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DOE OSTI2020

Area-Preserving Mapping of 3D Carotid Ultrasound Images Using Density-Equalizing Reference Map

Carotid atherosclerosis is a focal disease at the bifurcations of the carotid artery. To quantitatively monitor the local changes in the vessel-wall-plus-plaque thickness (VWT) and compare the VWT distributions for different patients or for the same patients at different ultrasound scanning sessions, a mapping technique is required to adjust for the geometric variability of different carotid artery models. In this work, we propose a novel method called density-equalizing reference map (DERM) for mapping 3D carotid surfaces to a standardized 2D carotid template, with an emphasis on preserving the local geometry of the carotid surface by minimizing the local area distortion. The initial map was generated by a previously described arc-length scaling (ALS) mapping method, which projects a 3D carotid surface onto a 2D non-convex L-shaped domain. A smooth and area-preserving flattened map was subsequently constructed by deforming the ALS map using the proposed algorithm that combines the density-equalizing map and the reference map techniques. This combination allows, for the first time, one-to-one mapping from a 3D surface to a standardized non-convex planar domain in an area-preserving manner. Evaluations using 20 carotid surface models show that the proposed method reduced the area distortion of the flattening maps by over 80% as compared to the ALS mapping method.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

FEDERATED LEARNING ON STOCHASTIC NEURAL NETWORKS

Federated learning is a machine learning paradigm that leverages edge computing on client devices to optimize models while maintaining user privacy by ensuring that local data remain on the device. However, since all data are collected by clients, federated learning is susceptible to latent noise in local datasets. Factors such as limited measurement capabilities or human errors may introduce inaccuracies in client data. To address this challenge, we propose the use of a stochastic neural network as the local model within the federated learning framework. Stochastic neural networks not only facilitate the estimation of the true underlying states of the data but also enable the quantification of latent noise. We refer to our federated learning approach, which incorporates stochastic neural networks as local models, as federated stochastic neural networks. In this work we will present numerical experiments demonstrating the performance and effectiveness of our method, particularly in handling nonindependent and identically distributed data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Evaluating the Effectiveness of Retrieval-Augmented Large Language Models in Scientific Document Reasoning

Despite the dramatic progress in Large Language Model (LLM) development, LLMs often provide seemingly plausible but not factual information, often referred as hallucinations. Retrieval-augmented LLMs provide a non-parametric approach to solve these issues by retrieving relevant information from external data sources and augment the training process. These models helps to trace evidence from an externally provided knowledge base allowing the model predictions to be better interpreted and verified. In this work, we critically evaluate these models in their ability to perform in scientific document reasoning tasks. To this end, we tuned multiple such model variants with science-focused instructions and evaluated them on a scientific document reasoning benchmark for the usefulness of the retrieved document passages. Our findings suggest that models justify predictions in science tasks with fabricated evidence and leveraging scientific corpus as pretraining data does not alleviate the risk of evidence fabrication.

• Artificial intelligence (AI) / machine learning ↗

DOE OSTI2024

CMIP6-based Multi-model Streamflow Projections over the Conterminous US, Version 1.1

This dataset presents an ensemble of streamflow projections covering the conterminous United States (CONUS), developed to support the SECURE Water Act Section 9505 Assessment for the US Department of Energy (DOE) Water Power Technologies Office (WPTO). Multiple Coupled Models Intercomparison Project phase 6 (CMIP6) Global Climate Models (GCMs) were downscaled using either statistical (DBCCA) or dynamical (RegCM) downscaling methods, based on two meteorological reference datasets (Daymet and Livneh). Subsequently, the downscaled precipitation, temperature, and wind speed data were used to drive two calibrated hydrologic models (VIC and PRMS), with total runoff routed through the Routing Application for Parallel computatIon of Discharge (RAPID) routing model, producing an ensemble of streamflow projections across 2.7 million NHDPlusV2 stream reaches across the CONUS. Each ensemble member covers the 1980-2019 baseline and 2020-2059 near-future periods under the high-end (SSP585) emission scenario. Additionally, using only DBCCA and Daymet, the projections extend to the 2060-2099 far-future period and encompass three additional emission scenarios (SSP370, SSP245, and SSP126). This dataset is designed to support the SECURE Water Act Section 9505 Assessment for the US Department of Energy (DOE) Water Power Technologies Office (WPTO). For further details, refer to Kao et al. (2022), Rastogi et al. (2022), and Ghimire et al. (2023).

