared illuminator, and image processing software. After reflective markers are firmly attached to the applicator and the patient body, applicator displacement can be measured by computing the relative change in distance between the markers. The reflective markers are magnetic resonance imaging (MRI) compatible, which is suitable for MRI-guided HDR brachytherapy paradigm. In our prototype, a Microsoft Kinect sensor with a resolution of 640 by 480 pixels is used as an infrared camera. A phantom study was carried out to compare RAPS' measurements with known displacements ranging from −15 to +15 mm. A reproducibility test was also conducted. Results: The RAPS can achieve 4 frames/s using a laptop with Intel{sup ®} Core™2 Duo processor. When the pixel size is 0.95 mm, the difference between RAPS' measurements and known shift values varied from 0 to 0.8 mm with the mean value of 0.1 mm and a standard deviation of 0.44 mm. The system reproducibility was within 0.6 mm after ten reposition trials. Conclusions: This work demonstrates the feasibility of a real-time infrared camera based gynecologic intracavitary brachytherapy applicator monitoring system. Less than 1 mm accuracy is achieved when using an off-the-shelf infrared camera.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

ZFS Interface For Accelerators

As data volume increases in HPC centers, storing data in reasonable amounts of space and time while maintaining data integrity and recoverability becomes ever more difficult. ZFS is a filesystem that provides these features, among many others, that make it attractive for usage in HPC environments. It has the ability to compress data, compute checksums, and compute redundancy codes within the same runtime, rather than compute each separately, without knowledge of the underlying structure of the filesystem. However, measurements have shown that compression on CPUs can be incredibly inefficient and significantly reduce the performance of ZFS. The ZFS Interface for Accelerators (Z.I.A.) was developed to provide an interface to route data to accelerators while being processed by ZFS, so that the ZFS infrastructure and features are maintained, while allowing for ZFS administrators to provide faster implementations of compression, or other features, to their instance of ZFS.

Lee, Jason↗
DOE OSTI2023

Wildfire Smoke PM2.5 per Zipcode

This dataset contains daily aggregated measurements of daily PM2.5 from ambient wildfire smoke in the contiguous United States, spanning from 2006 to 2016. The data is sourced from a study by Childs et al. (2022), titled "Daily Local-Level Estimates of Ambient Wildfire Smoke PM2.5 for the Contiguous US" published in Environmental Science & Technology. To compute the standardized weight across different zip codes, we computed the weight calculation on a 10km grids. To compute the weight, we obtain area-weights that add up to 1 in each polygon of zipcodes. This enabled us to calculate the smoke values per zipcode for the aforementioned period. Those interested in replicating our data processing pipeline can access it at https://github.com/NSAPH-Data-Processing/smoke_aggregation.

PM2.5↗
DOE OSTI2017

Physics Verification Overview

The purpose of the verification project is to establish, through rigorous convergence analysis, that each ASC computational physics code correctly implements a set of physics models and algorithms (code verification); Evaluate and analyze the uncertainties of code outputs associated with the choice of temporal and spatial discretization (solution or calculation verification); and Develop and maintain the capability to expand and update these analyses on demand. This presentation describes project milestones.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

Repopulation of interacting tumor cells during fractionated radiotherapy: Stochastic modeling of the tumor control probability

