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At least 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Enhancing atlas based segmentation with multiclass linear classifiers

Purpose: To present a method to enrich atlases for atlas based segmentation. Such enriched atlases can then be used as a single atlas or within a multiatlas framework. Methods: In this paper, machine learning techniques have been used to enhance the atlas based segmentation approach. The enhanced atlas defined in this work is a pair composed of a gray level image alongside an image of multiclass classifiers with one classifier per voxel. Each classifier embeds local information from the whole training dataset that allows for the correction of some systematic errors in the segmentation and accounts for the possible local registration errors. The authors also propose to use these images of classifiers within a multiatlas framework: results produced by a set of such local classifier atlases can be combined using a label fusion method. Results: Experiments have been made on the in vivo images of the IBSR dataset and a comparison has been made with several state-of-the-art methods such as FreeSurfer and the multiatlas nonlocal patch based method of Coupé or Rousseau. These experiments show that their method is competitive with state-of-the-art methods while having a low computational cost. Further enhancement has also been obtained with a multiatlas version of their method. It is also shown that, in this case, nonlocal fusion is unnecessary. The multiatlas fusion can therefore be done efficiently. Conclusions: The single atlas version has similar quality as state-of-the-arts multiatlas methods but with the computational cost of a naive single atlas segmentation. The multiatlas version offers a improvement in quality and can be done efficiently without a nonlocal strategy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

A formally certified end-to-end implementation of Shor’s factorization algorithm

Quantum computing technology may soon deliver revolutionary improvements in algorithmic performance, but it is useful only if computed answers are correct. While hardware-level decoherence errors have garnered significant attention, a less recognized obstacle to correctness is that of human programming errors—“bugs.” Techniques familiar to most programmers from the classical domain for avoiding, discovering, and diagnosing bugs do not easily transfer, at scale, to the quantum domain because of its unique characteristics. To address this problem, we have been working to adapt formal methods to quantum programming. With such methods, a programmer writes a mathematical specification alongside the program and semiautomatically proves the program correct with respect to it. The proof’s validity is automatically confirmed—certified—by a “proof assistant.” Formal methods have successfully yielded high-assurance classical software artifacts, and the underlying technology has produced certified proofs of major mathematical theorems. As a demonstration of the feasibility of applying formal methods to quantum programming, we present a formally certified end-to-end implementation of Shor’s prime factorization algorithm, developed as part of a framework for applying the certified approach to general applications. By leveraging our framework, one can significantly reduce the effects of human errors and obtain a high-assurance implementation of large-scale quantum applications in a principled way.

Science & Technology - Other Topics↗
DOE OSTI2025

Improvement and Verification of Online Cross Section Generation Capability of Griffin for TRISO-fueled Reactors

Griffin, a MOOSE-based reactor multiphysics code jointly developed by Idaho National Laboratory and Argonne National Laboratory under the DOE Office of Nuclear Energy’s NEAMS program, has pursued the development of an online multigroup cross section generation capability for a few years to enable high-fidelity, problem-dependent neutronics analyses of advanced thermal reactors. Recent advancements in Griffin’s online multigroup cross section generation capability have significantly improved the accuracy, robustness, and efficiency of self-shielding calculations for both prismatic and pebble-bed TRISO-fueled reactor applications. Key developments include a unified fuel self-shielding method applicable to both TRISO and annular compact/spherical shell fuel zone geometries; an advanced Dancoff Category-based Equivalence Theory using a bell function for non-fuel resonance treatment, achieving more than an order-of-magnitude speedup compared to the Tone method; an on-the-fly multigroup equivalence approach to mitigate group condensation errors; and a streaming correction method for pebble-bed homogenization. A proof-of-concept demonstration of on-the-fly group condensation with consistent P0 transport correction was also achieved. The method reproduced direct fine-group solutions with excellent accuracy (eigenvalue errors within 10 pcm and pin-power differences within 0.5%), but due to performance limitations of the current fixed-source solver, improvements to solver efficiency will be addressed in future work. Verification tests were performed on graphite-moderated TRISO-fueled two-dimensional core benchmark problems representing gas-cooled microreactors, heat pipe-cooled microreactors, gas-cooled pebble-bed reactors, and fluoride salt-cooled high-temperature reactors. Across all cases, Griffin showed excellent agreement with Serpent2 continuous energy Monte Carlo solutions: eigenvalue errors within 200 pcm, pin-power root-mean-square errors within 2%, and control rod and drum worth errors less than 2%. It should be noted that, for the benchmark problem, cross section generation contributed less than 3% of the total simulation times. These results demonstrate that Griffin’s online cross section generation capability delivers accurate and efficient reactor physics solutions across a wide spectrum of TRISO-fueled advanced reactor designs. With further improvements to the fine-group fixed-source solver and planned extensions to depletion, transients, and coupled neutron–gamma transport, Griffin will be well-positioned to become a powerful and comprehensive tool for advanced reactor analysis.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2015

