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DOE OSTI2020

Software Requirements for a Consequence Management Sample Data Simulator for Training and Drills

This document describes the requirements for a software tool that will enable FRMAC to simulate large sets of sample result data that is based realistically on simulated radionuclide deposition grids from NARAC. The user of this tool would be scientists involved in exercise and drill planning or part of the simulation cell of an exercise controller team. A key requirement is that this tool must be able to be run with a reasonable amount of training and job aids by any person within the Assessment, Laboratory Analysis, or Monitoring and Sampling divisions of the FRMAC to support any level of exercise from the small IPX to the national level full scale exercise. This tool should be relatively lean and stand-alone so that the user can run it in the field with limited IT resources. This document will describe the desired architecture, design characteristics, order of operations, and algorithms that can be given to a software development team to assist them in project scoping, costing, and eventually, development.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2020

NuSTAR Survey of Obscured Swift/BAT-selected Active Galactic Nuclei. II. Median High-energy Cutoff in Seyfert II Hard X-Ray Spectra

Broadband X-ray spectroscopy of the X-ray emission produced in the coronae of active galactic nuclei (AGNs) can provide important insights into the physical conditions very close to their central supermassive black holes. The temperature of the Comptonizing plasma that forms the corona is manifested through a high-energy cutoff that has been difficult to directly constrain even in the brightest AGN because it requires high-quality data at energies above 10 keV. In this paper we present a large collection of coronal cutoff constraints for obscured AGNs based on a sample of 130 AGNs selected in the hard X-ray band with Swift/BAT and observed nearly simultaneously with NuSTAR and Swift/XRT. Additionally, we find that under a reasonable set of assumptions regarding partial constraints the median cutoff is well constrained to 290 ± 20 keV, where the uncertainty is statistical and given at the 68% confidence level. We investigate the sensitivity of this result to our assumptions and find that consideration of various known systematic uncertainties robustly places the median cutoff between 240 and 340 keV. The central 68% of the intrinsic cutoff distribution is found to be between about 140 and 500 keV, with estimated uncertainties of 20 and 100 keV, respectively. In comparison with the literature, we find no clear evidence that the cutoffs in obscured and unobscured AGNs are substantially different. Our analysis highlights the importance of carefully considering partial and potentially degenerate constraints on the coronal high-energy cutoff in AGNs.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Analytical estimation of the signal to noise ratio efficiency in axion dark matter searches using a Savitzky-Golay filter

The signal to noise ratio efficiency ϵ SNR in axion dark matter searches has been estimated using large-statistic simulation data reflecting the background information and the expected axion signal power obtained from a real experiment. This usually requires a lot of computing time even with the assistance of powerful computing resources. Employing a Savitzky-Golay filter for background subtraction, in this work, we estimated a fully analytical ϵ SNR without relying on large-statistic simulation data, but only with an arbitrary axion mass and the relevant signal shape information. Hence, our work can provide ϵ SNR using minimal computing time and resources prior to the acquisition of experimental data, without the detailed information that has to be obtained from real experiments. Axion haloscope searches have been observing the coincidence that the frequency independent scale factor ξ is approximately consistent with the ϵ SNR . This was confirmed analytically in this work, when the window length of the Savitzky-Golay filter is reasonably wide enough, i.e., at least 5 times the signal window.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2019

High entropy alloys: A focused review of mechanical properties and deformation mechanisms