Purpose: Optimal treatment planning for fractionated external beam radiation therapy requires inputs from radiobiology based on recent thinking about the “five Rs” (repopulation, radiosensitivity, reoxygenation, redistribution, and repair). The need is especially acute for the newer, often individualized, protocols made feasible by progress in image guided radiation therapy and dose conformity. Current stochastic tumor control probability (TCP) models incorporating tumor repopulation effects consider “stem-like cancer cells” (SLCC) to be independent, but the authors here propose that SLCC-SLCC interactions may be significant. The authors present a new stochastic TCP model for repopulating SLCC interacting within microenvironmental niches. Our approach is meant mainly for comparing similar protocols. It aims at practical generalizations of previous mathematical models. Methods: The authors consider protocols with complete sublethal damage repair between fractions. The authors use customized open-source software and recent mathematical approaches from stochastic process theory for calculating the time-dependent SLCC number and thereby estimating SLCC eradication probabilities. As specific numerical examples, the authors consider predicted TCP results for a 2 Gy per fraction, 60 Gy protocol compared to 64 Gy protocols involving early or late boosts in a limited volume to some fractions. Results: In sample calculations with linear quadratic parameters α = 0.3 per Gy, α/β = 10 Gy, boosting is predicted to raise TCP from a dismal 14.5% observed in some older protocols for advanced NSCLC to above 70%. This prediction is robust as regards: (a) the assumed values of parameters other than α and (b) the choice of models for intraniche SLCC-SLCC interactions. However, α = 0.03 per Gy leads to a prediction of almost no improvement when boosting. Conclusions: The predicted efficacy of moderate boosts depends sensitively on α. Presumably, the larger values of α are the ones appropriate for individualized treatment protocols, with the smaller values relevant only to protocols for a heterogeneous patient population. On that assumption, boosting is predicted to be highly effective. Front boosting, apart from practical advantages and a possible advantage as regards iatrogenic second cancers, also probably gives a slightly higher TCP than back boosting. If the total number of SLCC at the start of treatment can be measured even roughly, it will provide a highly sensitive way of discriminating between various models and parameter choices. Updated mathematical methods for calculating repopulation allow credible generalizations of earlier results.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Graves' disease radioiodine-therapy: Choosing target absorbed doses for therapy planning

Purpose: The precise determination of organ mass (m{sub th}) and total number of disintegrations within the thyroid gland (A{sup ~}) are essential for thyroid absorbed-dose calculations for radioiodine therapy. Nevertheless, these parameters may vary according to the method employed for their estimation, thus introducing uncertainty in the estimated thyroid absorbed dose and in any dose–response relationship derived using such estimates. In consideration of these points, thyroid absorbed doses for Graves’ disease (GD) treatment planning were calculated using different approaches to estimating the m{sub th} and the A{sup ~}. Methods: Fifty patients were included in the study. Thyroid{sup 131}I uptake measurements were performed at 2, 6, 24, 48, 96, and 220 h postadministration of a tracer activity in order to estimate the effective half-time (T{sub eff}) of {sup 131}I in the thyroid; the thyroid cumulated activity was then estimated using the T{sub eff} thus determined or, alternatively, calculated by numeric integration of the measured time-activity data. Thyroid mass was estimated by ultrasonography (USG) and scintigraphy (SCTG). Absorbed doses were calculated with the OLINDA/EXM software. The relationships between thyroid absorbed dose and therapy response were evaluated at 3 months and 1 year after therapy. Results: The average ratio (±1 standard deviation) betweenm{sub th} estimated by SCTG and USG was 1.74 (±0.64) and that between A{sup ~} obtained by T{sub eff} and the integration of measured activity in the gland was 1.71 (±0.14). These differences affect the calculated absorbed dose. Overall, therapeutic success, corresponding to induction of durable hypothyroidism or euthyroidism, was achieved in 72% of all patients at 3 months and in 90% at 1 year. A therapeutic success rate of at least 95% was found in the group of patients receiving doses of 200 Gy (p = 0.0483) and 330 Gy (p = 0.0131) when m{sub th} was measured by either USG or SCTG and A{sup ~} was determined by the integration of measured {sup 131}I activity in the thyroid gland and based on T{sub eff}, respectively. No statistically significant relationship was found between therapeutic response and patients’ age, administered {sup 131}I activity (MBq), 24-h thyroid {sup 131}I uptake (%) or T{sub eff} (p ≥ 0.064); nonetheless, a good relationship was found between the therapeutic response and m{sub th} (p ≤ 0.035). Conclusions: According to the results of this study, the most effective thyroid absorbed dose to be targeted in GD therapy should not be based on a fixed dose but rather should be individualized based on the patient'sm{sub th} and A{sup ~}. To achieve a therapeutic success (i.e., durable euthyroidism or hypothyroidism) rate of at least 95%, a thyroid absorbed dose of 200 or 330 Gy is required depending on the methodology used for estimating m{sub th} and A{sup ~}.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

Automated registration of multispectral MR vessel wall images of the carotid artery