Systematic study of finite-size effects in quantum Monte Carlo calculations of real metallic systems

We present a systematic and comprehensive study of finite-size effects in diffusion quantum Monte Carlo calculations of metals. Several previously introduced schemes for correcting finite-size errors are compared for accuracy and efficiency, and practical improvements are introduced. In particular, we test a simple but efficient method of finite-size correction based on an accurate combination of twist averaging and density functional theory. Our diffusion quantum Monte Carlo results for lithium and aluminum, as examples of metallic systems, demonstrate excellent agreement between all of the approaches considered.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Modeling protein structures from predicted contacts with modern molecular dynamics potentials: accuracy, sensitivity, and refinement

Protein structure prediction has become increasingly popular and successful in recent years. An essential step for fragment-free, template-free methods is the generation of a final three-dimensional protein model from a set of predicted amino acid contacts that are often described by interresidue pairwise atomic distances. Here we explore the use of modern, open-source molecular dynamics (MD) engines, which have been continually developed over the last three decades with all-atom Hamiltonians to model biomolecular structure and dynamics, to generate accurate protein structures starting from a set of inferred pairwise distances. Additionally, the ability of MD empirical physical potentials to correct inaccuracies in the predicted geometries is tested. We rigorously characterize the effect of modeling parameters on results, the effect of different amounts of error in the predicted distances on the final structures, and test the ability of post-processing analysis to sort the best models out of a set of statistical replicas. We find that with exact distances and with noisy distances, the method can produce excellent structural models, and that the molecular dynamics force field seems to help correct errors in distance predictions, resisting the effects of applied noise.

Davidson, Russ↗
DOE OSTI2015

Study of orbit correction for eRHIC FFAG design

The unique feature of the orbits in the eRHIC Fixed Field Alternating Gradient (FFAG) design is that multiple accelerating and decelerating bunches pass through the same magnets with different horizontal offsets. Therefore, it is critical for the eRHIC FFAG to correct multiple orbits in the same vacuum pipe for better spin transmission and alignment of colliding beams. In this report, the effects on orbits from multiple error sources will be studied. The orbit correction method will be described and results will be presented.

43 PARTICLE ACCELERATORS↗
DOE OSTI2017

Better band gaps for wide-gap semiconductors from a locally corrected exchange-correlation potential that nearly eliminates self-interaction errors

Here, this work constitutes a comprehensive and improved account of electronic-structure and mechanical properties of silicon-nitride (${\rm Si}_{3}$ ${\rm N}_{4}$ ) polymorphs via van Leeuwen and Baerends (LB) exchange-corrected local density approximation (LDA) that enforces the exact exchange potential asymptotic behavior. The calculated lattice constant, bulk modulus, and electronic band structure of ${\rm Si}_{3}$ ${\rm N}_{4}$ polymorphs are in good agreement with experimental results. We also show that, for a single electron in a hydrogen atom, spherical well, or harmonic oscillator, the LB-corrected LDA reduces the (self-interaction) error to exact total energy to ~10%, a factor of three to four lower than standard LDA, due to a dramatically improved representation of the exchange-potential.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Correction of confidence intervals in excess relative risk models using Monte Carlo dosimetry systems with shared errors

