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At least 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Investigating the Effect of the Closure in Partially-Averaged Navier–Stokes Equations

For this study, the importance of the turbulence closure to the modeling accuracy of the partially-averaged Navier–Stokes equations (PANS) is investigated in prediction of the flow around a circular cylinder at Reynolds number of 3900. A series of PANS calculations at various degrees of physical resolution is conducted using three Reynolds-averaged Navier–Stokes equations (RANS)-based closures: the standard, shear-stress transport (SST), and turbulent/nonturbulent (TNT) k–ω models. The latter is proposed in this work. The results illustrate the dependence of PANS on the closure. At coarse physical resolutions, a narrower range of scales is resolved so that the influence of the closure on the simulations accuracy increases significantly. Among all closures, PANS–TNT achieves the lowest comparison errors. The reduced sensitivity of this closure to freestream turbulence quantities and the absence of auxiliary functions from its governing equations are certainly contributing to this result. It is demonstrated that the use of partial turbulence quantities in such auxiliary functions calibrated for total turbulent (RANS) quantities affects their behavior. On the other hand, the successive increase of physical resolution reduces the relevance of the closure, causing the convergence of the three models toward the same solution. Finally, this outcome is achieved once the physical resolution and closure guarantee the precise replication of the spatial development of the key coherent structures of the flow.

42 ENGINEERING↗
DOE OSTI2025

Regime Characterization of Offshore Wind Resource Using Unsupervised Learning

Predictability of wind resource conditions is critical for offshore wind design and operations. While many studies of extreme wind conditions focus on specific events such as low-level jets or ramps, these rely on threshold definitions that limit generality. Here we present a data-driven framework that combines principal component analysis (PCA), self-organizing maps (SOM), and k-means clustering to classify wind resource conditions as typical and anomalous from climatological data. Anomalies are defined not by fixed thresholds but by flagging samples located far from SOM node centers inside the baseline SOM structure. This reframes extremes as rare ebents and hence, likely difficult to anticipate by numerical weather prediction models. We applied this approach to 23 years (2000–2022) of hourly profiles from the NOW-23 hindcast model at the Humboldt Wind Energy Area. Classification is conducted on a feature space consisting of 10 m wind speed and direction, bulk shear and veer across 30–270 m, and a low-level jet index. Dimensionality reduction is achieved through PC. A 2 × 3 OM lattice trained on the PCA vectors identified six baseline regimes spanning weak to strong flow states. High quantization-error profiles are identified and re-clustered into four anomalous regimes. The baseline regimes exhibited clear seasonal and diurnal cycles. Meanwhile, the anomalous regimes represented <10 % of all hours but showed distinct combinations of speed, shear, and veer, when compared to the baseline regimes. Anomalous regimes are typically short-lived (~few hours), yet their transitions can lead to hub-height wind changes of −18 to +9 m s -1 . For a representative 15 MW turbine, these shifts imply rapid swings in capacity factor from near-full output to negligible generation. Validation with lidar buoy data showed 51% agreement in SOM labels across ~6,000 overlapping hours, with most mismatches confined to adjacent speed classes. HRRR comparisons further revealed that anomalous regimes were disproportionately associated with forecast biases exceeding 5 m s -1 . Together, these results reframe extremes in offshore wind from absolute maxima or minima to weather states that are difficult to anticipate from models.

17 WIND ENERGY↗
DOE OSTI2015

Model-based approaches to calibration and certification of nondestructive assay systems - 15615

