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DOE OSTI2015

SU-E-J-111: Finite Element-Based Deformable Image Registration of Pleural Cavity for Photodynamic Therapy

Purpose: The pleural volumes will deform during surgery portion of the pleural photodynamic therapy (PDT) of lung cancer when the pleural cavity is opened. This impact the delivered dose when using highly conformal treatment techniques. In this study, a finite element-based (FEM) deformable image registration is used to quantify the anatomical variation between the contours for the pleural cavities obtained in the operating room and those determined from pre-surgery computed tomography (CT) scans. Methods: An infrared camera-based navigation system (NDI) is used during PDT to track the anatomical changes and contour the lung and chest cavity. A series of CTs of the lungs, in the same patient, are also acquired before the surgery. The structure contour of lung and the CTs are processed and contoured in Matlab and MeshLab. Then, the contours are imported into COMSOL Multiphysics 5.0, where the FEM-based deformable image registration is obtained using the deformed mesh - moving mesh (ALE) model. The NDI acquired lung contour is considered as the reference contour, and the CT contour is used as the target one, which will be deformed. Results: The reconstructed three-dimensional contours from both NDI and CT can be converted to COMSOL so that a three-dimensional ALE model can be developed. The contours can be registered using COMSOL ALE moving mesh model, which takes into account the deformation along x, y and z-axes. The deformed contour has good matches to the reference contour after the dynamic matching process. The resulting 3D deformation map can be used to obtain the locations of other critical anatomic structures, e.g., heart, during surgery. Conclusion: Deformable image registration can fuse images acquired by different modalities. It provides insights into the development of phenomenon and variation in normal anatomical structures over time. The initial assessments of three-dimensional registration show good agreement.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Perovskite Sorbent Oxygen Separation Modeling with MFiX

This document chronicles the development and implementation of computational kinetic rate models that capture absorption and desorption characteristics of the National Energy Technology Laboratory (NETL) developed perovskite, Sr 1-x Ca x FeO 3-δ . Two paths to create accurate kinetic rates were followed: (1) an isothermal rate approach where thermogravimetric (TGA) data are recast as oxygen capacities through a pseudo-second order Lagergren equation (He et al., 2009); and (2) a more traditional Arrhenius approach where experimental data are fit with a power law model to derive associate activation energies (Bulfin et al., 2020a). For reference, the mathematics and associate experimental strategies that support these derivations are included in this report. In addition, computational fluid dynamics (CFD) models were developed to utilize both kinetic rate formulations and applied to simulate oxygen uptake and release in small scale scenarios. The program Multiphase Flow with interphase eXchanges (MFiX) was used to create: (1) discrete element method (DEM) simulations of a single tube of granular perovskite experiencing isothermal O 2 -absorption; and desorption and (2) two-fluid-model (TFM) non-isothermal simulations of perovskite O 2 -absorption and desorption tubes that share a wall. Conjugate heat transfer between steel walled tubes and the perovskite bed were managed with user-defined functions. As the project moves to simulating larger scale devices that will require more robust conjugate heat transfer methods, developed kinetic rates and associate methodologies have been recast for use in the ANSYS Fluent CFD program.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Improved pore network models to simulate single-phase flow in porous media by coupling with lattice Boltzmann method

In this paper, different pore network models to simulate single-phase flow in porous media are built and their accuracy is evaluated. In addition to the conventional pore network model (CPNM) which consists of regular pore bodies and throat bonds, three improved pore network models (IPNMs) are developed allowing to better describing the real pore and throat geometry. The first improved pore network model (IPNM1) replaces the regular throat bond with a throat bond showing the real throat cross section. The second improvement (IPNM2) uses a series of sub-throat bonds with varying cross sections to better describe the real throat geometry, which is firstly proposed in this paper. The third model (IPNM3) extracts the real pore-throat-pore geometry without simplification. The conductance of fluid flow through these more realistic throat bonds is calculated by the lattice Boltzmann method (LBM). The accuracy and computational efficiency of the different pore network models are evaluated taking the LBM simulation over the whole porous medium as reference solution. The global permeability and detailed pressure distributions in the pores for the different pore network models are validated. The results show that the accuracy of the pore network model increases from CPNM to IPNM3, but at the expense of increasing computational cost. This study suggests that IPNM3 can replace a whole-domain LBM simulation with similar accuracy but much lower computational cost. As a first-order approximation the newly proposed IPNM2 is suggested as good compromise between accuracy and computational cost.