Introduction: Measurement errors are ubiquitous in epidemiological studies, especially for doses arising from environmental and occupational exposures, which are difficult to assess. Correction methods for independent measurement errors, have been comprehensively described elsewhere, including regression calibration, simulation extrapolation (SIMEX), etc. However, when exposure estimates are constructed using complicated physical and biological models, uncertainties in the dosimetry system can become very complex. In such systems, uncertainties in some parameters may affect a large group of study participants simultaneously, and hence are “shared” as opposed to independent dosimetric uncertainties. Representing the structure of the uncertainty in the dosimetry by providing multiple realizations of possible dose has been described for several studies. The goal of this paper is to implement, and explore the properties of, a generalized estimating equation-based approach to shared uncertainties based on principles described in an earlier paper. Methods: The effects of shared and unshared dosimetry error on parameter estimates and confidence intervals in a generalized excess relative risk model are examined. A post-hoc correction method is implemented that constructs corrected confidence intervals based on an underlying variance structure described in an earlier paper. In this correction method it is assumed that the estimated slope parameter in a linear excess relative risk model is distributed as a mixture of normal and lognormal components. A simulation study of the behavior of this correction was developed based on multiple realizations provided by the Monte Carlo dosimetry system used for the plutonium exposures in the Mayak Worker Cohort and a risk model with close similarity to that used in analyses of lung cancer data in that cohort. Results: In the simulation study we found that shared dose errors severely degraded the coverage probabilities of confidence limits for the slope parameter in the linear excess relative risk model relating uncertain exposure to lung cancer risk. Using our correction method to adjust the confidence intervals provided much improved coverage probabilities for this parameter. A smaller amount of degradation in confidence interval coverage for other parameters (e.g. those in the baseline and dose modification terms) was noted, and the proposed correction method also improved coverage for these parameters as well. Discussion: Compared to other recently described methods our proposed correction method relies on relatively familiar software to fit dose response models. The basic modeling philosophy described here first uses existing Poisson regression methods to estimate parameters in the excess relative risk model; in this first stage mean dose (computed from the multiple realizations) is used as the independent variable in the regression. Once the model is fit we then correct (widen) the standard errors for all parameters using the proposed correction method. The simulation studies indicate that the methods described here are an important contribution to the available tools for dealing with shared measurement errors in complex risk analysis.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2015

Optics correction for the multi-pass FFAG ERL machine eRHIC

Gradient errors in the multi-pass Fixed Field Alternating Gradient (FFAG) Energy Recovery Linac (ERL) machine, eRHIC, distort the beam orbit and therefore cause emittance increase. The localization and correction of gradient errors are essential for an effective orbit correction and emittance preservation. In this report, the methodology and simulation of optics correction for the multi-pass FFAG ERL machine eRHIC will be presented.

43 PARTICLE ACCELERATORS↗
DOE OSTI2016

NEMA NU 2-2012 performance studies for the SiPM-based ToF-PET component of the GE SIGNA PET/MR system

Purpose: The GE SIGNA PET/MR is a new whole body integrated time-of-flight (ToF)-PET/MR scanner from GE Healthcare. The system is capable of simultaneous PET and MR image acquisition with sub-400 ps coincidence time resolution. Simultaneous PET/MR holds great potential as a method of interrogating molecular, functional, and anatomical parameters in clinical disease in one study. Despite the complementary imaging capabilities of PET and MRI, their respective hardware tends to be incompatible due to mutual interference. In this work, the GE SIGNA PET/MR is evaluated in terms of PET performance and the potential effects of interference from MRI operation. Methods: The NEMA NU 2-2012 protocol was followed to measure PET performance parameters including spatial resolution, noise equivalent count rate, sensitivity, accuracy, and image quality. Each of these tests was performed both with the MR subsystem idle and with continuous MR pulsing for the duration of the PET data acquisition. Most measurements were repeated at three separate test sites where the system is installed. Results: The scanner has achieved an average of 4.4, 4.1, and 5.3 mm full width at half maximum radial, tangential, and axial spatial resolutions, respectively, at 1 cm from the transaxial FOV center. The peak noise equivalent count rate (NECR) of 218 kcps and a scatter fraction of 43.6% are reached at an activity concentration of 17.8 kBq/ml. Sensitivity at the center position is 23.3 cps/kBq. The maximum relative slice count rate error below peak NECR was 3.3%, and the residual error from attenuation and scatter corrections was 3.6%. Continuous MR pulsing had either no effect or a minor effect on each measurement. Conclusions: Performance measurements of the ToF-PET whole body GE SIGNA PET/MR system indicate that it is a promising new simultaneous imaging platform.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