13 HYDRO ENERGY↗

DOE OSTI2016

The three-dimensional modeling of plasma edge transport and divertor fluxes during application of resonant magnetic perturbations on ITER

Results from three-dimensional modeling of plasma edge transport and plasma–wall interactions during application of resonant magnetic perturbation (RMP) fields for control of edge-localized modes in the ITER standard 15 MA Q = 10 H-mode are presented. The full 3D plasma fluid and kinetic neutral transport code EMC3-EIRENE is used for the modeling. Four characteristic perturbed magnetic topologies are considered and discussed with reference to the axisymmetric case without RMP fields. Two perturbation field amplitudes at full and half of the ITER ELM control coil current capability using the vacuum approximation are compared to a case including a strongly screening plasma response. In addition, a vacuum field case at high q95 = 4.2 featuring increased magnetic shear has been modeled. Formation of a three-dimensional plasma boundary is seen for all four perturbed magnetic topologies. The resonant field amplitudes and the effective radial magnetic field at the separatrix define the shape and extension of the 3D plasma boundary. Opening of the magnetic field lines from inside the separatrix establishes scrape-off layer-like channels of direct parallel particle and heat flux towards the divertor yielding a reduction of the main plasma thermal and particle confinement. This impact on confinement is most accentuated at full RMP current and is strongly reduced when screened RMP fields are considered, as well as for the reduced coil current cases. The divertor fluxes are redirected into a three-dimensional pattern of helical magnetic footprints on the divertor target tiles. At maximum perturbation strength, these fingers stretch out as far as 60 cm across the divertor targets, yielding heat flux spreading and the reduction of peak heat fluxes by 30%. However, at the same time substantial and highly localized heat fluxes reach divertor areas well outside of the axisymmetric heat flux decay profile. Reduced RMP amplitudes due to screening or reduced RMP coil current yield a reduction of the width of the divertor flux spreading to about 20–25 cm and cause increased peak heat fluxes back to values similar to those in the axisymmetric case. The dependencies of these features on the divertor recycling regime and the perpendicular transport assumptions, as well as toroidal averaged effects mimicking rotation of the RMP field, are discussed in the paper.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Fast charging of Li-ion cells: Effect of separator membranes and mapping of “safe lines” to avoid Li plating

An experimental method is introduced that uses microprobe Li/Cu reference electrodes to map "safe" charging regimes to avoid Li metal plating on graphite anodes at rates to 8C. With this method, a Li-ion cell closely approaches the Li plating condition but avoids descending into this regime. This "safe" approach is used to demonstrate effects of the microporous separator on Li plating in cells consisting of a layered nickel-manganese -cobalt oxide cathode and graphite anode. We argue that most of the difference in behaviors for different separators arises from time delayed Li + ion percolation through the membrane. In conclusion, our study suggests that explicitly treating kinetics of phase transitions in the lithiated graphite anode is essential for electrochemical models predicting "safe" lines for fast charging cells.

25 ENERGY STORAGE↗

DOE OSTI2018

Shell-model coupled-cluster method for open-shell nuclei

An approach to derive effective shell-model interactions from microscopic nuclear forces is introduced here. The similarity transformed coupled-cluster Hamiltonian decouples the single-reference state of a closed-shell nucleus and provides us with a core for the shell model. We use a second similarity transformation to decouple a shell-model space from the excluded space. We show that the three-body terms induced by both similarity transformations are crucial for an accurate computation of ground and excited states. As a proof of principle we use a nucleon-nucleon interaction from chiral effective field theory, employ a 4 He core, and compute low-lying states of 6–8 He and 6–8 Li in p -shell model spaces. Our conclusions agree with benchmarks from full configuration interaction.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2014

OpenSHMEM Reference Implementation using UCCS-uGNI Transport Layer. In: PGAS '14 Proceedings of the 8th International Conference on Partitioned Global Address Space Programming Models, Article No. 18

OpenSHMEM is a library interface implementation and specification that enables the implementation of the Partitioned Global Address Space (PGAS) model. It exports modern RDMA network functionality and communication semantics to applications very efficiently. There are many closed source implementations of OpenSHMEM for modern RDMA interconnects such as InfiniBand and Cray's Gemini and Aries. Given the important role that Cray systems play in HPC, in this paper, we present an open source implementation of OpenSHMEM for Cray XE/XK/XC systems. To implement OpenSHMEM, we use the uGNI interface. uGNI is a generic interface that is designed for multiple programming models. The interface fits well the goal of UCCS. Having OpenSHMEM with UCCS-uGNI allows usage of the same implementation over multiple interconnects. This also translates into many advantages that come with common code such as resource sharing, increasing productivity because of less code maintenance, etc. Preliminary results show that OpenSHMEM-UCCS performs comparable to state-of-the-art Cray SHMEM for Put, Get, and AMO operations.