42 ENGINEERING↗

DOE OSTI2020

Magnesium abundances in cool metal-polluted white dwarfs

ABSTRACT The accretion of rocky material is responsible for the presence of heavy elements in the atmospheres of a large fraction of white dwarf stars. Those objects represent a unique opportunity to infer the bulk composition of exoplanetesimals. This chemical characterization requires the use of detailed atmosphere models to determine the elemental abundances at the photospheres of white dwarfs. In this work, we use a state-of-the-art model atmosphere code to reanalyse the first large survey of metal-polluted white dwarfs for which abundances are found for multiple elements. We show that the improved constitutive physics of our models lead to systematically higher Mg abundances than previous analyses. We find an average $\log \, {\rm Mg/Ca}$ number abundance ratio of 1.5. This value is significantly above the reference abundance for chondrites, which is expected as current diffusion models predict that for the cool helium-atmosphere white dwarfs of our sample, Mg should remain in the atmosphere longer than Ca. This helps resolve a recently identified Mg depletion problem, where the planetesimals accreted by white dwarfs were reported to be Mg-deficient compared to the expected composition of their planetary systems.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

How May the Choice of Downscaling Techniques and Meteorological Reference Observations Affect Future Hydroclimate Projections?

Abstract We present an intercomparison of a suite of high‐resolution downscaled climate projections based on a six‐member General Circulation Model (GCM) ensemble from Coupled Models Intercomparison Project (CMIP6). The CMIP6 GCMs have been downscaled using dynamical and statistical downscaling techniques based on two meteorological reference observations over the conterminous United States. We use the regional climate model, RegCM4, for dynamical downscaling, double bias correction constructed analogs method for statistical downscaling, and Daymet and Livneh datasets as the reference observations for statistical training and bias‐correction. We evaluate the performances of downscaled data in both historical and future periods under the SSP585 scenario. While dynamical downscaling improves the simulation of some performance evaluation indices, it adds an extra bias in others, highlighting the need for statistical correction before its use in impact assessments. Downscaled datasets after bias‐correction compare exceptionally well with observations. However, the choice of downscaling techniques and the underlying reference observations influence the hydroclimate characteristics of downscaled data. For instance, the statistical downscaling generally preserves the GCMs climate change signal but overestimates the frequency of hot extremes. Similarly, simulated future changes are sensitive to the choice of reference observations, particularly for precipitation extremes that exhibit a higher projected increase in the ensembles trained and/or corrected by Daymet than Livneh. Overall, these results demonstrate that multiple factors, including downscaling techniques and reference observations, can substantially influence the outcome of downscaled climate projections and stress the need for a comprehensive understanding of such method‐based uncertainties.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Modeling Noise: Paths toward AI-Enabled Stochastic Earth System Models and Parameterizations

Some of the key challenges in Earth system prediction arise from an uncertain representation of unpredictable natural variability, across time and space scales. This variability, hereafter referred to as noise, represents the quantity against which the strength of a signal of interest is measured to assess predictability. Underestimating or overestimating this noise in Earth system models can lead to issues ranging between overconfidence in an erroneous prediction and a lack thereof in an otherwise accurate one. Noise is part of the physical processes in the Earth system and can amplify or damp a signal of interest in a complex manner that is not systematically characterized. Specifically, while there has been significant progress in our understanding of multiscale interactions among known modes of variability (potentially predictable signals), how these are impacted by the noise is not clear. Recent effort toward stochastic parametrization schemes that provide a representation of noise due to uncertain sub-grid processes in climate models (Berner et al., 2017 and references therein) has shown promise not only in reducing biases and improving probabilistic prediction but also in improving the representation of natural variability in the model toward what is observed. However, today’s standard schemes for stochastic parametrization are still simplistic as they do not take the state of the atmosphere into account (other than by the use of multiplicative noise for model tendencies). Furthermore they require hand-tuning and trial-and-error testing for the magnitude of the added noise, which is difficult in a chaotic system that is as complex as the Earth system.