The Importance of Addressing Disagreements Between Nominal and Effective Treatments During Bat Mortality Minimization Validation Studies

As the wind energy industry grows, so too does our need for effective and low-cost bat mortality minimization solutions. Despite knowledge gaps in our understanding of what drives bats to collide with spinning turbines, minimization solutions have shown success during validation studies. Curtailment has been consistently effective, reducing bat mortality from 33%-79%, depending on the curtailment scenario and species present. Several validation studies have demonstrated deterrent solutions, specifically ultrasonic deterrents, to be effective, but overall, more variable compared to curtailment solutions. Further, a study combining curtailment with ultrasonic deterrents produced encouraging results, finding that adding ultrasonic deterrents to turbines that were designated to curtail, significantly reduced mortality rates compared to curtailment only turbines. Despite positive results, the strength of inference achieved with validation studies is limited by methodological constraints associated with appropriately assigning fatalities to treatments. Because of the temporal separation between when a bat collides with a turbine and when it is discovered during a ground-based carcass survey, we must assign carcasses to a treatment that ran during the prior night(s). This process may introduce errors at multiple stages. First, for studies that rotate treatments among turbines, mortality surveyors must be confident that carcasses are 'fresh' such that mortalities are correctly assigned to the treatment from the previous night(s). Second, we must reconcile any misalignments between how we assign treatments and how we implement treatments (e.g., turbines assigned with a deterrent treatment may be implemented as another treatment when deterrent devices are not operating as designed). Finally, for curtailment solutions, it is critical to recognize that measured effects are a function of not just the treatment as implemented but the proportion of the night the treatment is realized (e.g., if wind speeds are greater than the curtailment treatment cut-in speed for the entire night, we cannot expect there to me any differences in mortality reduction relative to control turbines). Using a dataset collected between June and October 2017, that rotated 3 treatments (Deterrent Only, 5 m/s Curtail only, and 5 m/s Curtail & Deterrent) and 1 control condition across 16 turbines each night, we explored the importance and implications of accounting for potential errors in assigning fatalities to treatments. We present preliminary results comparing the mortality associated with error-corrected treatments and control conditions highlighting how the measured effect of a treatment (mortality) greatly depends on site specific implementation.

bats↗
DOE OSTI2019

Publisher Correction: High-harmonic generation from solids

In the version of this Review Article originally published, in Fig. 2b, the label ‘Inter-band current’ should have read ‘Intra-band current’. This error has now been corrected in the online versions.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2015

Fault tolerance in an inner-outer solver: A GVR-enabled case study

Resilience is a major challenge for large-scale systems. It is particularly important for iterative linear solvers, since they take much of the time of many scientific applications. We show that single bit flip errors in the Flexible GMRES iterative linear solver can lead to high computational overhead or even failure to converge to the right answer. Informed by these results, we design and evaluate several strategies for fault tolerance in both inner and outer solvers appropriate across a range of error rates. We implement them, extending Trilinos’ solver library with the Global View Resilience (GVR) programming model, which provides multi-stream snapshots, multi-version data structures with portable and rich error checking/recovery. Lastly, experimental results validate correct execution with low performance overhead under varied error conditions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Does DFT+U mimic hybrid density functionals?

Here, this work examines the question of how a Hubbard U correction to a local exchange–correlation functional compares with adding Hartree–Fock exchange to a local functional for both solid-state and molecular properties. We compute a solid-state property, namely the band gap, and thermochemical molecular properties, in particular main-group bond energies, transition-metal–ligand bond energies, and barrier heights, to elucidate whether the DFT+U method mimics hybrid DFT. We find that a calculation with a Hubbard U correction may or may not mimic a hybrid functional – depending on the atom, the subshell, and the property to which it is applied. For band gaps, we find that adding a Hubbard U correction to the valence d orbitals of transition metals increases the band gap, which thereby gets closer to the experimental value, while adding a Hubbard U correction to valence s or p orbitals of main group elements need not always increase the band gap. For molecular thermochemistry, we find that adding a Hubbard U correction to a local density functional need not have the same effect as adding Hartree–Fock exchange to a local density functional. For example when compared to a local DFT, hybrid DFT increases the barrier height in all cases, but DFT+U does not always increase the barrier height. For the band gaps of transition metal monoxides, the Hubbard-corrected results lowered the mean errors significantly and were comparable to what could be achieved with a much more expensive hybrid functional, but for reaction barrier heights and bond energies the Hubbard correction can lower the mean error by approximately a kcal/mol. As part of the analysis, we also compare VASP and Gaussian 09 calculations for the same density functional.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Active phase correction of high resolution silicon photonic arrayed waveguide gratings

