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Maximum likelihood estimation of difference scaling functions for suprathreshold judgments

Maximum likelihood estimation (MLE) has been used to produce perceptual scales from binary judgments of triads and quadruples. This method relies on Thurstone’s theory of a stochastic perceptual process where the perceived difference of two stimuli is the difference in their perceived strengths. It is possible that the perception of a suprathreshold difference is overestimated when adding smaller differences, a phenomenon referred to as diminishing returns. The current approach to construct a perceptual scale using MLE does not account for this phenomenon. We present a way to model the perception of differences using MLE and Thurstone’s theory, adapted to allow the possibility of diminishing returns. This method is validated using Monte Carlo simulated responses to experimental triads and can correctly model diminishing returns, the absence of diminishing returns, and the opposite of diminishing returns both in the cases when a perceptual scale is known and when the true perceived strengths of the stimuli are unknown. Additionally, this method was applied to empirical data sets to determine its feasibility in investigations of perception. Ultimately, it was found that this analysis allows for more accurate modeling of suprathreshold difference judgments, a more complete understanding of the perceptual processes underlying comparisons, and the evaluation of Thurstone’s theory of difference judgments.

97 MATHEMATICS AND COMPUTING↗

Investigating the Atmospheric Sources and Sinks of Perfluorooctanoic Acid Using a Global Chemistry Transport Model

Perfluorooctanoic acid, PFOA, is one of the many concerning pollutants in our atmosphere; it is highly resistant to environmental degradation processes, which enables it to accumulate biologically. With direct routes of this chemical to the environment decreasing, as a consequence of the industrial phase out of PFOA, it has become more important to accurately model the effects of indirect production routes, such as environmental degradation of precursors; e.g., fluorotelomer alcohols (FTOHs). The study reported here investigates the chemistry, physical loss and transport of PFOA and its precursors, FTOHs, throughout the troposphere using a 3D global chemical transport model, STOCHEM-CRI. Furthermore, this investigation includes an important loss process of PFOA in the atmosphere via the addition of the stabilised Criegee intermediates, hereby referred to as the “Criegee Field.” Whilst reaction with Criegee intermediates is a significant atmospheric loss process of PFOA, it does not result in its permanent removal from the atmosphere. Additionally, the atmospheric fate of the resultant hydroperoxide product from the reaction of PFOA and Criegee intermediates resulted in a ≈0.04 Gg year-1 increase in the production flux of PFOA. Furthermore, the physical loss of the hydroperoxide product from the atmosphere (i.e., deposition), whilst decreasing the atmospheric concentration, is also likely to result in the reformation of PFOA in environmental aqueous phases, such as clouds, precipitation, oceans and lakes. As such, removal facilitated by the “Criegee Field” is likely to simply result in the acceleration of PFOA transfer to the surface (with an expected decrease in PFOA atmospheric lifetime of ≈10 h, on average from ca. 80 h without Criegee loss to 70 h with Criegee loss).

54 ENVIRONMENTAL SCIENCES↗

Exploratory Studies of Mechanical Properties, Residual Stress, and Grain Evolution at the Local Regions near Pores in Additively Manufactured Metals

Directed energy deposition (DED) is gaining widespread acceptance in various industrial applications since its unique manufacturing features allow the DED to print metallic parts with very complex geometries. However, DED inevitably generates a lot of internal pores which can limit the widespread applications of the DED technique. The current studies on DED porosity are mostly focused on analyzing pores’ bulk-scale influences on mechanical properties and performances. Since DED pores have a micro-scale existence, with dimensions ranging from a few microns to several hundred microns, it is fundamental to explore the pores’ influences on the micro-scale, including local mechanical properties, residual stress, and grains near pores. However, this important research direction has been neglected. The objective of this work is to fill the above gap in DED porosity research and acquire a fundamental understanding of the role of porosity on a microscopic scale. The authors used nanoindentation approaches to investigate internal pores’ effects on mechanical properties and residual stress in local regions surrounding the pores. In addition, the grains near pores were observed through EBSD, and simulated with the Kinetic Monte Carlo model. The research findings can be provided for DED researchers and industrial practitioners as technical guidance. Most importantly, the research results can work as a good reference for tracing the source of bulk-scale mechanical performances and properties of DED parts with internal pores.

