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At least 1,477 records · Page 82

In Vitro Evolution and Computational Approaches to Predict, Prevent and Control Future Pandemics

The natural tendency of virus to mutate and the under-sampling of the environment makes it difficult to become aware of the emergence of new viral strains with pandemic potential. Being able to predict what mutations make a virus more infective might allow to spot such strains with minimal sampling and potentially allow to predict/prevent the next pandemic. The team attempted to mimic natural viral mutations and recombination through computational and experimental methods producing a variety of mutants of a SARS-COV-2 protein (receptor binding domain, RBD, of spike protein) responsible for viral entry in mammalian cells. The library of mutants was then interrogated for ability and lack-there-of to interact with the host cell receptor ushering viral entry, Angiotensin-converting enzyme 2 (ACE2). The negative and positive data set is intended to “teach the rules” of virus-host receptor interaction. Additionally, the positive clones were used to screen a set of antibody mutants designed to widen the breadth of viral mutants recognition, to demonstrate that this kind of libraries could also be a tool to produce antibody therapeutics impervious to viral mutation, even before a pandemic strain is discovered.

59 BASIC BIOLOGICAL SCIENCES↗

Key Degradation Products in Nitroplasticizer Thermal Aging

Upon thermal aging, nitroplasticizer (NP) can thermally degrade and release numerous degradation products depending on aging conditions. In this report, we summarize our recent findings, a library of key degradation products in the NP thermal aging is provided. The library contains 25 identified species with their corresponding MS/MS spectrum and intensity profiles, which are derived from our 44-month thermal aging experiment of NP conducted in air, nitrogen, and water at room temperature (RT), 38, 45, 55, and 64°C. To provide a comprehensive yet simplified overview of NP degradation, we summarized the proposed mechanisms of HONO elimination and decomposition, acid generation, PBNA nitrosation and nitration, acid-catalyzed hydrolyses of NP and polynitrated PBNAs, as well as the formation of NP degradants. As the last part of a series of publications and reports on the investigation of NP degradation mechanisms, this work further unfolds complex chemistry that occurs in the entire aging process of NP.

36 MATERIALS SCIENCE↗

Enhanced PDV waveform search and analysis method using parallel circular-convolution / cross-correlation for improved dynamic surface velocity extraction [Poster]

Previous work on exhaustive search methodologies for extracting best-match parameters pertaining to dynamic surface quantities from PDV was done by cross-correlating synthetically generated PDV waveforms with observed counterparts using the circular-convolution theorem. This work was further developed into an open-source PDV analysis toolkit called CCPDVANALYSIS which expands upon and enhances the previously tested methods by parallelizing serial algorithmic components and incorporating a comprehensive script library for different flavors of instantaneous frequency functions utilized in generating synthetic PDV waveforms. Results of these enhancements have been shown to markedly decrease execution times of exhaustive search and extraction algorithms and produce improved velocity recoveries for low-velocity and dynamically varying velocity signals. The CCPDVANALYSIS script library demonstrates an advanced method for extracting velocities from low-velocity and non-constant velocity signals further extending and improving the methods beyond capabilities of traditional frequency domain tools.

97 MATHEMATICS AND COMPUTING↗

Bringing randomized algorithms to mainstream numerical linear algebra

Numerical linear algebra (NLA) underpins huge swaths of computational science and engineering. For scientists and engineers to make the most of the DOE’s computing resources, it is essential that they have access to high-performance implementations of algorithms with best-in-class scalability and reliability. Despite this, prevailing NLA libraries have little to no support for breakthrough algorithms from the field of randomized numerical linear algebra (RandNLA) that have been developed over the past twenty years. The goal of this LDRD was to break a log-jam that had prevented broad adoption of RandNLA. Our work had two thrusts. The first was to develop RandBLAS: a trustworthy and high-performance C++ library for randomized dimension reduction (an operation widely known as sketching). The second was the development of a novel randomized algorithm for computing a challenging type of matrix decomposition known as Householder QR with column pivoting (Householder QRCP). In this one-year late-start LDRD we successfully delivered RandBLAS 1.0 and new CPU and GPU codes for Householder QRCP. RandBLAS has extensive documentation at https://randblas.readthedocs.io/en/stable/. Papers on RandBLAS and and our high-performance QRCP codes are forthcoming.