Increasingly, model-based methods founded in physics are employed to calibrate, or extend the calibration of, nondestructive assay (NDA) systems used to characterize materials contaminated with plutonium, uranium, and other radioactive isotopes. In addition, modeling and mathematical methods are used to establish system parameters, correction factors, and measurement uncertainty components in NDA measurements. The methods combine the characteristics of the measurement configuration (detector structure, object shape and dimensions, source-detector distance and orientation, and collimation), generator knowledge of the waste composition, and known physical properties of the system in order to establish these parameters, factors, and components. These methods offer several important benefits over traditional methods used to test, calibrate, operate, and certify radiation measurement systems. First, instruments can be set up and put into service more quickly and correctly using a model-based approach. Second, calibrations can be performed, tested, and modified with reduced use of plutonium and uranium standards when modeling and mathematical methods are employed. Also, modeled approaches avoid calibration error resulting from heterogeneous source distribution. Moreover, the parameters can be installed quickly and simply in an office setting without the need for the safety, security, and safeguards considerations that are present when standards are used. Calibrations can also be tailored to fit unique or nonstandard container configurations (for example, over-packed drums), new container types, or specialized matrices. Finally, when modeling methods are applied, correction factors and measurement uncertainty elements can be developed, tested, and validated relatively quickly and without the need for surrogate matrix materials and a large number of test measurements. A combined gamma and neutron NDA system has recently been moved from Idaho National Laboratory to the TA 55 facility at Los Alamos National Laboratory (LANL). The system will be used to assay transuranic waste packaged in drums. After the move, the system was modified to replace degraded components and improve system performance. Afterwards, it was set up to assay different container types and to extend the calibration range. Model-based approaches were used to adapt the system to its new purpose at LANL. This report will describe the setup, calibration, and certification of the combined system at LANL Included in this discussion will be the measurement applications and details of the measurement methods. The steps in these processes that involved the use of modeling and mathematical calculations to replace or supplement more traditional methods will be identified and discussed. Finally, an overarching discussion of the methods and advantages of model-based methods to establish the properties of NDA systems will be presented. We conclude that validated mathematical methods offer a robust, flexible, and mature approach which is technically defensible from first principle physics. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2017

Importance of elastic finite-size effects: Neutral defects in ionic compounds

Small system sizes are a well known source of error in DFT calculations, yet computational constraints frequently dictate the use of small supercells, often as small as 96 atoms in oxides and compound semiconductors. In ionic compounds, electrostatic finite size effects have been well characterised, but self-interaction of charge neutral defects is often discounted or assumed to follow an asymptotic behaviour and thus easily corrected with linear elastic theory. Here we show that elastic effect are also important in the description of defects in ionic compounds and can lead to qualitatively incorrect conclusions if inadequatly small supercells are used; moreover, the spurious self-interaction does not follow the behaviour predicted by linear elastic theory. Considering the exemplar cases of metal oxides with fluorite structure, we show that numerous previous studies, employing 96-atom supercells, misidentify the ground state structure of (charge neutral) Schottky defects. We show that the error is eliminated by employing larger cells (324, 768 and 1500 atoms), and careful analysis determines that elastic effects, not electrostatic, are responsible. The spurious self-interaction was also observed in non-oxide ionic compounds and irrespective of the computational method used, thereby resolving long standing discrepancies between DFT and force-field methods, previously attributed to the level of theory. The surprising magnitude of the elastic effects are a cautionary tale for defect calculations in ionic materials, particularly when employing computationally expensive methods (e.g. hybrid functionals) or when modelling large defect clusters. We propose two computationally practicable methods to test the magnitude of the elastic self-interaction in any ionic system. In commonly studies oxides, where electrostatic effects would be expected to be dominant, it is the elastic effects that dictate the need for larger supercells | greater than 96 atoms.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

RELAP-7 Beta Release: Summary of Capabilities

RELAP-7 is a nuclear systems safety analysis code being developed at the Idaho National Laboratory (INL). Building upon the decades of software development at the INL, we began the development of RELAP-7 in 2011 to support the Risk Informed Safety Margins Characterization (RISMC) Pathway. As part of this development, the first lines of RELAP-7 code were committed to the software revision control repository on November 7th, 2011. The overall design goal of RELAP-7 is to take advantage of the previous thirty years of advancements in computer architecture, software design, numerical methods, and physical models in order to provide capabilities needed for the RISMC methodology and to support nuclear power safety analysis. RELAP-7 is built using the INL’s modern scientific software development framework, MOOSE (Multi-physics Object Oriented Simulation Environment). MOOSE provides improved numerical calculations (including higher-order integration in both space and time, yielding converged second-order accuracy). The RELAP-7 code structure is based on multiple physical component models such as pipes, junctions, pumps, etc. Each component can have options for different fluid models such as single- and two-phase flow. This component-based and physics-based software architecture allows RELAP-7 to adopt different physical models for different applications. A relatively new two-phase hydrodynamic model, termed the ''7-Equation model'' for two phasic pressures, velocities, energies, and volumetric fraction, is incorporated into RELAP-7 for liquid-gas (water-steam) flows. This new model allows second-order integration because it is well-posed, which will reduce the numerical error associated with traditional systems analysis codes. In this paper, we provide a RELAP-7 capability list describing analysis features, range of applicability, and reactor components that will be available for the December 15th, 2014 beta release of the software.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