Janjusic, Tomislav↗

DOE OSTI2015

Modeling to Support the Development of Habitat Targets for Piping Plovers on the Missouri River

This report describes analyses done in support of the establishment of quantitative targets for piping plovers on the Missouri River using predictive numerical models for emergent sandbar habitat and piping plovers developed for the Missouri River Effects Analysis. Several approaches were considered and modeled: current operations of the reservoirs to serve as a reference (Existing Conditions), an unregulated hydrograph to simulate historical conditions (Unregulated), a scenario where dams were present but not operated (No-Operations), and a scenario where the amount of habitat necessary to provide a desired level of population viability (5% risk of extinction in 50 years) was constructed (Calibrated Target). These scenarios were compared in terms of the distribution of standardized habitat produced, the proportion of time available habitat exceeded a given acreage, and the risk of quasi-extinction for plover populations. Sensitivity analyses were also conducted to demonstrate the effects of initial population size and target habitat acreage on extinction risk and the effects of viability criteria on habitat targets. Limitations and uncertainties in the modeling, including caveats on the use of these models to estimate historical conditions and the availability of information to build a metapopulation model are discussed. The challenges inherent in setting population targets and a possible alternative approach to assessing management alternatives in terms of population effects are also included.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Exploring the nexus of many-body theories through neural network techniques: the tangent model

Abstract In this paper, we present a physically informed neural network (NN) representation of the effective interactions associated with coupled-cluster downfolding models to describe chemical systems and processes. The NN representation not only allows us to evaluate the effective interactions efficiently for various geometrical configurations of chemical systems corresponding to various levels of complexity of the underlying wave functions, but also reveals that the bare and effective interactions are related by a tangent function of some latent variables. We refer to this characterization of the effective interaction as a tangent model. We discuss the connection between this tangent model for the effective interaction with the previously developed theoretical analysis that examines the difference between the bare and effective Hamiltonians in the corresponding active spaces.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Camelina sativa , an oilseed at the nexus between model system and commercial crop

The rapid assessment of metabolic engineering strategies in plants is aided by crops that provide simple, high throughput transformation systems, a sequenced genome, and the ability to evaluate the resulting plants in field trials. Camelina sativa provides all of these attributes in a robust oilseed platform. The ability to perform field evaluation of Camelina is a useful, and in some studies essential benefit that allows researchers to evaluate how traits perform outside the strictly controlled conditions of a greenhouse. In the field the plants are subjected to higher light intensities, seasonal diurnal variations in temperature and light, competition for nutrients, and watering regimes dictated by natural weather patterns, all which may affect trait performance. There are difficulties associated with the use of Camelina . The current genetic resources available for Camelina pale in comparison to those developed for the model plant Arabidopsis thaliana; however, the sequence similarity of the Arabidopsis and Camelina genomes often allows the use of Arabidopsis as a reference when additional information is needed. Camelina ’s genome, an allohexaploid, is more complex than other model crops, but the diploid inheritance of its three subgenomes is straightforward. The need to navigate three copies of each gene in genome editing or mutagenesis experiments adds some complexity but also provides advantages for gene dosage experiments. In conclusion, the ability to quickly engineer Camelina with novel traits, advance generations, and bulk up homozygous lines for small-scale field tests in less than a year, in our opinion, far outweighs the complexities associated with the crop.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

End-Use Savings Shapes Upgrade Package Documentation: Wall and Roof Insulation and New Windows

Building on the successfully completed effort to calibrate and validate the U.S. Department of Energy's ResStock and ComStock models over the past 3 years, the objective of this work is to produce national data sets that empower analysts working for federal, state, utility, city, and manufacturer stakeholders to answer a broad range of analysis questions. The goal of this work is to develop energy efficiency, electrification, and demand flexibility end-use load shapes (electricity, gas, propane, or fuel oil) that cover a majority of the high-impact, market-ready (or nearly market-ready) upgrade measures, or upgrades. "Measures" refers to energy efficiency variables that can be applied to buildings during modeling. An end-use savings shape is the difference in energy consumption between a baseline building and a building with an energy efficiency, electrification, or demand flexibility upgrade applied. It results in a time-series profile that is broken down by end use and fuel (electricity or on-site gas, propane, or fuel oil use) at each time step. ComStock is a highly granular, bottom-up model that uses multiple data sources, statistical sampling methods, and advanced building energy simulations to estimate the annual subhourly energy consumption of the commercial building stock across the United States. The baseline model intends to represent the U.S. commercial building stock as it existed in 2018. The methodology and results of the baseline model are discussed in the final technical report of the End-Use Load Profiles project. This documentation focuses on an upgrade package of three end-use savings shapes upgrades - Window Replacement, Exterior Wall Insulation, and Roof Insulation, which we will refer to collectively as the "High Efficiency Envelope" package. More details on the individual upgrades can be found on the ComStock Measures Documentation page. An upgrade package applies two or more EUSS upgrades to a single building model simulation. Since ComStock is a bottom-up physics-based model, an upgrade package will go beyond aggregating or summing the individual upgrade results and produce novel results by simulating interactions between the upgrades. For example, pairing an envelope upgrade with an electrification upgrade would likely result in higher savings results than the sum of these upgrades individually, and the size of the heating, ventilating, and air conditioning (HVAC) equipment may be reduced if the envelope upgrade reduces the loads significantly.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2016