36 MATERIALS SCIENCE↗

HYBRD (High Resolution HYBrid Regional Downscaling) Model: Input data and Code

The HYBRD (HYBrid Regional Downscaling) model is a high-resolution urban land downscaling model that can be used to downscale intermediate urban land use and land cover (LULC) products into a high-resolution (30-meters). HYBRD uses a sequential hybrid process, combining statistical models with cellular-automata-based spatial algorithms. This repository contains all the necessary model code and inputs needed to successfully run HYBRD for Los Angeles, California. The repo also contains example outputs of each model step, except the final simulated raster outputs. Examples of simulated raster outputs for multiple scenarios for Los Angeles are available at DOI: 10.57931/2575233. Please refer to Related Works below.

Land↗

"Source Term Modeling for Advanced Gas Micro-Reactors"

Maintaining the safety of the public, environment, and operating personnel is the most important factor in designing, operating, maintaining, and decommissioning nuclear reactors. In recent years, there has been a growing interest in the development of micro-reactors employing TRi-structural ISOtropic (TRISO)-coated particle fuel. In gas reactors, TRISO fuel plays an important role in the safety case for high temperature reactors because of the fission product retention properties of the fuel. This ability enables the use of a functional containment strategy for the reactor where multiple barriers are used to prevent fission product release to the environment. Part of the safety analysis of these advanced reactors is the assessment of radionuclide releases under normal and accident conditions through the multiple credited safety barriers. Using conservative assumptions, a mechanistic analysis can be performed to quantify these releases that combines the probabilistic assessment of failure with analytic solutions to radionuclide transport equations. Source term modeling for TRISO fuel has been performed for previous reactor designs; however, these models are outdated, in many cases proprietary, and need updates to be applied to the current state of TRISO fuel technology and alternative gas reactor core configurations [1]. Currently, the only publicly available source term assessment for gas reactors is an expert-based Monte Carlo simulation based on the effectiveness of the fuel kernel, coating layers, and graphite block in a modular high temperature gas reactor [2]. Thus, there is a need to develop a simple, versatile, and mechanistic model of fission product release and transport in gas reactor cores that could be applied to a variety of reactors through user inputs and reactor-specific radionuclide inventories. The release is calculated by the diffusion of the key safety important fission products through the kernel, silicon carbide (SiC), graphite for both intact and defective TRISO particles based on fuel and graphite temperatures in the reactor under normal operation. These releases from the fuel enter the coolant where they can plate-out on cooler surfaces. A clean-up model is included for designs with a coolant purification system to remove fission gases. This initial distribution of fission products in the reactor serves as an initial condition for potential releases under postulated accident conditions. The model then can calculate the fission product release for any transient temperature profile and fission product releases can then be used to assess radiological dose to the workers and the public using conventional dose tools. Data on the diffusion of fission products is based on historic German TRISO experiments and the more current Department of Energy (DOE) Advanced Gas Reactor (AGR) TRISO fuel development program. The model is coded in python with inputs and outputs in excel spreadsheets, as well as python plotting utilities to aid in the interpretation of the results. References: [1] INL, NGNP Mechanistic Source Term White Paper, INL-10-17997, July 2010. [2] David A. Petti, Richard R. Hobbins, Peter Lowry, Hans Gougar, “Representative Source Terms and The Influence of Reactor Attributes on Functional Containment in Modular High Temperature Gas-cooled Reactors,” Nuclear Technology, Vol. 184, p. 181-197, Nov. 2013.

07 ISOTOPE AND RADIATION SOURCES↗

Distributed model predictive control for coordinated, grid-interactive buildings

Continued focus on reducing carbon emissions and improving energy efficiency requires buildings to become grid-interactive and not just behave as static consumers. A distributed model predictive control (DMPC) algorithm known as Limited-Communication (LC) DMPC is modified to enable grid-interactive buildings. A grid-aggregator subsystem is added that allows for a bulk grid power reference signal to be followed while the individual building subsystems also achieve their local comfort objectives. The LC-DMPC algorithm is applied for the first time to systems with multiple buildings. Adequate power tracking is shown for different simulation scenarios involving heterogeneous buildings, and next steps are discussed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