The high-entropy alloy (HEA) concept was based on the idea that high mixing entropy can promote formation of stable single-phase microstructures. During the past 15 years, various alloy systems have been explored to identify HEA systems with improved property combinations, leading to an extraordinary growth of this field. In the large pool of alloys with varying characteristics, the first single-phase HEA with good tensile properties, the equiatomic CrMnFeCoNi alloy has become the benchmark material, and it forms the basis of much of our current fundamental understanding of HEA mechanical behavior. As the field is evolving to the more broadly defined complex concentrated alloys (CCAs) and the available data in the literature increase exponentially, a fundamental question remains unchanged: how special are these new materials? In the first part of this review, select mechanical properties of HEAs and CCAs are compared with those of conventional engineering alloys. This task is difficult because of the limited tensile data available for HEAs and CCAs. Additionally, the wider suite of mechanical properties needed to assess structural materials is woefully lacking. Nonetheless, our evaluations have not revealed many HEAs or CCAs with properties far exceeding those of conventional engineering alloys, although specific alloys can show notable enhancements in specific properties. Consequently, it is reasonable to first approach the understanding of HEAs and CCAs through the assessment of how the well-established deformation mechanisms in conventional alloys operate or are modified in the presence of the high local complexity of the HEAs and CCAs. The second part of the paper provides a detailed review of the deformation mechanisms of HEAs with the FCC and BCC structures. For the former, we chose the CrMnFeCoNi (Cantor) alloy because it is the alloy on which the most rigorous and thorough investigations have been performed and, for the latter, we chose the TiZrHfNbTa (Senkov) alloy because this is one of the few refractory HEAs that exhibits any tensile ductility at room temperature. As expected, our review shows that the fundamental deformation mechanisms in these systems, and their dependence on basic physical properties, are broadly similar to those of conventional FCC and BCC metals. The third part of this review examines the theoretical and modeling efforts to date that seek to provide either qualitative or quantitative understanding of the mechanical performance of FCC and BCC HEAs. Since experiments reveal no fundamentally new mechanisms of deformation, this section starts with an overview of modeling perspectives and fundamental considerations. Next, the review turns to the evolution of modeling and predictions as compared to recent experiments, highlighting both successes and limitations. Finally, in spite of some significant successes, important directions for further theory development are discussed. Overall, while the individual deformation mechanisms or properties of the HEAs and CCAs are not, by and large, “special” relative to conventional alloys, the present HEA rush remains valuable because the compositional freedom that comes from the multi-element space will allow exploration of whether multiple mechanisms can operate sequentially or simultaneously, which may yet lead to the creation of new alloys with a spectrum of mechanical properties that are significantly superior to those of current engineering alloys.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Effects of spatial energy distribution-induced porosity on mechanical properties of laser powder bed fusion 316L stainless steel

Laser powder bed fusion (LPBF) additive manufacturing (AM) offers a variety of advantages over traditional manufacturing, however its usefulness for manufacturing of high-performance components is currently hampered by internal defects (porosity) created during the LPBF process that have an unknown impact on global mechanical performance. By inducing porosity distributions through variations in print energy density and inspecting the resulting tensile samples using computed tomography, nearly 50,000 pores across 75 samples were identified. Porosity characteristics were quantitatively extracted from inspection data and compared with mechanical properties to understand the strength of relationships between porosity and global tensile performance. Useful porosity characteristics were identified for prediction of part performance. Results indicate that ductility and strain at ultimate tensile strength are the global tensile properties most significantly impacted by porosity and can be predicted with reasonable accuracy using simple porosity shape descriptors such as volume, diameter, and surface area. Moreover, it was found that the largest pores influenced behavior most significantly. Specifically, pores in excess of 125 µm in diameter were found to be a sufficient threshold for property estimation. These results establish an initial understanding of the complex defect-performance relationship in AM 316L stainless steel and can be leveraged to develop certification standards and improve confidence in part quality and reliability for the broader set of engineering alloys.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Automatic and rapid calibration of urban building energy models by learning from energy performance database

Urban building energy modeling (UBEM) is attracting increasing attention in the energy modeling filed. Unlike modeling a single building using detailed building systems information, UBEM generally uses limited high-level building stock data to infer default assumptions about building characteristics and operations. Additionally, this practice inherently brings uncertainty to UBEM. This study introduced a novel method of automatic and rapid calibration of UBEM based on the annual electricity and natural gas energy use data by learning the correlations between crucial model input parameters and the building energy use from the reference building models. A case study was presented to calibrate 72 large office buildings built before 1978 in San Francisco. Seventeen model parameters were selected and Monte Carlo sampling was used to create 1000 samples that reasonably represent the parameter space. Then 1000 simulations were performed for the reference building model to create an energy performance database. The results showed that by learning from the energy performance database, it took less than four simulation runs on average to calibrate a building model. After the calibration, the distributions of each parameter were obtained to replace their single predefined default values. For example, the default lighting power density of 21.39 W/m 2 was calibrated to be 7.50 W/m 2 on average. The case study successfully demonstrated the effectiveness of the novel calibration method for UBEM in the mild climate. The method will be further tested in future for other climate zones and other building types.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