Technical Report: Reference photon dosimetry data for Varian accelerators based on IROC-Houston site visit data

Purpose: Accurate data regarding linear accelerator (Linac) radiation characteristics are important for treatment planning system modeling as well as regular quality assurance of the machine. The Imaging and Radiation Oncology Core-Houston (IROC-H) has measured the dosimetric characteristics of numerous machines through their on-site dosimetry review protocols. Photon data are presented and can be used as a secondary check of acquired values, as a means to verify commissioning a new machine, or in preparation for an IROC-H site visit. Methods: Photon data from IROC-H on-site reviews from 2000 to 2014 were compiled and analyzed. Specifically, data from approximately 500 Varian machines were analyzed. Each dataset consisted of point measurements of several dosimetric parameters at various locations in a water phantom to assess the percentage depth dose, jaw output factors, multileaf collimator small field output factors, off-axis factors, and wedge factors. The data were analyzed by energy and parameter, with similarly performing machine models being assimilated into classes. Common statistical metrics are presented for each machine class. Measurement data were compared against other reference data where applicable. Results: Distributions of the parameter data were shown to be robust and derive from a student’s t distribution. Based on statistical and clinical criteria, all machine models were able to be classified into two or three classes for each energy, except for 6 MV for which there were eight classes. Quantitative analysis of the measurements for 6, 10, 15, and 18 MV photon beams is presented for each parameter; supplementary material has also been made available which contains further statistical information. Conclusions: IROC-H has collected numerous data on Varian Linacs and the results of photon measurements from the past 15 years are presented. The data can be used as a comparison check of a physicist’s acquired values. Acquired values that are well outside the expected distribution should be verified by the physicist to identify whether the measurements are valid. Comparison of values to this reference data provides a redundant check to help prevent gross dosimetric treatment errors.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

'Constraint consistency' at all orders in cosmological perturbation theory

We study the equivalence of two—order-by-order Einstein's equation and Reduced action—approaches to cosmological perturbation theory at all orders for different models of inflation. We point out a crucial consistency check which we refer to as 'Constraint consistency' condition that needs to be satisfied in order for the two approaches to lead to identical single variable equation of motion. The method we propose here is quick and efficient to check the consistency for any model including modified gravity models. Our analysis points out an important feature which is crucial for inflationary model building i.e., all 'constraint' inconsistent models have higher order Ostrogradsky's instabilities but the reverse is not true. In other words, one can have models with constraint Lapse function and Shift vector, though it may have Ostrogradsky's instabilities. We also obtain single variable equation for non-canonical scalar field in the limit of power-law inflation for the second-order perturbed variables.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2013

Moving Away from the Reference Genome: Evaluating a Peptide Sequencing Tagging Approach for Single Amino Acid Polymorphism Identifications in the Genus Populus

The genetic diversity across natural populations of the model organism, Populus, is extensive, containing a single nucleotide polymorphism roughly every 200 base pairs. When deviations from the reference genome occur in coding regions, they can impact protein sequences. Rather than relying on a static reference database to profile protein expression, we employed a peptide sequence tagging (PST) approach capable of decoding the plasticity of the Populus proteome. Using shotgun proteomics data from two genotypes of P. trichocarpa, a tag-based approach enabled the detection of 6,653 unexpected sequence variants. Through manual validation, our study investigated how the most abundant chemical modification (methionine oxidation) could masquerade as a sequence variant (AlaSer) when few site-determining ions existed. In fact, precise localization of an oxidation site for peptides with more than one potential placement was indeterminate for 70% of the MS/MS spectra. We demonstrate that additional fragment ions made available by high energy collisional dissociation enhances the robustness of the peptide sequence tagging approach (81% of oxidation events could be exclusively localized to a methionine). We are confident that augmenting fragmentation processes for a PST approach will further improve the identification of single amino acid polymorphism in Populus and potentially other species as well.