97 MATHEMATICS AND COMPUTING↗

FY24 Mole Development Updates and SAM-Mole Coupling for MSR Species Transport Applications

In this report, a new coupling strategy linking Mole to SAM is demonstrated where SAM is used to drive the solution and Mole is used primarily as a library for mass transport coefficient models. Groundwork is laid to transition Mole into a harbor for various mass transfer coefficient models, which generally take the form of scalar, auxiliary Multiphysics Object-Oriented Simulation Environment (MOOSE) kernels. It is envisioned that these models will be agnostic to the spatial discretization scheme and can be used across the MOOSE ecosystem, providing a centralized library for certain mass transfer coefficients to MOOSE codes that must account for liquid-to-vapor and vapor-to-liquid mass transport phenomena for both high-volatility and low-volatility species.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Spin-Controllable Dynamics in Defect-Engineered Carbon Nanotubes as Single Photon Emitters: Data-Driven Modeling and Computations

Quantum technologies, such as quantum computing and sensing, require efficient single-photon emission (SPE) sources that operate at room temperature in telecom wavelengths. While several materials can serve as SPE sources, no single platform meets all the criteria for efficiency, ambient operation, and scalability. Single-walled carbon nanotubes (SWCNTs) with covalently attached molecules offer a promising solution. Their SPE can be easily tuned via modifications of the SWCNT's diameter, chirality, and bonded molecules, enabling emission across near-IR to telecom wavelengths at ambient conditions. However, to fully realize the potential of SWCNTs and unlock their quantum capabilities, a deeper understanding of how structural defects from molecular adducts affect their emission and competing photoexcited processes is essential. To address this gap in our knowledge, this project combined quantum chemistry calculations with data-driven methods of cheminformatics (QSAR) and machine learning (ML). The developed computational approaches have provided several design strategies for covalent functionalization of SWCNTs to improve their optical response. The collaboration with Los Alamos National Lab (LANL) enabled direct comparison of computational and experimental data, facilitating method validation. This partnership was enhanced through access to LANL's Center for Integrated Nanotechnologies (CINT) utilizing User Facility Program and summer internships, which provided three NDSU graduate students with hands-on experience at LANL. The outcomes of this project included (1) Advancing the current stage of computational methods in accurate modeling of non-adiabatic spin-dependent photoexcited dynamics and its applicability to nanosystems consisting of thousands of atoms, realized as open-access codes linked to existing DFT-based software; (2) Establishing the relationship between the structure of adducts and SWCNTs and intrinsic excitonic and spin properties of defect states for guiding novel synthetic strategies and experimental probes of chemically functionalized SWCNTs as near-IR emitting materials; (3) Generating virtual libraries of hypothetical functionalized SWCNTs for virtual screening of their chemical structures and optical properties, leveraging new functionalities of SWCNTs; (4) Offering a unique experience for NDSU graduate students that prepared them for future scientific careers related to materials modeling and big data processing. These results were summarized in 12 published journal papers and 3 recently submitted papers. One of a key finding is that the position of defect sites on the SWCNT surface primarily drives the emission redshift (up to 100 meV), while the polarity of the defect-inducing molecules has a much smaller effect (~10 meV). However, the electron-donating or withdrawing properties of a molecule influence selecting reactivity of defect sites. These insights important for optimizing synthetic protocols for desired emissions in SWCNTs. We also revealed that the interaction between two defects at various positions on the SWCNT enhances the redshift and optical activity of states, favoring strong near-IR emission. This suggests that manipulations in defect concentrations is a promising strategy for controlling efficient emission. Mostly important, the defect position was found controllable by the spin states of photoexcited intermediates: Excited aromatic molecules form ortho defects with SWCNTs at their singlet states in the presence of oxygen, while oxygen-free conditions favor para defects via the triplet-state mechanism. Additionally, a heat-activated [2+2] cycloaddition reaction facilitates divalent defect formation with fewer bonding positions that narrows emission bands. These groundbreaking findings have been experimentally validated and significantly advance our understanding of defect chemistry in SWCNTs. Using a novel encoding technique and 3D-MoRSE descriptors, we developed highly accurate ML/QSAR models to predict both the 3D structure and optical properties of SWCNTs with chemical defects. This model enabled the creation of a virtual library of 125,556 structures, providing new insights into the relationship between SWCNT-defect structure and emission.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Light Output Fitting Software