PV Reference Cells for Outdoor Use: An Investigation of Calibration Factors

Reference cells are widely used in the photovoltaic (PV) industry to measure irradiance. For field applications and outdoor use, a variety of products are on the market, and they are often perceived as a low-cost alternative to thermopile radiometers. But reference cell characteristics differ substantially from the latter, therefore measurements made by one category of instrument cannot be substituted for or directly compared with the other. The National Renewable Energy Laboratory's (NREL's) Solar Radiation Research Laboratory is currently in a multiyear effort to develop guidance and recommendations for the design and use of outdoor reference cells, with a view to reducing inconsistencies and measurement uncertainty. The core of this effort is the long-term deployment of 39 units of 10 distinct types made by 6 manufacturers. This report compares the calibration factors provided by manufacturers - which most users rely upon - to those measured at a high level of accuracy by NREL's Cell Lab. It also reports on the application of the Broadband Outdoor Radiometer Calibration (BORCAL) method to reference cells. As a group, the factory calibrations for the crystalline silicon cells showed a small positive bias of +0.7%, with a tight distribution around this value. This is a very good result for the manufacturers. The two World Photovoltaic Scale cells constituted outliers, with a mean deviation of -0.8%, which is still within the reported uncertainty ranges. The data collected during the BORCAL procedures show a strong and systematic fluctuation of the apparent responsivity of the reference cells over the course of a day, which was anticipated. Consequently, the standard BORCAL R@45 calibration factors underestimated the reference cell responsivities by 1%-4%. An alternate responsivity indicator was developed, R'@30, incorporating adjustments for temperature response, spectral response, and directional response. This reduced the mean deviation to -0.4% compared to the Cell Lab. Further, two independent BORCAL sessions were able to produce the same values to within ±0.2%. This could be a viable approach for verifying reference cells using existing BORCAL infrastructure, for example, to evaluate their long-term stability. The daily profiles of responsivity obtained during the BORCAL sessions (provided in Appendix A) show clear patterns of differences between models, which provides evidence that their directional responses differ from each other; thus, two sensors that are calibrated correctly might give the same reading at 30° zenith angle but systematically different readings at 60°. The impact of these inconsistencies in field operation will be quantified using the long-term observations started in 2020.

14 SOLAR ENERGY↗

EGS Collab Experiment 1: 3D Seismic Velocity Model and Updated Microseismic Catalog Using Transfer-Learning Aided Double-Difference Tomography

This package contains a 3D Seismic velocity model and an updated microseismic catalog associated with a proceedings paper (Chai et al., 2020) published in the 45th Workshop on Geothermal Reservoir Engineering. The 3D_seismic_velocity_model text file contains x (m), y(m), z(m), P-wave velocity (km/s), P-wave velocity quality indicator (1 for well-constrained; 0 for poorly constrained), S-wave velocity (km/s), and S-wave velocity quality indicator (1 for well-constrained; 0 for poorly constrained). The Updated_MEQ_catalog text file contains event origin time, x(m), y(m), z(m), error in x (m), error in y (m), error in z (m), and RMS misfit (millisecond). The 3D_seismic_P-wave_velocity_model animation file shows slices of the 3D P-wave velocity model. The 3D_seismic_S-wave_velocity_model animation file shows slices of the 3D S-wave velocity model. The Interactive_MEQ_locations API file is an interactive visualization of the updated microseismic event locations. The visualization allows users to view the event locations by dragging, rotating, and zooming in. References: Chai, C., Maceira, M., Santos-Villalobos, H. J., Venkatakrishnan, S. V., Schoenball, M., and EGS Collab Team, 2020, Automatic Seismic Phase Picking Using Deep Learning for the EGS Collab Project, in PROCEEDINGS, 45th Workshop on Geothermal Reservoir Engineering, edited, Stanford University, Stanford, California, 45, 1266-1276.