NSFnets (Navier-Stokes flow nets): Physics-informed neural networks for the incompressible Navier-Stokes equations

In the last 50 years there has been a tremendous progress in solving numerically the Navier-Stokes equations using finite differences, finite elements, spectral, and even meshless methods. Yet, in many real cases, we still cannot incorporate seamlessly (multi-fidelity) data into existing algorithms, and for industrial-complexity applications the mesh generation is time consuming and still an art. Moreover, solving ill-posed problems (e.g., lacking boundary conditions) or inverse problems is often prohibitively expensive and requires different formulations and new computer codes. Here, we employ physics-informed neural networks (PINNs), encoding the governing equations directly into the deep neural network via automatic differentiation, to overcome some of the aforementioned limitations for simulating incompressible laminar and turbulent flows. We develop the Navier-Stokes flow nets (NSFnets) by considering two different mathematical formulations of the Navier-Stokes equations: the velocity-pressure (VP) formulation and the vorticity-velocity (VV) formulation. Since this is a new approach, we first select some standard benchmark problems to assess the accuracy, convergence rate, computational cost and flexibility of NSFnets; analytical solutions and direct numerical simulation (DNS) databases provide proper initial and boundary conditions for the NSFnet simulations. The spatial and temporal coordinates are the inputs of the NSFnets, while the instantaneous velocity and pressure fields are the outputs for the VP-NSFnet, and the instantaneous velocity and vorticity fields are the outputs for the VV-NSFnet. This is unsupervised learning and, hence, no labeled data are required beyond boundary and initial conditions and the fluid properties. The residuals of the VP or VV governing equations, together with the initial and boundary conditions, are embedded into the loss function of the NSFnets. No data is provided for the pressure to the VP-NSFnet, which is a hidden state and is obtained via the incompressibility constraint without extra computational cost. Unlike the traditional numerical methods, NSFnets inherit the properties of neural networks (NNs), hence the total error is composed of the approximation, the optimization, and the generalization errors. Here, we empirically attempt to quantify these errors by varying the sampling (“residual”) points, the iterative solvers, and the size of the NN architecture. For the laminar flow solutions, we show that both the VP and the VV formulations are comparable in accuracy but their best performance corresponds to different NN architectures. The initial convergence rate is fast but the error eventually saturates to a plateau due to the dominance of the optimization error. For the turbulent channel flow, we show that NSFnets can sustain turbulence at , but due to expensive training we only consider part of the channel domain and enforce velocity boundary conditions on the subdomain boundaries provided by the DNS data base. We also perform a systematic study on the weights used in the loss function for balancing the data and physics components, and investigate a new way of computing the weights dynamically to accelerate training and enhance accuracy. In the last part, we demonstrate how NSFnets should be used in practice, namely for ill-posed problems with incomplete or noisy boundary conditions as well as for inverse problems. We obtain reasonably accurate solutions for such cases as well without the need to change the NSFnets and at the same computational cost as in the forward well-posed problems. As a result, we also present a simple example of transfer learning that will aid in accelerating the training of NSFnets for different parameter settings.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Definition of fragmentation functions and the violation of sum rules