High energy collisional dissociation↗

DOE OSTI2015

Overview of the Biomass Scenario Model

This report describes the structure of the October 2012 version of the Biomass Scenario Model (BSM) in considerable detail, oriented towards readers with a background or interest in the underlying modeling structures. Readers seeking a less-detailed summary of the BSM may refer to Peterson (2013). BSM aims to provide a framework for exploring the potential contribution of biofuel technologies to the transportation energy supply for the United States over the next several decades. The model has evolved significantly from the prototype developed as part of the Role of Biomass in America" tm s Energy Future (RBAEF) project. BSM represents the supply chain surrounding conversion pathways for multiple fuel products, including ethanol, butanol, and infrastructure-compatible biofuels such as diesel, jet fuel, and gasoline.

09 BIOMASS FUELS↗

DOE OSTI2022

MELCOR Accident Progression and Source Term Demonstration Calculations for a FHR

MELCOR is an integrated thermal hydraulics, accident progression, and source term code for reactor safety analysis that has been developed at Sandia National Laboratories for the United States Nuclear Regulatory Commission (NRC) since the early 1980s. Though MELCOR originated as a light water reactor (LWR) code, development and modernization efforts have expanded its application scope to include non-LWR reactor concepts. Current MELCOR development efforts include providing the NRC with the analytical capabilities to support regulatory readiness for licensing non-LWR technologies under Strategy 2 of the NRC's near- term Implementation Action Plans. Beginning with the Next Generation Nuclear Project (NGNP), MELCOR has undergone a range of enhancements to provide analytical capabilities for modeling the spectrum of advanced non-LWR concepts. This report describes the generic plant model developed to demonstrate MELCOR capabilities to perform fluoride-salt-cooled high-temperature reactor (FHR) safety evaluations. The generic plant model is based on publicly-available FHR design information. For plant aspects (e.g., reactor building leak rate and details of the cover-gas system) that are not described in the FHR references, the analysts made assumptions needed to construct a MELCOR full-plant model. The FHR model uses a TRi-structural ISOtropic (TRISO)-particle fuel pebble-bed reactor with a primary system rejecting heat to two coiled tube air heat ex changers. Three passive direct reactor auxiliary cooling systems provide heat removal to supplement or replace the emergency secondary system heat removal during accident conditions. Surrounding the reactor vessel is a low volume reactor cavity that insulates the reactor with fire bricks and thick concrete walls. A refractory reactor liner system provides water cooling to reduce the concrete wall temperatures. Example calculations are performed to show the plant response and MELCOR capabilities to characterize a range of accident conditions. The accidents selected for evaluation consider a range of degraded and failed modes of operation for key safety functions providing reactivity control, the primary system decay heat removal and also a piping leak of the line to the coolant drain tank.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2017

Three-Dimensional Modeling of Fracture Clusters in Geothermal Reservoirs

The objective of this is to develop a 3-D numerical model for simulating mode I, II, and III (tensile, shear, and out-of-plane) propagation of multiple fractures and fracture clusters to accurately predict geothermal reservoir stimulation using the virtual multi-dimensional internal bond (VMIB). Effective development of enhanced geothermal systems can significantly benefit from improved modeling of hydraulic fracturing. In geothermal reservoirs, where the temperature can reach or exceed 350oC, thermal and poro-mechanical processes play an important role in fracture initiation and propagation. In this project hydraulic fracturing of hot subsurface rock mass will be numerically modeled by extending the virtual multiple internal bond theory and implementing it in a finite element code, WARP3D, a three-dimensional finite element code for solid mechanics. The new constitutive model along with the poro-thermoelastic computational algorithms will allow modeling the initiation and propagation of clusters of fractures, and extension of pre-existing fractures. The work will enable the industry to realistically model stimulation of geothermal reservoirs. The project addresses the Geothermal Technologies Office objective of accurately predicting geothermal reservoir stimulation (GTO technology priority item). The project goal will be attained by: (i) development of the VMIB method for application to 3D analysis of fracture clusters; (ii) development of poro- and thermoelastic material sub-routines for use in 3D finite element code WARP3D; (iii) implementation of VMIB and the new material routines in WARP3D to enable simulation of clusters of fractures while accounting for the effects of the pore pressure, thermal stress and inelastic deformation; (iv) simulation of 3D fracture propagation and coalescence and formation of clusters, and comparison with laboratory compression tests; and (v) application of the model to interpretation of injection experiments (planned by our industrial partner) with reference to the impact of the variations in injection rate and temperature, rock properties, and in-situ stress.

15 GEOTHERMAL ENERGY↗