15 GEOTHERMAL ENERGY↗

SCALE 6.2 Lattice Physics Performance Assessment

The US Nuclear Regulatory Commission relies on the lattice physics analysis capabilities of the SCALE code system to perform confirmatory licensing analyses. Either SCALE lattice physics code—TRITON/NEWT or Polaris—can be used to generate cross section data used by the PARCS nodal core simulator for full-core neutronics calculations. This report presents an assessment of the accuracy of SCALE lattice physics codes for preparation of lattice physics data that are used to support simulator codes such as the NRC’s PARCS, for UO 2 -mixed oxide (MOX)/Zr fueled light water reactor (LWR) analyses. Due to the nature of lattice physics calculations, critical reactor experiment benchmarks cannot be modeled in explicit detail in a lattice physics code. However, this limitation does not mean that these measurement data are not usable for lattice physics studies. Therefore, either geometry approximations or axial buckling must be implemented to determine the critical water height. These modeling limitations have led to development of a three-phase assessment strategy. In the first phase, selected critical experiment benchmarks are modeled using the SCALE 3D continuous-energy (CE) Monte Carlo (MC) code KENO, which is the most rigorous neutron transport method available in SCALE, with no approximations in the spatial, angle, or energy treatments. Biases and statistical uncertainties in quantities of interest such as k eff and pin power distributions are determined by comparing CE KENO results to experimental data. This first phase in the accuracy assessment is to demonstrate and establish the use of CE KENO as a reference solution for the second phase. In the second phase, 14 numerical test suites are used to compare SCALE lattice physics calculations with CE KENO as a reference solution. In the third phase, SCALE lattice physics depletion calculations are performed, and the spent fuel isotopic results are compared with available radiochemical assay measurements. Isotopic measurement comparisons provide quantitative assessment of isotopic density distribution predictions with the depletion models in SCALE lattice physics codes. This report documents results for all test suites. The assessment was performed using standard production techniques unless otherwise noted. Both TRITON/NEWT and Polaris exhibited acceptable accuracy for most test cases. For the few test cases in which acceptable accuracy criteria were not met, further code and data development are planned. The computer codes used in this assessment are as follows: SCALE 6.2 rev19189 (pre-release of 6.2.1) was used for CE KENO, TRITON/NEWT and Polaris (PWR only) calculations; SCALE 6.2.2 was used for Polaris calculations to address several updates in support of support boiling water reactor (BWR) lattice geometries. For this work, there is no difference between SCALE 6.2.1 and SCALE 6.2.2 beyond the inclusion of the Polaris BWR analysis capability; The ENDF/B-VII.1 continuous energy and 252 group libraries deployed in SCALE 6.2 were generated with AMPX 6.2 that is distributed with SCALE.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Operating Wind Turbine as Synchronous Generator: Modeling and Power-Hardware-in-the-Loop Demonstration

Grid-forming (GFM) control of Type 3 and Type 4 wind turbine generators (WTGs) has attracted substantial attention in power systems research; however, the limited overcurrent capability of power electronics converters continues to deteriorate the grid strength of the evolving power systems. Synchronous wind, also referred to as a Type 5 WTG, offers a unique GFM solution to address grid integration and grid strength issues by keeping the grid largely synchronous at very high integration levels of renewable generation. A Type 5 WTG interfaces with the electric grid via a synchronous generator driven by a variable speed hydraulic torque converter; hence, the wind rotor operates in variable-speed mode for maximum power generation, and the generator shaft remains synchronous to the grid. This paper develops and tests a high-fidelity model of a Type 5 WTG in a power-hardware-in-the-loop testing environment, and it presents its operation characteristics under different grid contingencies. The power-hardware-in-the-loop demonstration shows that a Type 5 WTG inherently behaves as a GFM unit and can obtain similar performance in terms of power response, wind rotor dynamics, and stability enhancement compared to a Type 3 WTG in GFM control mode. Furthermore, the paper provides further insight into how Type 5 WTGs can support the smooth transition to power systems with high integration levels of inverter-based resources.