We point out a problem with the formulation and derivations of sum rules for quark fragmentation functions that impacts their validity in QCD, but which potentially points toward an improved understanding of final states in inclusive hard processes. Fragmentation functions give the distribution of final-state hadrons arising from a parton exiting a hard scattering, and the sum rules for momentum, electric charge, etc. express conservation of these quantities. The problem arises from a mismatch between the quark quantum numbers of the initial quark and the fact that all observed final-state hadrons are confined bound states with color zero. We point that, in a confining theory like QCD, the Wilson line in the operator definition of a fragmentation function entails that the final state in a fragmentation function includes a bound state in the external field generated by the Wilson line. We justify this with the aid of general features of string hadronization. The anomalous bound states are restricted to fractional momentum z = 0 . They tend to invalidate sum rules like the one for charge conservation when applied to the fragmentation functions inferred from experimental data but not the momentum sum rule. We propose to exploit our ideas in future studies as a way to relate the fragmentation functions extracted from inclusive cross sections to more detailed nonperturbative descriptions of final state hadronization. We also describe scenarios wherein the traditional sum rules might remain approximately valid with a reasonably high degree of accuracy. Published by the American Physical Society 2024

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

An Assessment of Homogeneous Mixture Method Cavitation Models in Predicting Cavitation in Nozzle Flow

The homogeneous mixture method (HMM) is a popular class of models used in the computational prediction of cavitation. Several cavitation models have been developed for use with HMM to govern the development and destruction of vapor in a fluid system. Two models credited to Kunz and Schnerr–Sauer are studied in this paper. The goal of this work is to provide an assessment of the two cavitation submodels in their ability to predict cavitation in nozzle flow. Validation data were obtained via experiments which employ both passive cavitation detection, (PCD) via acoustic sensing and optical cavitation detection (OCD) via camera imaging. The experiments provide quantitative information on cavitation inception and qualitative information on the vapor in the nozzle. The results show that initial vapor formation is not predicted precisely but within reason. A sensitivity analysis of the models to input parameters shows that the Schnerr–Sauer method does not depend upon the estimation of nuclei size and number density. Small changes in the vapor formation rate but not the total vapor volume can be seen when weighting parameters are modified. In contrast, changes to the input parameters for the Kunz model greatly change the final total vapor volume prediction. The assessment also highlights the influence of vapor convection within the method. Finally, the analysis shows that if the fluid and nozzle walls do not support nuclei larger than 40 μm, the methods would still predict cavitation when indeed there would be none in practice.

Engineering↗

DOE OSTI2020

Independent Review of Paducah Gaseous Diffusion Plant Freon Release Authorized Limits and Evaluation of Corresponding Radiological Doses

The Portsmouth/Paducah Project Office (PPPO) proposes to use the American National Standard Institute (ANSI)/Health Physics Society (HPS) N13.12 (ANSI 2013) volumetric screening levels as Authorized Limits (ALs) for the release of cryofluorane R-114 (Freon) at the Paducah Gaseous Diffusion Plant (PGDP) in Paducah, Kentucky. A review of the proposed ALs document indicated that potential exposure scenarios from the release of Freon are adequately discussed therein. However, questions arose regarding the assumptions made for the ANSI N13.12 clearance values, and whether or not all pathway doses were adequately considered in the Authorized Limits Request. For example, PPPO used the inverse square rule to estimate dose to the truck driver. A more appropriate evaluation would have considered the material as a cylindrical source for this pathway. In addition, the inverse square rule was inadequately applied to the inhalation and ingestion pathways. Furthermore, while the ANSI N13.12 volumetric clearance values are used in the ALs, questions arose concerning whether the values are appropriate for materials of greater than 1 metric ton, and whether or not the ANSI N13.12 standard could be used for liquids that are sent to an incinerator. For these reasons, dose modeling was conducted to demonstrate that using ANSI/HPS N13.12 screening levels as ALs for release of PGDP Freon meets the dose criteria set in U.S. Department of Energy (DOE) Order 458.1. This report provides a bounding dose analysis using scenarios described in PPPO document. Realistic parameters, such as the incinerator characteristics data, are used when available.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2022

High concentrations of ice: Investigations using polarimetric radar observations combined with in situ measurements and cloud modeling (Final Report)