Determining the Ensemble N -Representability of Reduced Density Matrices

The N-representability problem for reduced density matrices remains a fundamental challenge in electronic structure theory. Following our previous work that employs a unitary-evolution algorithm based on an adaptive derivative-assembled pseudo-Trotter variational quantum algorithm to probe pure-state N-representability of reduced density matrices [J. Chem. Theory Comput. 2024, 20, 9968], in this work we propose a practical framework for determining the ensemble N-representability of a p-body matrix. This is accomplished using a purification strategy that embeds an ensemble state into a pure state defined on an extended Hilbert space, such that the reduced density matrices of the purified state reproduce those of the original ensemble. By iteratively applying variational unitaries to an initial purified state, the proposed algorithm minimizes the Hilbert-Schmidt distance between its p-body reduced density matrix and a specified target p-body matrix, which serves as a measure of the N-representability of the target. This methodology facilitates both error correction of defective ensemble reduced density matrices and quantum-state reconstruction on a quantum computer, offering a route for density-matrix refinement. We validate the algorithm with numerical simulations on systems of two, three, and four electrons in both simple models as well as molecular systems at finite temperature, demonstrating its robustness.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

A dynamically bi-orthogonal method for time-dependent stochastic partial differential equations I: Derivation and algorithms

We propose a dynamically bi-orthogonal method (DyBO) to solve time dependent stochastic partial differential equations (SPDEs). The objective of our method is to exploit some intrinsic sparse structure in the stochastic solution by constructing the sparsest representation of the stochastic solution via a bi-orthogonal basis. It is well-known that the Karhunen–Loeve expansion (KLE) minimizes the total mean squared error and gives the sparsest representation of stochastic solutions. However, the computation of the KL expansion could be quite expensive since we need to form a covariance matrix and solve a large-scale eigenvalue problem. The main contribution of this paper is that we derive an equivalent system that governs the evolution of the spatial and stochastic basis in the KL expansion. Unlike other reduced model methods, our method constructs the reduced basis on-the-fly without the need to form the covariance matrix or to compute its eigendecomposition. In the first part of our paper, we introduce the derivation of the dynamically bi-orthogonal formulation for SPDEs, discuss several theoretical issues, such as the dynamic bi-orthogonality preservation and some preliminary error analysis of the DyBO method. We also give some numerical implementation details of the DyBO methods, including the representation of stochastic basis and techniques to deal with eigenvalue crossing. In the second part of our paper [11], we will present an adaptive strategy to dynamically remove or add modes, perform a detailed complexity analysis, and discuss various generalizations of this approach. An extensive range of numerical experiments will be provided in both parts to demonstrate the effectiveness of the DyBO method.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Validity of Five Satellite-Based Latent Heat Flux Algorithms for Semi-arid Ecosystems