17 - WIND ENERGY↗

Evaluation of PBR Spent Fuel Criticality and Dose Rate Compliance for Storage and Transportation

Spent tri-structural isotropic (TRISO)–based fuels have a strong track record in storage and transportation without documented incidents. This work seeks to reduce uncertainty to aid in more informed spent fuel management of TRISO-based fuels by modeling both fresh and spent pebble bed reactor (PBR) fuel and comparing the results to the regulatory standards from 10 CFR 71. SCALE was used for all modeling due to it having fast and accurate methods for handling PBR fuel modeling, as well as having an efficient method for shielding calculations in monaco with automated variance reduction using importance calculations (MAVRIC), which utilizes the consistent adjoint-driven importance sampling (CADIS) and the forward-weighted consistent adjoint-driven importance sampling (FW-CADIS) methods. KENO-VI was used for all criticality calculations, TSUNAMI was used for uncertainty quantification on k-effective, TRITON and the Oak Ridge isotope generation code (ORIGEN) were both used for depletion of the fuel, and MAVRIC was used for shielding calculations. For criticality assessments, this study focused on the requirement that the value of the neutron multiplication factor, k-effective (k-eff), would not exceed a peak value of 0.95, including uncertainty, with 95% confidence. Criticality was initially examined by modeling fresh fuel from three different designs—HTR-10 fuel, PBMR-400 fuel, and demonstration fuel representative of a TRISO-fueled modern high-temperature gas reactor (HTGR) design, henceforth referred to as Demo HTGR—and placing them into various sized containers with conditions described in 10 CFR 71 to quantify the peak k-eff state. When the peak value of 0.95 k-eff was exceeded, mitigation methods were examined in those scenarios. Burnup credit, pebble displacement in areas of strong neutron multiplication, and random pebble replacement using pebbles of various compositions and replacement fractions were examined. In summary, the criticality of PBR fuels can be well accounted for by restricting container size, taking credit for burnup, or by displacing/replacing pebbles. Uncertainty of the k-eff due to nuclear data uncertainties was recorded at ~0.6644%Δk/k, or roughly 664% mil (pcm). The nuclear data–induced uncertainty was relatively small and should not require significant modification in the design to be accounted for. Revisions to the evaluated nuclear data file values have been shown to have a larger impact than nuclear data–induced uncertainty. For dose rate aspects, U.S. Nuclear Regulatory Commission regulations require a maximum dose rate of 10 millirem per hour (mrem/h) at 2 meters. In examining the dose rate behavior of spent PBR fuel, the representative Demo HTGR fuel was modeled exclusively due to it possessing the highest target burnup of the examined fuels. Equilibrium cycle modeling methods were used to produce a higher-fidelity discharge isotopic composition than simple assumptions, such as reflected pebbles. The discharge composition was used as a source term in the fixed-source transport shielding calculations, and dose rates were calculated at 2 m for the shortest possible cooling time. The low concentration of fuel material led to dose rates that were in line with regulatory limits, despite the high burnup when compared to traditional light water reactor fuels. In conclusion, the methods employed in this study would require more work to further verify and validate and are limited to the criticality and dose rate analyses performed.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Doppler Backscattering Data Analysis and Integrated Modeling with OMFIT

One Modeling Framework for Integrated Tasks (OMFIT) is a widely used software tool in the magnetic fusion research community. OMFIT provides magnetic fusion energy researchers with a framework for the development of special-purpose physics modules. This paper describes an OMFIT physics module pertaining to the Doppler Backscattering (DBS) fusion plasma diagnostic. DBS measures density fluctuations and flow velocity through plasma scattering of electromagnetic waves. The OMFIT DBS module was developed to analyze experimental DBS data and facilitate modeling of DBS systems installed on multiple tokamak devices. The OMFIT DBS module is designed to support several analysis workflows: detailed analysis of experimental data, experimental planning, and theory-based synthetic diagnostic modeling. The DBS module uses integrated modeling by leveraging other OMFIT physics modules to perform tasks related to DBS, e.g. ray/beam–tracing simulations, edge-localized mode–synchronized data analysis, magnetic equilibrium reconstruction, and fitting kinetic profile data. Furthermore, this paper describes several supported workflows and serves a reference for the OMFIT DBS module.