This DOE-funded joint project had the over-arching goal of understanding the reasons for observed size distributions of ice particles in cold clouds. Its approach involves the use of cloud models and field observations by radar and aircraft of real storms. The project addresses three major research objectives: (1) Utilize a novel polarimetric radar technique to retrieve size distributions and amounts of ice from radar data collected during the previous DOE ARM field campaigns; (2) Evaluate the results of ice microphysical retrievals using available in situ aircraft measurements and other remote sensors (e.g., vertically pointing cloud radars and wind profilers); (3) Improve the treatment of microphysical processes leading to cloud glaciation and ice multiplication in numerical cloud models. The study was performed by three research organizations: University of Oklahoma, The Hebrew University of Jerusalem, Israel, and Lund University, Sweden. The Israel and Swedish partners were funded by the sub-awards from the University of Oklahoma. Cloud modeling studies have been performed by the research teams at The Hebrew University of Jerusalem (HUJ) and Lund University to identify the origins of high concentrations of cloud ice in areas of high ice water content (HIWC). The Hebrew University Cloud Model (HUCM) with full spectral bin microphysics and the Lund University aerosol-cloud (AC) model with a hybrid bin / bulk microphysics scheme complementing HUCM were utilized for simulations. Both research teams had particular focus on secondary ice production (SIP) as one of the possible sources of enhanced ice concentration. The HUJ group suggested a novel concept of ice multiplication during droplet freezing. It is assumed that splintering and droplet fragmentation during droplet freezing takes place because of dendritic growth within a supercooled drop. The resulting simulations of SIP generated small ice in concentrations exceeding hundreds per liter similar to what was observed in the HIWC regions of the tropical storms. The Lund team explored the SIP mechanisms such as breakup of ice particles due to ice-ice collisions and ice sublimation that are expected to dominate the continental storms. They also quantified the impact of homogeneous nucleation of cloud droplets on the total number concentration of ice at very low temperatures near the tops of the clouds. Additionally, the Lund AC model is able to simulate the effect of aerosols of various types (including biological) on the cloud life cycle and the corresponding ice production. The HUCM / AC model was used to simulate one of the “golden” cases of the DOE MC3E campaign on 20 May 2011. The model output was converted into the fields of polarimetric radar variables using the polarimetric radar forward operator developed at the University of Oklahoma and compared with radar observations and in situ microphysical measurements onboard research aircraft. It was demonstrated that specific differential phase KDP is the best radar parameter to identify the HIWC areas and quantify the corresponding ice parameters. For the first time, the shape of the vertical profile of KDP was realistically reproduced by the cloud model with the KDP maximum in the dendritic growth layer (DGL) centered at the -15°C isotherm. The University of Oklahoma team has developed a methodology for polarimetric radar retrievals of such microphysical parameters of ice as ice water content (IWC), mean volume diameter (Dm), and total number concentration (Nt) of ice particles. These retrievals have been validated using in situ aircraft measurements during 6 field campaigns and proved to be quite robust and reliable. This allowed to build the first climatology of the vertical profiles of polarimetric radar variables and retrieved microphysical parameters for the three types of weather systems: continental MCSs, maritime MCSs, and tropical cyclones / hurricanes (Hu and Ryzhkov 2022). The data were collected by a multitude of the WSR-88D radars in 13 continental and 10 maritime MCSs and 11 landfalling hurricanes. The HIWC areas were identified within the examined storms and the corresponding “HIWC statistics” was compared with the “background” one without HIWC. An overarching conclusion of the study is that maritime tropical storms (MCSs and hurricanes) are characterized by smaller size ice in higher concentration compared to the continental MCSs. High ice water content in the HIWC areas is primarily caused by a strong jump in a number concentration of ice particles rather than the increase of their size compared to the “background” environment. This may point to the homogeneous nucleation of excessive amounts of supercooled droplets and / or secondary ice production as the possible origins of HIWC. Such a climatology provides a good observational reference for the modelers to evaluate the performance of their models. As an example, the in-depth analysis of the 20 May 2011 MC3E case shows that the advanced cloud models developed in the course of this study still tend to underestimate the number concentration of ice in the HIWC areas although they succeed in reproducing realistically looking vertical profiles of IWC and Nt. The results of the project research are summarized in 13 journal papers.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Vibration Studies for the CLARA Interferometer