Arrayed waveguide gratings provide flexible spectral filtering functionality for integrated photonic applications. Achieving narrow channel spacing requires long optical path lengths which can greatly increase the footprint of devices. High index contrast waveguides, such as those fabricated in silicon-on-insulator wafers, allow tight waveguide bends which can be used to create much more compact designs. Both the long optical path lengths and the high index contrast contribute to significant optical phase error as light propagates through the device. Thus, silicon photonic arrayed waveguide gratings require active or passive phase correction following fabrication. We present the design and fabrication of compact silicon photonic arrayed waveguide gratings with channel spacings of 50, 10 and 1 GHz. The largest device, with 11 channels of 1 GHz spacing, has a footprint of only 1.1 cm 2 . Using integrated thermo-optic phase shifters, the phase error is actively corrected. We present two methods of phase error correction and demonstrate state-of-the-art cross-talk performance for high index contrast arrayed waveguide gratings. As a demonstration of possible applications, we perform RF channelization with 1 GHz resolution. In addition, we generate unique spectral filters by applying non-zero phase offsets calculated by the Gerchberg Saxton algorithm.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Characterization of Cameras for the COSMO K-coronagraph

Digital image sensors are ubiquitous in astronomical instrumentation and it is well known that they suffer from issues that must be corrected for data to be scientifically useful. I present discussion on errors resulting from digitization and characterization of nonlinearity and ADC errors of the PhotonFocus MV-D1024E cameras selected for the K-coronagraph of the Coronal Solar Magnetism Observatory. I derive an analytic expression for quantization errors. The MV-D1024E camera has adequate bit depth for which quantization error is not an issue. I show that this is not the case for all cameras, particularly those with deep wells and low read noise. The impact of nonlinearity and ADC errors on science observations of the K-coronagraph is analyzed using a simplified telescope model. Errors caused by the camera ADCs result in systematic errors in the measurement of the polarimetric signal of several times 10{sup −9} B {sub ⊙}, which is about an order of magnitude above the desired sensitivity. I demonstrate a method for post-facto data correction using a lookup table and derive parameters from camera characterization measurements that were made with a lab setup. Nonlinearity is traditionally addressed with a global correction. I show through analysis of calibration data that for the MV-D1024E this correction leaves residual systematic errors after dark and gain correction of up to 1% of the signal. I demonstrate that a pixel-wise correction of nonlinearity reduces the errors to below 0.1%. These corrections are necessary for the K-coronagraph data products to meet the science requirements. They have been implemented in the instrument data acquisition system and data reduction pipeline. While no other instruments besides the K-coronagraph or cameras besides the MV-D1024E are discussed here, the results are illustrative for all instruments and cameras.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Subtlety of TiO 2 phase stability: Reliability of the density functional theory predictions and persistence of the self-interaction error

TiO 2 is an important material with broad applications that can exist in different phases with dramatically different properties. Theoretical prediction of their polymorph energetics is therefore critical for the material design and for identifying thermodynamically accessible structures. Determining TiO 2 relative phase stabilities remains challenging for first-principles methods, and density functional theory is the only approach available for studying phase stabilities at finite temperatures with acceptable computational efficiency. Here, we show that density functional theory using the recently developed efficient strongly constrained and appropriately normed (SCAN) [Sun et al., Phys. Rev. Lett. 115, 036402 (2015)] exchange-correlation functional for the first time predicts the phase stability in qualitative agreement with the experimental results at realistic conditions. Further analysis shows that the self-interaction error intrinsic in the density functional persists in the stability prediction. By correcting the self-interaction error through an empirical approach, SCAN predicts the relative stability as well as defect properties in excellent agreement with the experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