Accurate estimation of latent heat flux (LE) is critical in characterizing semiarid ecosystems. Many LE algorithms have been developed during the past few decades. However, the algorithms have not been directly compared, particularly over global semiarid ecosystems. In this paper, we evaluated the performance of five LE models over semiarid ecosystems such as grassland, shrub, and savanna using the Fluxnet dataset of 68 eddy covariance (EC) sites during the period 2000–2009. We also used a modern-era retrospective analysis for research and applications (MERRA) dataset, the Normalized Difference Vegetation Index (NDVI) and Fractional Photosynthetically Active Radiation (FPAR) from the moderate resolution imaging spectroradiometer (MODIS) products; the leaf area index (LAI) from the global land surface satellite (GLASS) products; and the digital elevation model (DEM) from shuttle radar topography mission (SRTM30) dataset to generate LE at region scale during the period 2003–2006. The models were the moderate resolution imaging spectroradiometer LE (MOD16) algorithm, revised remote sensing based Penman–Monteith LE algorithm (RRS), the Priestley–Taylor LE algorithm of the Jet Propulsion Laboratory (PT-JPL), the modified satellite-based Priestley–Taylor LE algorithm (MS-PT), and the semi-empirical Penman LE algorithm (UMD). Direct comparison with ground measured LE showed the PT-JPL and MS-PT algorithms had relative high performance over semiarid ecosystems with the coefficient of determination (R2) ranging from 0.6 to 0.8 and root mean squared error (RMSE) of approximately 20 W/m 2 . Empirical parameters in the structure algorithms of MOD16 and RRS, and calibrated coefficients of the UMD algorithm may be the cause of the reduced performance of these LE algorithms with R2 ranging from 0.5 to 0.7 and RMSE ranging from 20 to 35 W/m 2 for MOD16, RRS and UMD. Sensitivity analysis showed that radiation and vegetation terms were the dominating variables affecting LE Fluxes in global semiarid ecosystem.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Quantified Gamow shell model interaction for p s d -shell nuclei

Background: The structure of weakly bound and unbound nuclei close to particle drip lines is one of the major science drivers of nuclear physics. A comprehensive understanding of these systems goes beyond the traditional configuration interaction approach formulated in the Hilbert space of localized states (nuclear shell model) and requires an open quantum system description. The complex-energy Gamow shell model (GSM) provides such a framework as it is capable of describing resonant and nonresonant many-body states on equal footing. Purpose: To make reliable predictions, quality input is needed that allows for the full uncertainty quantification of theoretical results. In this study, we carry out the optimization of an effective GSM (one-body and two-body) interaction in the psdf-shell-model space. The resulting interaction is expected to describe nuclei with 5 ≤ A ≲ 12 at the p-sd-shell interface. Method: The one-body potential of the 4 He core is modeled by a Woods-Saxon + spin-orbit + Coulomb potential, and the finite-range nucleon-nucleon interaction between the valence nucleons consists of central, spin-orbit, tensor, and Coulomb terms. The GSM is used to compute key fit observables. The χ 2 optimization is performed using the Gauss-Newton algorithm augmented by the singular value decomposition technique. The resulting covariance matrix enables quantification of statistical errors within the linear regression approach. Results: The optimized one-body potential reproduces nucleon- 4 He scattering phase shifts up to an excitation energy of 20 MeV. The two-body interaction built on top of the optimized one-body field is adjusted to the bound and unbound ground-state binding energies and selected excited states of the helium, lithium, and beryllium isotopes up to A = 9 . A very good agreement with experimental results was obtained for binding energies. First applications of the optimized interaction include predictions for two-nucleon correlation densities and excitation spectra of light nuclei with quantified uncertainties. In conclusion: The new interaction will enable comprehensive and fully quantified studies of structure and reactions aspects of nuclei from the psd region of the nuclear chart.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Bond Order Conservation Strategies in Catalysis Applied to the NH 3 Decomposition Reaction

On the basis of an extensive set of density functional theory calculations, it is shown that a simple scheme provides a fundamental understanding of variations in the transition state energies and structures of reaction intermediates on transition metal surfaces across the periodic table. The scheme is built on the bond order conservation principle and requires a limited set of input data, still achieving transition state energies as a function of simple descriptors with an error smaller than those of approaches based on linear fits to a set of calculated transition state energies. Here, we have applied this approach together with linear scaling of adsorption energies to obtain the energetics of the NH 3 decomposition reaction on a series of stepped fcc(211) transition metal surfaces. Moreover, this information is used to establish a microkinetic model for the formation of N 2 and H 2 , thus providing insight into the components of the reaction that determines the activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Modeling the dosimetry of organ-at-risk in head and neck IMRT planning: An intertechnique and interinstitutional study