The purpose of the CLARA experiment is to study the nature of undulator radiation emitted by single electrons circulating in the IOTA storage ring. The classical and quantum properties of the radiation are investigated by measuring its coherence length, intensity fluctuations and time correlations. The experiment took data in IOTA Run 4 (2022-2023). The key component of the apparatus is a Mach-Zehnder interferometer (MZI), in which the optical length of one of the arms can be precisely controlled. For some measurements, the fine regulation of the arm length must be smaller than the radiation wavelength. For this reason, the apparatus is particularly sensitive to mechanical vibrations. In this note, we model and measure the effect of vibrations on the performance of the MZI under various conditions. Several improvements of the setup were implemented to minimize systematic distortions of the observed interference patterns. In this report, we present a mathematical model of the effect of mechanical vibrations on observed detector and coincidence rates. We also describe the measurements that were made to estimate the magnitude and spectra of rate fluctuations and their sources in the CLARA MZI under various conditions. Finally, we estimate the magnitude of arm length fluctuations and we deduce the sensitivity to coincidence-rate variations in our apparatus.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

Assessing Simulations of Forest Hurricane Disturbance and Recovery in Puerto Rico by ELM-FATES Using Field Measurements

In the past three decades, Puerto Rico (PR) experienced five hurricanes that met or exceeded category three, and they caused severe forest structural damage and elevated tree mortality. To improve our mechanistic understanding of hurricane impacts on tropical forests and assess hurricane-affected forest dynamics in Earth system models, we use in situ forest measurements at the Bisley Experimental Watersheds in Northeast PR to evaluate the Functionally Assembled Terrestrial Ecosystem Simulator coupled with the Energy Exascale Earth System Model Land Model (ELM-FATES). The observations show that before Hurricane Hugo, 77.3% of the aboveground biomass (AGB) is from the shade-tolerant plant function type (PFT). The Hugo-induced mortality rates are over ~50%, and they induce a ~39% AGB reduction, which recovers to a level like the pre-Hugo condition in 2014, following a second, lower intensity hurricane, Georges. We perform numerical experiments that simulate damage from Hugo and Georges on the forests, including defoliation, sapwood and structural biomass damage, and hurricane-induced mortality. ELM-FATES can reasonably represent coexistence between the two PFTs–light-demanding and shade-tolerant–for both the pre-Hugo and post-Hugo conditions. The model represents a reasonable size distribution of mid-and large-sized trees although it underestimates AGB, likely due to the overestimated nonhurricane mortality. ELM-FATES temporarily stimulated leaf biomass and diameter increment after Georges, an effect that should be tested with observations of future hurricane defoliation events. This research indicates that addressing model-data mismatches in tree mortality and understory dynamics are essential to simulation of more extreme hurricane effects under climate change.

58 GEOSCIENCES↗

DOE OSTI2023

Comparison of MHD stability properties between QH-mode and ELMy H-mode plasmas by considering plasma rotation and ion diamagnetic drift effects

Magnetohydrodynamic (MHD) stability at tokamak edge pedestal in a quiescent H-mode (QH-mode) and type-I ELMy H-mode plasmas in DIII-D experiment was analyzed by considering plasma rotation and ion diamagnetic drift effects. QH-mode plasma is marginally stable to kink/peeling mode (K/PM), but ELMy H-mode one is almost unstable to peeling-ballooning mode (PBM). It was identified that there are three physics features responsible for the difference in the MHD stability properties between QH-mode plasma and ELMy H-mode one. These are the distance of pedestal foot from the last closed flux surface (LCFS), the amount of the ion diamagnetic drift frequency at pedestal, and impact of coupled rotation and ion diamagnetic drift effects. These features were confirmed through the numerical experiments that the stability properties of the QH-mode plasma can be changed to that of the ELMy H-mode one by shifting the plasma profiles inward in the radial direction and halving the ion diamagnetic drift frequency. The reasons of the change in the stability properties are thought as that K/PM is stabilized due to the inward shift of the bootstrap current profile, and PBM is destabilized due to the reduction of the coupled rotation and ion diamagnetic drift stabilizing effect. Importance of these features was validated through numerical experiments with experimental data of other QH-mode plasmas in DIII-D. All the results show that MHD stability properties of QH-mode plasma can be obtained in case that pedestal foot is close to LCFS, ion diamagnetic drift frequency is large due to high ion temperature, and strong rotation shear exists near pedestal.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