58 GEOSCIENCES↗

DOE OSTI2014

A Novel Fast Helical 4D-CT Acquisition Technique to Generate Low-Noise Sorting Artifact–Free Images at User-Selected Breathing Phases

Purpose: To develop a novel 4-dimensional computed tomography (4D-CT) technique that exploits standard fast helical acquisition, a simultaneous breathing surrogate measurement, deformable image registration, and a breathing motion model to remove sorting artifacts. Methods and Materials: Ten patients were imaged under free-breathing conditions 25 successive times in alternating directions with a 64-slice CT scanner using a low-dose fast helical protocol. An abdominal bellows was used as a breathing surrogate. Deformable registration was used to register the first image (defined as the reference image) to the subsequent 24 segmented images. Voxel-specific motion model parameters were determined using a breathing motion model. The tissue locations predicted by the motion model in the 25 images were compared against the deformably registered tissue locations, allowing a model prediction error to be evaluated. A low-noise image was created by averaging the 25 images deformed to the first image geometry, reducing statistical image noise by a factor of 5. The motion model was used to deform the low-noise reference image to any user-selected breathing phase. A voxel-specific correction was applied to correct the Hounsfield units for lung parenchyma density as a function of lung air filling. Results: Images produced using the model at user-selected breathing phases did not suffer from sorting artifacts common to conventional 4D-CT protocols. The mean prediction error across all patients between the breathing motion model predictions and the measured lung tissue positions was determined to be 1.19 ± 0.37 mm. Conclusions: The proposed technique can be used as a clinical 4D-CT technique. It is robust in the presence of irregular breathing and allows the entire imaging dose to contribute to the resulting image quality, providing sorting artifact–free images at a patient dose similar to or less than current 4D-CT techniques.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2022

Impact of doped barriers on the recombination coefficients of c -plane InGaN/GaN single quantum well light-emitting diodes

Differential carrier lifetime measurements were performed on c-plane InGaN/GaN single quantum well (QW) light-emitting diodes (LEDs) of different QW indium compositions as well as with and without doped barriers. Mg-doped p-type and Si-doped n-type barriers close to the QW were used to reduce the net internal electric field in the QW, thereby improving the electron–hole wavefunction overlap on the LEDs. LEDs with doped barriers show short lifetimes and low carrier densities in the active region compared to the reference LEDs. The recombination coefficients in the ABC model were estimated based on the carrier lifetime and quantum efficiency measurements. The improvement in the radiative coefficients in the LEDs with doped barriers coupled with the blueshift of the emission wavelengths indeed indicates an enhancement in wavefunction overlap and a reduction of quantum confined Stark effect as a result of the reduced internal electric field. However, doped barriers also introduce non-radiative recombination centers and thereby increase the Shockley–Read–Hall (SRH) coefficient, although the increment is less for LEDs with high indium composition QWs. As a result, at high indium composition (22%), LEDs with doped barriers outperform the reference LEDs even though the trend is reversed for LEDs with lower indium composition (13.5%). In conclusion, despite the trade-off of higher SRH coefficients, doped barriers are shown to be effective in reducing the internal electric field and increasing the recombination coefficients.

42 ENGINEERING↗

DOE OSTI2021

PyOECP: A flexible open-source software for the measurement and modeling of the dielectric spectrum from the reflection coefficient

We present PyOECP, a Python-based flexible open-source software for estimating and modeling the complex permittivity obtained from the open-ended coaxial probe (OECP) technique. The transformation of the measured reflection coefficient to complex permittivity is performed based on two different models, including the capacitance model and the antenna model. The software library contains dielectric spectra of common reference liquids, which can be used to transform the reflection coefficient into the dielectric spectra. Several Python routines that are commonly employed (e.g., SciPy and NumPy) are only required so that the users can alter the software structure depending on their needs. The modeling algorithm exploits the Markov chain Monte Carlo method for the data regression. The discrete relaxation models can be built by a proper combination of well-known relaxation models. In addition to these models, the electrode polarization, which is a common measurement artifact for interpreting the dielectric spectra, can be incorporated in the modeling algorithm. A continuous relaxation model, which solves the Fredholm integral equation of the first kind (a mathematically ill-posed problem) is also included.