Purpose: To build a statistical model to quantitatively correlate the anatomic features of structures and the corresponding dose-volume histogram (DVH) of head and neck (HN) Tomotherapy (Tomo) plans. To study if the model built upon one intensity modulated radiation therapy (IMRT) technique (such as conventional Linac) can be used to predict anticipated organs-at-risk (OAR) DVH of patients treated with a different IMRT technique (such as Tomo). To study if the model built upon the clinical experience of one institution can be used to aid IMRT planning for another institution. Methods: Forty-four Tomotherapy intensity modulate radiotherapy plans of HN cases (Tomo-IMRT) from Institution A were included in the study. A different patient group of 53 HN fixed gantry IMRT (FG-IMRT) plans was selected from Institution B. The analyzed OARs included the parotid, larynx, spinal cord, brainstem, and submandibular gland. Two major groups of anatomical features were considered: the volumetric information and the spatial information. The volume information includes the volume of target, OAR, and overlapped volume between target and OAR. The spatial information of OARs relative to PTVs was represented by the distance-to-target histogram (DTH). Important anatomical and dosimetric features were extracted from DTH and DVH by principal component analysis. Two regression models, one for Tomotherapy plan and one for IMRT plan, were built independently. The accuracy of intratreatment-modality model prediction was validated by a leave one out cross-validation method. The intertechnique and interinstitution validations were performed by using the FG-IMRT model to predict the OAR dosimetry of Tomo-IMRT plans. The dosimetry of OARs, under the same and different institutional preferences, was analyzed to examine the correlation between the model prediction and planning protocol. Results: Significant patient anatomical factors contributing to OAR dose sparing in HN Tomotherapy plans have been analyzed and identified. For all the OARs, the discrepancies of dose indices between the model predicted values and the actual plan values were within 2.1%. Similar results were obtained from the modeling of FG-IMRT plans. The parotid gland was spared in a comparable fashion during the treatment planning of two institutions. The model based on FG-IMRT plans was found to predict the median dose of the parotid of Tomotherapy plans quite well, with a mean error of 2.6%. Predictions from the FG-IMRT model suggested the median dose of the larynx, median dose of the brainstem and D2 of the brainstem could be reduced by 10.5%, 12.8%, and 20.4%, respectively, in the Tomo-IMRT plans. This was found to be correlated to the institutional differences in OAR constraint settings. Re-planning of six Tomotherapy patients confirmed the potential of optimization improvement predicted by the FG-IMRT model was correct. Conclusions: The authors established a mathematical model to correlate the anatomical features and dosimetric indexes of OARs of HN patients in Tomotherapy plans. The model can be used for the setup of patient-specific OAR dose sparing goals and quality control of planning results. The institutional clinical experience was incorporated into the model which allows the model from one institution to generate a reference plan for another institution, or another IMRT technique.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

Modelling the BAO feature in bispectrum

We investigate how well a simple leading order perturbation theory model of the bispectrum can fit the baryon acoustic oscillation (BAO) feature in the measured bispectrum monopole of galaxies. Previous works showed that perturbative models of the galaxy bispectrum start failing at the wavenumbers of k ∼ 0.1 h Mpc −1 . We show that when the BAO feature in the bispectrum is separated, it can be successfully modelled up to much higher wavenumbers. We validate our modelling on GLAM simulations that were run with and without the BAO feature in the initial conditions. We also quantify the amount of systematic error due to BAO template being offset from the true cosmology. We find that the systematic errors do not exceed 0.3 per cent for reasonable deviations of up to 3 per cent from the true value of the sound horizon.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Lipkin model on a quantum computer

Atomic nuclei are important laboratories for exploring and testing new insights into the universe, such as experiments to directly detect dark matter or explore properties of neutrinos. The targets of interest are often heavy, complex nuclei that challenge our ability to reliably model them (as well as quantify the uncertainty of those models) with classical computers. Hence there is great interest in applying quantum computation to nuclear structure for these applications. As an early step in this direction, especially with regards to the uncertainties in the relevant quantum calculations, we develop circuits to implement variational quantum eigensolver (VQE) algorithms for the Lipkin-Meshkov-Glick model, which is often used in the nuclear physics community as a testbed for many-body methods. Here, we present quantum circuits for VQE for two and three particles and discuss the construction of circuits for more particles. Implementing the VQE for a two-particle system on the IBM Quantum Experience, we identify initialization and two-qubit gates as the largest sources of error. We find that error mitigation procedures reduce the errors in the results significantly, but additional quantum hardware improvements are needed for quantum calculations to be sufficiently accurate to be competitive with the best current classical methods.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2013