Doppler backscattering↗

SMART Mobility. Urban Science Capstone Report

The U.S. Department of Energy’s Systems and Modeling for Accelerated Research in Transportation (SMART) Mobility Consortium is a multiyear, multi-laboratory collaborative, managed by the Energy Efficient Mobility Systems Program of the Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office, dedicated to further understanding the energy implications and opportunities of advanced mobility technologies and services. The Urban Science (US) Pillar focuses on maximum-mobility and minimum-energy opportunities associated with emerging transportation and transportation-related technologies specifically within the urban context. Such technologies, often referred to as automated, connected, efficient (or electrified), and shared (ACES), have the potential to greatly improve mobility and related quality of life in urban areas. Although all the SMART Mobility research pillars share some commonalities, Urban Science strives to model, analyze, and gain insights from the perspective of human settlements (the “city”) as a living organism. This is especially critical as the United States is one of the most urbanized countries, and as more and more of the global population migrates to urban areas.1 The urban mobility system consists of a complex network that reaches well beyond roads and vehicles and includes significant investments in public transit, private mobility services (such as taxis and transportation network companies, or TNCs), significant parking reserves, and curb management practices, not to mention the abundance of emerging on-demand micromobility services for the movement of people and goods such as e-bikes and scooters, which make the urban space a dynamic laboratory for mobility. Urban spaces also concentrate employment, markets, services, and attractions, which are the destinations for most trips. The concentration of human activities and ensuing density also creates the need and emphasis for space efficiency in urban environments, which is often less of a constraint in suburban or rural contexts. This mixture of transportation and mobility infrastructure and practice, combined with global urbanization trends, make urban spaces a critical focus of research for developing energy-efficient mobility systems (EEMS).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Review: Pre-Darcy flows in low-permeability porous media

The widely used Darcy’s law specifies a linear relation between the Darcy velocity of fluid flow and the pressure gradient that drives the flow. However, studies have shown that Darcy velocity can exhibit a nonlinear dependence on the pressure gradient in low-permeability porous media such as clay and shale when the pressure gradient is adequately low. This phenomenon is referred to as low-velocity non-Darcian flow or pre-Darcy flow. This paper provides a comprehensive review of the theories, experimental data, and modeling methods for pre-Darcy flow in low-permeability porous media. The review begins by outlining the fundamental mechanisms underlying pre-Darcy flow that regulate the unique characteristics such as nonlinear dependence of the Darcy velocity on the pressure gradient and its relevance to fluid–rock interactions. The review then proceeds to present a thorough compilation of experimental investigations performed in various low-permeability geomaterials including tight sandstones, shales, and clays. Next, empirical and theoretical models and simulation methods that have been developed to fit and interpret experimental data are reviewed. Finally, the review underscores the challenges encountered in conducting and interpreting pre-Darcy flow experiments and suggests future research directions. By analyzing previous experimental investigations, this review aims to offer a valuable resource for researchers and practitioners seeking to enhance their understanding of fluid dynamics in low-permeability geomaterials. This provides insights into the application of pre-Darcy flow in numerous natural and engineered processes such as shale oil and gas recovery, contaminant transport in low-permeability aquifers, and geological disposal of nuclear waste.

58 GEOSCIENCES↗

Virtual refrigerant charge sensing algorithm for residential CO₂ heat pumps

Natural refrigerants are increasingly adopted in next-generation heat pump systems, among which CO₂ heat pumps have attracted significant attention. However, due to their high operating pressures, the leakage risk is higher, resulting in undercharge conditions and degraded heat pump performance. Thus, developing an accurate refrigerant charge level detection technique is necessary to guarantee safe and efficient operation. Although virtual refrigerant charge (VRC) level calculation algorithms for CO₂ heat pumps exist, they typically rely on empirically selected features without a systematic selection framework, leading to multicollinearity and potential overfitting, which limit their prediction accuracy and generalizability. To address these issues, this study proposes a VRC algorithm framework with a systematic feature selection method that identifies physically meaningful and statistically significant features, and is applied using a residential CO₂ heat pump as a case study. The method is extended from previous work on conventional refrigerants to account for charge behavior in CO₂ gas coolers. The selected features include gas cooler outlet density, evaporator pressure, and superheat temperature. The results demonstrate that the proposed feature selection method significantly improves prediction accuracy compared to existing VRC approaches. A relatively small training dataset (∼30 samples) is sufficient for feature identification and model development. The developed algorithm achieves less than 3% prediction error under both undercharge and overcharge conditions, representing reductions of 46.7% and 35.3% compared to two recent reference VRC algorithms for transcritical CO₂ heat pumps reported in the literature. The proposed algorithm and feature selection method enhance leakage detection capability, facilitate the deployment of CO₂ heat pump systems, and contribute to reduced energy waste and maintenance costs.