Yoon, Tae-Jun↗

DOE OSTI2023

OC6 project Phase III: validation of the aerodynamic loading on a wind turbine rotor undergoing large motion caused by a floating support structure

Abstract. This paper provides a summary of the work done within Phase III of the Offshore Code Comparison Collaboration, Continued, with Correlation and unCertainty (OC6) project, under the International Energy Agency Wind Technology Collaboration Programme Task 30. This phase focused on validating the aerodynamic loading on a wind turbine rotor undergoing large motion caused by a floating support structure. Numerical models of the Technical University of Denmark 10 MW reference wind turbine were validated using measurement data from a 1:75 scale test performed during the UNsteady Aerodynamics for FLOating Wind (UNAFLOW) project and a follow-on experimental campaign, both performed at the Politecnico di Milano wind tunnel. Validation of the models was performed by comparing the loads for steady (fixed platform) and unsteady (harmonic motion of the platform) wind conditions. For the unsteady wind conditions, the platform was forced to oscillate in the surge and pitch directions under several frequencies and amplitudes. These oscillations result in a wind variation that impacts the rotor loads (e.g., thrust and torque). For the conditions studied in these tests, the system aerodynamic response was almost steady. Only a small hysteresis in airfoil performance undergoing angle of attack variations in attached flow was observed. During the experiments, the rotor speed and blade pitch angle were held constant. However, in real wind turbine operating conditions, the surge and pitch variations would result in rotor speed variations and/or blade pitch actuations, depending on the wind turbine controller region that the system is operating. Additional simulations with these control parameters were conducted to verify the fidelity of different models. Participant results showed, in general, a good agreement with the experimental measurements and the need to account for dynamic inflow when there are changes in the flow conditions due to the rotor speed variations or blade pitch actuations in response to surge and pitch motion. Numerical models not accounting for dynamic inflow effects predicted rotor loads that were 9 % lower in amplitude during rotor speed variations and 18 % higher in amplitude during blade pitch actuations.

17 WIND ENERGY↗

DOE OSTI2019

TRANSIENT ANALYSES OF THE VERSATILE TEST REACTOR USING RELAP5-3D

The DOE Office of Nuclear Energy established the Versatile Test Reactor (VTR) program in February 2017 in response to reports outlining the need for a fast spectrum test reactor. In this framework, Idaho National Laboratory (INL), as the proposed hosting site for the VTR, is expanding its capabilities leveraging on its staff nuclear expertise on experiments design and reactors operation, codes development and assessment, advanced safety analyses. One of the key points of this strategy is to develop capabilities necessary to perform transient analyses in order to understand the plant behavior during upset conditions and appropriately quantify margins. In this context system thermal-hydraulic models of the VTR are being developed using the SAS4A/SASSYS-1 code developed at Argonne National Laboratory as well as the INL code RELAP5-3D. The former provides reference analyses whereas the latter could provide an independent assessment of the reference analyses if deemed necessary by the project. This paper focuses on the RELAP5-3D modeling, highlighting the different solutions adopted for correctly analyzing sodium fast reactor behavior. After showing the modeling activities, we present a set of reference transient analyses for protected and unprotected transients, highlighting the intrinsic safety characteristics of the VTR design.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2020