Study of exclusive B → X u ℓ ν decays and extraction of | V u b | using full reconstruction tagging at the Belle experiment

Here, we report the results of a study of the exclusive semileptonic decays B - → π 0 ℓ - ν ¯ ℓ , B ¯ 0 → π + ℓ - ν ¯ ℓ , B - → ρ 0 ℓ - ν ¯ ℓ , B ¯ 0 → ρ + ℓ - ν ¯ ℓ and B - → ω ℓ - ν ¯ ℓ , where ℓ represents an electron or a muon. The events are tagged by fully reconstructing a second B meson in the event in a hadronic decay mode. The measured branching fractions are B ( B - → π 0 ℓ - ν ¯ ℓ ) = ( 0.80 ± 0.08 ± 0.04 ) × 10 - 4 , B ( B ¯ 0 → π + ℓ - ν ¯ ℓ ) = ( 1.49 ± 0.09 ± 0.07 ) × 10 - 4 , B ( B - → ρ 0 ℓ - ν ¯ ℓ ) = ( 1.83 ± 0.10 ± 0.10 ) × 10 - 4 , B ( B ¯ 0 → ρ + ℓ - ν ¯ ℓ ) = ( 3.22 ± 0.27 ± 0.24 ) × 10 - 4 , and B ( B - → ω ℓ - ν ¯ ℓ ) = ( 1.07 ± 0.16 ± 0.07 ) × 10 - 4 , where the first error is statistical and the second one is systematic. The obtained branching fractions are inclusive of soft photon emission. Furthermore, we determine the branching fractions as a function of the 4-momentum transfer squared to the leptonic system q 2 = ( p ℓ + p ν ) 2 , where p ℓ and p ν are the lepton and neutrino 4-momenta, respectively. Using the pion modes, a recent light cone sum rule calculation, lattice QCD results and a model-independent description of the hadronic form factor, a value of the Cabibbo-Kobayashi-Maskawa matrix element | V u b | = ( 3.52 ± 0.29 ) × 10 - 3 is extracted. A structure in the two-pion invariant mass distribution near 1.3 GeV / c 2 , which might be dominated by the decay B - → f 2 ( 1270 ) ℓ - ν ¯ ℓ , f 2 → π + π - , is seen. These results are obtained from a 711 fb - 1 data sample that contains 772 × 10 6 B B ¯ pairs, collected near the Υ ( 4 S ) resonance with the Belle detector at the KEKB asymmetric-energy e + e - collider.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Iterative Learning Control for Video-rate Atomic Force Microscopy

We present a control scheme for video-rate atomic force microscopy with rosette pattern. The controller structure involves a feedback internal-model-based controller and a feedforward iterative learning controller. The iterative learning controller is designed to improve tracking performance of the feedback-controlled scanner by rejecting the repetitive disturbances arising from the system nonlinearities. We investigate the performance of two inversion techniques for constructing the learning filter. We conduct tracking experiments using a two-degree-of-freedom microelectromechanical system (MEMS) nanopositioner at frame rates ranging from 5 to 20 frames per second. Furthermore, the results reveal that the algorithm converges rapidly and the iterative learning controller significantly reduces both the transient and steady-state tracking errors. We acquire and report a series of high-resolution time-lapsed video-rate AFM images with the rosette pattern.