CUF-Links: Continuous and Ubiquitous FAIRness Linkages for Reproducible Research

Despite much creative work on methods and tools, reproducibility— the ability to repeat the computational steps used to obtain a research result—remains elusive. One reason for these difficulties is that extant tools for capturing research processes, while powerful, often fail to capture vital connections as research projects grow in extent and complexity. We explain here how these interstitial connections can be preserved via simple methods that integrate easily with current work practices to capture basic information about every data product consumed or produced in a project. By thus extending the scope of findable, accessible, interoperable, and reusable (FAIR) data in both time and space to enable the creation of a continuous chain of Continuous and Ubiquitous FAIRness linkages (CUFlinks) from inputs to outputs, such mechanisms can facilitate capture of the provenance linkages that are essential to reproducible research. Herein we give examples of mechanisms that can facilitate the use of these methods, and review how they have been applied in practice.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Transmission Interface Limits for High-Spatial Resolution Capacity Expansion Modeling

Large-scale capacity expansion models typically rely on estimates of the power transfer limits between modeled zones. Accurate estimation of these interface transfer limits (ITLs) requires modeling the underlying transmission network. Here we expand on a maximum flow optimization method that uses linearized power flow to estimate transfer limits. We apply this method to a data set of the U.S. transmission network to estimate ITLs between U.S. counties. By calculating ITLs using different subsets of the network, we evaluate how the size of the network used in the estimation affects the results. The results show diminishing returns to ITL accuracy after six hops, suggesting that a network subset can reasonably be used to approximate ITLs. The county-level estimates produced in this study will support more spatially resolved capacity expansion modeling and will help inform policy making at local and national levels.

capacity planning↗

DOE OSTI2021

Reconstruction of the Room D, B, G, and Q Closure Histories at the Waste Isolation Pilot Plant

Experimental measurements of room closure in salt repositories are valuable for understanding the evolution of the underground and for validating geomechanical models. Room closure was measured during a number of experiments at the Waste Isolation Pilot Plant (WIPP) during the 1980's and 1990's. Most rooms were excavated using a multi-pass mining sequence, where each pass necessarily destroyed some of the mining sequence closure measurement points. These destroyed points were promptly reinstalled to capture the closure after the mining pass. After the room was complete, the mining sequence closure measurement stations were supplemented with remotely read closure measurement stations. Although many aspects of these experiments were thoroughly documented, the digital copies of the closure data were inadvertently destroyed, the non-trivial process of zeroing and shifting the raw closure measurements after each mining pass was not precisely described, the various closure measurements within a given room were not directly compared on the same plot, and the measurements were collected for several years longer than previously reported. Consequently, the hand-written mining sequence closure measurements for Rooms D, B, G, and Q were located in the WIPP archives, digitized, and reanalyzed for this report. The process of reconstructing the mining sequence closure histories was documented in detail and the raw data can be found in the appendices. Within the mid-section of a given room, the reconstructed closure histories were largely consistent with other mining sequence and remotely read closure histories, which builds confidence in the experiments and suggests that plane strain is an appropriate modeling assumption. The reconstructed closure histories were also reasonably consistent with previously published results, except in one notable case: the reconstructed Room Q closure histories 30 days after excavation were about 45 % less than the corresponding closures reported in Munson's 1997 capstone paper.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