Guo, Fangzhou [Lawrence Berkeley National Laborato↗

Accelerating eigenvalue computation for nuclear structure calculations via perturbative corrections

Subspace projection methods utilizing perturbative corrections have been proposed for computing the lowest few eigenvalues and corresponding eigenvectors of large Hamiltonian matrices. In this paper, we build upon these methods and introduce the term Subspace Projection with Perturbative Corrections (SPPC) method to refer to this approach. We tailor the SPPC for nuclear many-body Hamiltonians represented in a truncated configuration interaction subspace, i.e., the no-core shell model (NCSM). We use the hierarchical structure of the NCSM Hamiltonian to partition the Hamiltonian as the sum of two matrices. The first matrix corresponds to the Hamiltonian represented in a small configuration space, whereas the second is viewed as the perturbation to the first matrix. Eigenvalues and eigenvectors of the first matrix can be computed efficiently. Because of the split, perturbative corrections to the eigenvectors of the first matrix can be obtained efficiently from the solutions of a sequence of linear systems of equations defined in the small configuration space. These correction vectors can be combined with the approximate eigenvectors of the first matrix to construct a subspace from which more accurate approximations of the desired eigenpairs can be obtained. We show by numerical examples that the SPPC method can be more efficient than conventional iterative methods for solving large-scale eigenvalue problems such as the Lanczos, block Lanczos and the locally optimal block preconditioned conjugate gradient (LOBPCG) method. The method can also be combined with other methods to avoid convergence stagnation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Interface Nucleus Templating of Modular Intermetallic Morphologies: Chemical Pressure Complementarity, Columnar Domains, and Complex Disorder in Y 13 Ag 42.7 Zn 29.7

One element of the diversity of intermetallic phases is the formation of complex structures from the assembly of fragments of simpler structures. Recently, we devised the Interface Nuclear Approach as a model for understanding such modular arrangements, in which the intergrowth of different structures is driven by chemical pressure (CP) relief at shared motifs at the domain interfaces, referred to as interface nuclei. In this Article, we present the synthesis, crystal structure, and CP analysis of a new compound that expands on this theme, Y 13 Ag 42.7 Zn 29.7 . Its hexagonal structure contains interpenetrating domains based on the CaPd 5+x and EuMg 5 types. The CaPd 5+x -based regions are reminiscent of the lamellar intergrowth structures previously observed in the Y−Ag−Zn system. In Y 13 Ag 42.7 Zn 29.7 , however, the domains have a different morphology, forming columns that adopt a hexagonal rod-packing. The geometrical features of the remaining spaces are assigned, using the program GrowDomain, to the cores of trigonal units of the EuMg 5 type, while layers of disordered atoms occur at heights along z where the parent structures are mismatched. At the CaPd 5+x -type/EuMg 5 -type interfaces, simple interface nucleus motifs with strong CP-complementarity can be identified, while their distribution within the parent structures supports the notion of templated architectures in modular intermetallics.

Chemical structure↗

phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids

Phosphorylated amino acids are involved in many cell regulatory networks; proteins containing these post-translational modifications are widely studied both experimentally and computationally. Simulations are used to investigate a wide range of structural and dynamic properties of biomolecules, such as ligand binding, enzyme-reaction mechanisms, and protein folding. However, the development of force field parameters for the simulation of proteins containing phosphorylated amino acids using the Amber program has not kept pace with the development of parameters for standard amino acids, and it is challenging to model these modified amino acids with accuracy comparable to proteins containing only standard amino acids. In particular, the popular ff14SB and ff19SB models do not contain parameters for phosphorylated amino acids. Here, the dihedral parameters for the side chains of the most common phosphorylated amino acids are trained against reference data from QM calculations adopting the ff14SB approach, followed by validation against experimental data. Finally, library files and corresponding parameter files are provided, with versions that are compatible with both ff14SB and ff19SB.

77 NANOSCIENCE AND NANOTECHNOLOGY↗