Light output response of scintillators is crucial to the utilization of organic scintillators as effective tools in radiation detection and measurement. While the response is a continuous distribution, the light output corresponding to the maximum energy deposition is crucial in effectively understanding and simulating a detector. There are a variety of fits derived in literature that will vary for every detector material. The Light Output Response Fitter, or LORF Program is a python script designed to easily and quickly compute and plot fits for a variety of scintillator light output models. It includes a stopping power library constructed from SRIM including Organic Glass, EJ309, EJ301, Stilbene, EJ276, and their deuterated counterparts by default, with the ability for the user to add custom stopping power libraries. The user is also capable of importing the python package and utilizing its in-built functions as appropriate. Uses for this capability include plotting and computing a model with known parameters.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

End-to-End Optimization for Battery Materials and Molecules by Combining Graph Neural Networks and Reinforcement Learning

The National Renewable Energy Laboratory (NREL), together with the Colorado School of Mines (CSM) and Colorado State University (CSU), has developed a machine learning-enhanced approach to the design of new battery materials. Currently, such materials are designed in part via numerous expensive high-fidelity computational simulations that predict the performance of a given composition. Even with computational screening tools, the vast landscape of possible molecular or crystal structures exceeds current and future computational capacity. Improving the efficiency by which new materials can be optimized will therefore disrupt the cost, risk, and time required to bring new energy solutions to the marketplace. Predicting the properties of an organic molecule or periodic crystalline material given its structure has grown increasingly common. These approaches leverage large-scale computational and experimental databases and ML approaches such as graph neural networks. The inverse design problem of finding a material that possesses desired properties is substantially more challenging, since enumerating all valid material structures is not feasible. In this project, we leveraged recent success in reinforcement learning to efficiently navigate this high-dimensional search space. Just as algorithms can find the optimal chess moves from nearly limitless options, we train an approach to evolve a simple starting structure into a complex structure that possess the desired properties. Our solution has been demonstrated by applying it to two related design application tasks for short- and long-term energy storage, respectively: (1) the design of solid-state ion conductors and (2) the design of organic redox-active materials. The project has resulted an open-source software library for material design, documented examples of applying the library to both organic and inorganic material optimization, and peer-reviewed publications detailing the data, computational models, and resulting candidate materials.

25 ENERGY STORAGE↗

Developing and Managing Data Acquisition Software Using Spack

The Data Acquisition systems of particle physics experiments regularly push the boundaries of high-throughput computing, demanding low-latency collection of data from thousands of devices, collating data into time-sliced events, processing these events and making trigger decisions, and writing the selected data streams to disk. To accomplish these tasks, the DAQ Engineering and Operations department at Fermilab leverages multiple software libraries and builds reusable DAQ frameworks on top. These libraries must be delivered in well-defined bundles and are thoroughly tested for compatibility and functionality before being deployed to live detectors. We have several techniques used to ensure that a consistent set of dependencies can be delivered and re-created at need. We must also support active development of DAQ software components, ideally in an environment as close as possible to that of the detectors. This development often occurs across multiple packages which have to be built in concert and features tested in a consistent and reproducible manner. I will present our scheme for accomplishing these goals using Spack environments, bundle packages, and Github Actions-based CI.

Flumerfelt, Eric [Fermilab]↗

Advances in Modeling Capabilities for Critical Mineral Separation Technologies: A PrOMMiS Overview