42 ENGINEERING↗
DOE OSTI2014

Physics-based shape matching for intraoperative image guidance

Purpose: Soft-tissue deformations can severely degrade the validity of preoperative planning data during computer assisted interventions. Intraoperative imaging such as stereo endoscopic, time-of-flight or, laser range scanner data can be used to compensate these movements. In this context, the intraoperative surface has to be matched to the preoperative model. The shape matching is especially challenging in the intraoperative setting due to noisy sensor data, only partially visible surfaces, ambiguous shape descriptors, and real-time requirements. Methods: A novel physics-based shape matching (PBSM) approach to register intraoperatively acquired surface meshes to preoperative planning data is proposed. The key idea of the method is to describe the nonrigid registration process as an electrostatic–elastic problem, where an elastic body (preoperative model) that is electrically charged slides into an oppositely charged rigid shape (intraoperative surface). It is shown that the corresponding energy functional can be efficiently solved using the finite element (FE) method. It is also demonstrated how PBSM can be combined with rigid registration schemes for robust nonrigid registration of arbitrarily aligned surfaces. Furthermore, it is shown how the approach can be combined with landmark based methods and outline its application to image guidance in laparoscopic interventions. Results: A profound analysis of the PBSM scheme based on in silico and phantom data is presented. Simulation studies on several liver models show that the approach is robust to the initial rigid registration and to parameter variations. The studies also reveal that the method achieves submillimeter registration accuracy (mean error between 0.32 and 0.46 mm). An unoptimized, single core implementation of the approach achieves near real-time performance (2 TPS, 7–19 s total registration time). It outperforms established methods in terms of speed and accuracy. Furthermore, it is shown that the method is able to accurately match partial surfaces. Finally, a phantom experiment demonstrates how the method can be combined with stereo endoscopic imaging to provide nonrigid registration during laparoscopic interventions. Conclusions: The PBSM approach for surface matching is fast, robust, and accurate. As the technique is based on a preoperative volumetric FE model, it naturally recovers the position of volumetric structures (e.g., tumors and vessels). It cannot only be used to recover soft-tissue deformations from intraoperative surface models but can also be combined with landmark data from volumetric imaging. In addition to applications in laparoscopic surgery, the method might prove useful in other areas that require soft-tissue registration from sparse intraoperative sensor data (e.g., radiation therapy)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

COMPASS: A Framework for Automated Performance Modeling and Prediction

Flexible, accurate performance predictions offer numerous benefits such as gaining insight into and optimizing applications and architectures. However, the development and evaluation of such performance predictions has been a major research challenge, due to the architectural complexities. To address this challenge, we have designed and implemented a prototype system, named COMPASS, for automated performance model generation and prediction. COMPASS generates a structured performance model from the target application's source code using automated static analysis, and then, it evaluates this model using various performance prediction techniques. As we demonstrate on several applications, the results of these predictions can be used for a variety of purposes, such as design space exploration, identifying performance tradeoffs for applications, and understanding sensitivities of important parameters. COMPASS can generate these predictions across several types of applications from traditional, sequential CPU applications to GPU-based, heterogeneous, parallel applications. Our empirical evaluation demonstrates a maximum overhead of 4%, flexibility to generate models for 9 applications, speed, ease of creation, and very low relative errors across a diverse set of architectures.

Lee, Seyong↗
DOE OSTI2019

De novo Nanopore read quality improvement using deep learning

BACKGROUND: Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. The limited sensitivity of existing read-based error correction methods can cause large-scale mis-assemblies in the assembled genomes, motivating further innovation in this area. RESULTS: Here we developed a Convolutional Neural Network (CNN) based method, called MiniScrub, for identification and subsequent "scrubbing" (removal) of low-quality Nanopore read segments to minimize their interference in downstream assembly process. MiniScrub first generates read-to-read overlaps via MiniMap2, then encodes the overlaps into images, and finally builds CNN models to predict low-quality segments. Applying MiniScrub to real world control datasets under several different parameters, we show that it robustly improves read quality, and improves read error correction in the metagenome setting. Compared to raw reads, de novo genome assembly with scrubbed reads produces many fewer mis-assemblies and large indel errors. CONCLUSIONS: MiniScrub is able to robustly improve read quality of Oxford Nanopore reads, especially in the metagenome setting, making it useful for downstream applications such as de novo assembly. We propose MiniScrub as a tool for preprocessing Nanopore reads for downstream analyses. MiniScrub is open-source software and is available at https://bitbucket.org/berkeleylab/jgi-miniscrub .

59 BASIC BIOLOGICAL SCIENCES↗