Efficient DNA sequence compression with neural networks

Abstract Background The increasing production of genomic data has led to an intensified need for models that can cope efficiently with the lossless compression of DNA sequences. Important applications include long-term storage and compression-based data analysis. In the literature, only a few recent articles propose the use of neural networks for DNA sequence compression. However, they fall short when compared with specific DNA compression tools, such as GeCo2. This limitation is due to the absence of models specifically designed for DNA sequences. In this work, we combine the power of neural networks with specific DNA models. For this purpose, we created GeCo3, a new genomic sequence compressor that uses neural networks for mixing multiple context and substitution-tolerant context models. Findings We benchmark GeCo3 as a reference-free DNA compressor in 5 datasets, including a balanced and comprehensive dataset of DNA sequences, the Y-chromosome and human mitogenome, 2 compilations of archaeal and virus genomes, 4 whole genomes, and 2 collections of FASTQ data of a human virome and ancient DNA. GeCo3 achieves a solid improvement in compression over the previous version (GeCo2) of $2.4\%$, $7.1\%$, $6.1\%$, $5.8\%$, and $6.0\%$, respectively. To test its performance as a reference-based DNA compressor, we benchmark GeCo3 in 4 datasets constituted by the pairwise compression of the chromosomes of the genomes of several primates. GeCo3 improves the compression in $12.4\%$, $11.7\%$, $10.8\%$, and $10.1\%$ over the state of the art. The cost of this compression improvement is some additional computational time (1.7–3 times slower than GeCo2). The RAM use is constant, and the tool scales efficiently, independently of the sequence size. Overall, these values outperform the state of the art. Conclusions GeCo3 is a genomic sequence compressor with a neural network mixing approach that provides additional gains over top specific genomic compressors. The proposed mixing method is portable, requiring only the probabilities of the models as inputs, providing easy adaptation to other data compressors or compression-based data analysis tools. GeCo3 is released under GPLv3 and is available for free download at https://github.com/cobilab/geco3.

Silva, Milton↗

DOE OSTI2017

Maxdose-SR and popdose-SR routine release atmospheric dose models used at SRS

MAXDOSE-SR and POPDOSE-SR are used to calculate dose to the offsite Reference Person and to the surrounding Savannah River Site (SRS) population respectively following routine releases of atmospheric radioactivity. These models are currently accessed through the Dose Model Version 2014 graphical user interface (GUI). MAXDOSE-SR and POPDOSE-SR are personal computer (PC) versions of MAXIGASP and POPGASP, which both resided on the SRS IBM Mainframe. These two codes follow U.S. Nuclear Regulatory Commission (USNRC) Regulatory Guides 1.109 and 1.111 (1977a, 1977b). The basis for MAXDOSE-SR and POPDOSE-SR are USNRC developed codes XOQDOQ (Sagendorf et. al 1982) and GASPAR (Eckerman et. al 1980). Both of these codes have previously been verified for use at SRS (Simpkins 1999 and 2000). The revisions incorporated into MAXDOSE-SR and POPDOSE-SR Version 2014 (hereafter referred to as MAXDOSE-SR and POPDOSE-SR unless otherwise noted) were made per Computer Program Modification Tracker (CPMT) number Q-CMT-A-00016 (Appendix D). Version 2014 was verified for use at SRS in Dixon (2014).

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2019

GridAPPS-D™ a distribution management platform to develop applications for rural electric utilities

Rural electric utilities, many of which operate with a co-op management approach, have unique operational challenges not shared with their municipal or IOU counterparts. Rural electric utilities typically have fewer customers per feeder mile, and are generally less able to afford the costs, or provide robust support for today’s Advanced Distribution Management System (ADMS) offerings. Additionally, co-ops typically do not need the full suite of ADMS offerings but would benefit from a subset of applications such as OMS, Unbalanced Power-Flow, Volt-VAR optimization and FLISR (Fault Location Isolation and Service Restoration). Their needs, even within these applications, are simpler and more standardized. Lastly, due to their size, their IT capabilities and resources are commonly limited; hence hardware and software needs to be standards-based and easy to maintain with only most expansions of current capabilities. GridAPPS-D™ is an open-source, application development environment that’s part of the Department of Energy’s Grid Modernization Efforts, being led by the Pacific Northwest National Laboratory. The GridAPPS-D project is developing a reference architecture and implementation with the goal of reducing the time and cost to integrate distribution applications for both planning and operations through the use of standardized interfaces and data models. In this paper, we present a view of the reference architecture for GridAPPS-D and highlight its applicability to the rural electric utilities’ needs, including descriptions of applications being developed using this platform, and how they can be applied to other rural electric utilities.