Purpose: Atherosclerosis is the primary cause of heart disease and stroke. The detailed assessment of atherosclerosis of the carotid artery requires high resolution imaging of the vessel wall using multiple MR sequences with different contrast weightings. These images allow manual or automated classification of plaque components inside the vessel wall. Automated classification requires all sequences to be in alignment, which is hampered by patient motion. In clinical practice, correction of this motion is performed manually. Previous studies applied automated image registration to correct for motion using only nondeformable transformation models and did not perform a detailed quantitative validation. The purpose of this study is to develop an automated accurate 3D registration method, and to extensively validate this method on a large set of patient data. In addition, the authors quantified patient motion during scanning to investigate the need for correction. Methods: MR imaging studies (1.5T, dedicated carotid surface coil, Philips) from 55 TIA/stroke patients with ipsilateral <70% carotid artery stenosis were randomly selected from a larger cohort. Five MR pulse sequences were acquired around the carotid bifurcation, each containing nine transverse slices: T1-weighted turbo field echo, time of flight, T2-weighted turbo spin-echo, and pre- and postcontrast T1-weighted turbo spin-echo images (T1W TSE). The images were manually segmented by delineating the lumen contour in each vessel wall sequence and were manually aligned by applying throughplane and inplane translations to the images. To find the optimal automatic image registration method, different masks, choice of the fixed image, different types of the mutual information image similarity metric, and transformation models including 3D deformable transformation models, were evaluated. Evaluation of the automatic registration results was performed by comparing the lumen segmentations of the fixed image and moving image after registration. Results: The average required manual translation per image slice was 1.33 mm. Translations were larger as the patient was longer inside the scanner. Manual alignment took 187.5 s per patient resulting in a mean surface distance of 0.271 ± 0.127 mm. After minimal user interaction to generate the mask in the fixed image, the remaining sequences are automatically registered with a computation time of 52.0 s per patient. The optimal registration strategy used a circular mask with a diameter of 10 mm, a 3D B-spline transformation model with a control point spacing of 15 mm, mutual information as image similarity metric, and the precontrast T1W TSE as fixed image. A mean surface distance of 0.288 ± 0.128 mm was obtained with these settings, which is very close to the accuracy of the manual alignment procedure. The exact registration parameters and software were made publicly available. Conclusions: An automated registration method was developed and optimized, only needing two mouse clicks to mark the start and end point of the artery. Validation on a large group of patients showed that automated image registration has similar accuracy as the manual alignment procedure, substantially reducing the amount of user interactions needed, and is multiple times faster. In conclusion, the authors believe that the proposed automated method can replace the current manual procedure, thereby reducing the time to analyze the images.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2025

New charged-particle transport computational capability: the SIT code An L-4 milestone

We have developed a new high-fidelity code for direct transport of charged particles using the simple integral transport method. The code can be coupled to the outputs of any hydrodynamical simulation code in 1-D, 2-D or 3-D. In this report we summarize the formalism involved in treating complex transport problems. We present physical examples wherein we have used the code to calculate the transport of alpha particles. Future work is planned to study the sensitivity of hydrodynamical mix to charged-particle radiochemistry and reaction-in-flight neutrons for the complex inertial confinement fusion problems encountered at NIF and at the Z-machine.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2016

RAY-RAMSES: a code for ray tracing on the fly in N-body simulations

We present a ray tracing code to compute integrated cosmological observables on the fly in AMR N-body simulations. Unlike conventional ray tracing techniques, our code takes full advantage of the time and spatial resolution attained by the N-body simulation by computing the integrals along the line of sight on a cell-by-cell basis through the AMR simulation grid. Moroever, since it runs on the fly in the N-body run, our code can produce maps of the desired observables without storing large (or any) amounts of data for post-processing. We implemented our routines in the RAMSES N-body code and tested the implementation using an example of weak lensing simulation. We analyse basic statistics of lensing convergence maps and find good agreement with semi-analytical methods. The ray tracing methodology presented here can be used in several cosmological analysis such as Sunyaev-Zel'dovich and integrated Sachs-Wolfe effect studies as well as modified gravity. Our code can also be used in cross-checks of the more conventional methods, which can be important in tests of theory systematics in preparation for upcoming large scale structure surveys.

79 ASTRONOMY AND ASTROPHYSICS↗