distribution management, GridAPPS-D, rural electri↗

DOE OSTI2017

Synthetic Proxy Infrastructure for Task Evaluation

The Synthetic Proxy Infrastructure for Task Evaluation is a proxy application designed to support application developers in gauging the performance of various task granularities when determining how best to utilize task based programming models.The infrastructure is designed to provide examples of common communication patterns with a synthetic workload intended to provide performance data to evaluate programming model and platform overheads for the purpose of determining task granularity for task decomposition purposes. This is presented as a reference implementation of a proxy application with run-time configurable input and output task dependencies ranging from an embarrassingly parallel scenario to patterns with stencil-like dependencies upon their nearest neighbors. Once all, if any, inputs are satisfied each task will execute a synthetic workload (a simple DGEMM of in this case) of varying size and output all, if any, outputs to the next tasks.The intent is for this reference implementation to be implemented as a proxy app in different programming models so as to provide the same infrastructure and to allow for application developers to simulate their own communication needs to assist in task decomposition under various models on a given platform.

Junghans, Christoph↗

DOE OSTI2024

Metabolic Costs of Walking with Weighted Vests

ABSTRACT Introduction The US Army Load Carriage Decision Aid (LCDA) metabolic model is used by militaries across the globe and is intended to predict physiological responses, specifically metabolic costs, in a wide range of dismounted warfighter operations. However, the LCDA has yet to be adapted for vest-borne load carriage, which is commonplace in tactical populations, and differs in energetic costs to backpacking and other forms of load carriage. Purpose The purpose of this study is to develop and validate a metabolic model term that accurately estimates the effect of weighted vest loads on standing and walking metabolic rate for military mission-planning and general applications. Methods Twenty healthy, physically active military-age adults (4 women, 16 men; age, 26 ± 8 yr old; height, 1.74 ± 0.09 m; body mass, 81 ± 16 kg) walked for 6 to 21 min with four levels of weighted vest loading (0 to 66% body mass) at up to 11 treadmill speeds (0.45 to 1.97 m·s −1 ). Using indirect calorimetry measurements, we derived a new model term for estimating metabolic rate when carrying vest-borne loads. Model estimates were evaluated internally byk-fold cross-validation and externally against 12 reference datasets (264 total participants). We tested if the 90% confidence interval of the mean paired difference was within equivalence limits equal to 10% of the measured walking metabolic rate. Estimation accuracy, precision, and level of agreement were also evaluated by the bias, standard deviation of paired differences, and concordance correlation coefficient (CCC), respectively. Results Metabolic rate estimates using the new weighted vest term were statistically equivalent (P< 0.01) to measured values in the current study (bias, −0.01 ± 0.54 W·kg −1 ; CCC, 0.973) as well as from the 12 reference datasets (bias, −0.16 ± 0.59 W·kg −1 ; CCC, 0.963). Conclusions The updated LCDA metabolic model calculates accurate predictions of metabolic rate when carrying heavy backpack and vest-borne loads. Tactical populations and recreational athletes that train with weighted vests can confidently use the simplified LCDA metabolic calculator provided as Supplemental Digital Content to estimate metabolic rates for work/rest guidance, training periodization, and nutritional interventions.

Sport Sciences↗

DOE OSTI2017

Synthetic Proxy Infrastructure for Task Evaluation

Junghans, Christoph↗

DOE OSTI2025

PV Reference Cells for Outdoor Use: Stability Over Four Years of Deployment

Photovoltaic (PV) reference cells are frequently used to evaluate the performance of PV power plants. They provide a measure of irradiance that strongly correlates with the electrical output of PV modules, which makes them very useful for detecting short-term anomalies or long-term degradation in PV power plant output. One very important quality is long-term stability. This report presents observations about the stability of a set of 22 commercial reference cells that have been in continuous operation for a period of four years at the Solar Radiation Research Laboratory (SRRL) site at the National Renewable Energy Laboratory (NREL). The 22 reference cells at the SRRL represent 10 different models from 6 manufacturers.

14 SOLAR ENERGY↗