This is an oral presentation at the TechConnect conference on the work developed by PrOMMiS. PrOMMiS builds on and extends capabilities developed within the Department of Energy’s (DOE) Institute for the Design of Advanced Energy Systems (IDAES), Integrated Platform, and Water Treatment Technoeconomic Assessment Platform (WaterTAP), which have been successfully leveraged by other Department of Energy research areas. The open-source toolkit facilitates validation, reproducibility, and accountability, allowing for easy extension of the framework to other systems. This talk presents an overview of the PrOMMiS capabilities, including unit model library, advances in thermophysical properties models, and capital cost libraries for simulation and optimization of mineral processing technologies. The PrOMMiS applications include (1) conceptual design and superstructure optimization for screening different process configurations and identifying promising technologies; (2) dynamic modeling and optimization to enable the creation of digital twins; (3) surrogate modeling tools to leverage data when predictive thermodynamic models are not currently available; (4) technical risk reduction via uncertainty quantification and robust optimization to identify process designs that are robust to process variability and uncertainties; and (5) deployment of uncertainty quantification tools to maximize knowledge gained from experimental campaigns, while reducing the number of experiments required

critical minerals and materials↗

(U) STATEMENT OF WORK, UCD RadHard Collaboration

The following subcontract engages UC Davis (UCD) to collaborate with Lawrence Livermore National Laboratory (LLNL) on the design and analysis of microelectronic circuits (macrocells). As part of the proposed statement of work UCD will be given access to information that is export controlled. Within this statement of work UCD is to acquire and install any applicable foundry PDK(s) and collaborate with LLNL on the design of new macrocells and assist in making improvements to existing macrocells as well as the design of ASICs using collections of macrocells. The intent is to increase the application space of the existing LLNL macrocell library and demonstrate the use of the macrocell library, including new designs, by making reference design ASICs.

42 ENGINEERING↗

AMPX Status 2024 [Slides]

This presentation focus on AMPX development for 2024 it also touches on ENDF/B-VIII.1. The slides touches on Thermal Neutron Scattering Library, AMPX Development Highlights, and Transport libraries for SCALE 7.0.0.

ENDF/B-VIII.1↗

Resolving the Discontinuity Between Thermal Scattering Data and Fast Data

The task of resolving discontinuities between thermal cross sections and fast cross sections in AMPX processing is part of a broader project to provide guidance on the potential effect of unknown thermal neutron scattering law (TNSL) data, primarily from the standpoint of criticality safety. The primary goal of this work is to deliver code fixes in AMPX that increase confidence that SCALE libraries provide physically correct cross sections across the full range of neutron energies encountered in transport applications. This report discusses the resolution of two sources of discontinuity. The first issue occurs when the Bragg edges in an evaluated nuclear data file do not extend to 5 eV. The second issue concerns parameters chosen during the processing of the nuclear data library—specifically, the parameter that defines the energy at which the thermal data ends and the fast nuclide data begins. This report also discusses a third issue, which is related to the calculation of probability distributions from a densely gridded double-differential cross section.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Electromagnetic Transient Modeling of Large Data Centers for Grid-Level Studies

The magnitude and complexity of electricity usage patterns from large data centers are having significant impacts on the operation and dynamics of the power grid; grid operators and planners require a range of specialized data center models to properly evaluate these impacts and specify technical solutions as needed. Towards addressing this need, Pacific Northwest National Laboratory (PNNL) has developed a library of electromagnetic transient (EMT) models for grid-level studies of data centers called the data center model library (DML). This report describes how the DML was created and how it may properly be used. The models present in the DML are generic models; subject matter expertise and additional technical data are needed to modify these models before they can represent any real data center. However, they will significantly reduce the level of effort required to develop site-specific models and can serve as a common starting point to guide industry towards a more refined consensus. Most of the models within DML are dedicated to representing the power electronics interfaces commonly used in modern data centers, such as double-conversion uninterruptible power supplies and single-phase power factor correction converters. These models are intended for use in grid-level studies and are a simplified aggregation of many small components. That said, background material on the physical and electrical design of large data centers is provided as companion material so that users can be aware of many of the details which have been omitted or streamlined as a matter of practical necessity. Additionally, guidance on the application of EMT analysis for data center interconnection studies is provided, which aids users in identifying when the DML is necessary and what sort of additional model development may be necessary for conducting real-world studies.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Demonstration of Monte Carlo Reference Equilibrium Core Solutions for Pebble Bed Reactors Using Shift in kugelpy

This report describes how to produce reference solutions for the equilibrium core search of pebble bed reactors using the pyrates Python library. The pyrates library uses the kugelpy methodology to perform running-in calculations to reach an equilibrium core. This approach relies on full-core Monte Carlo neutron transport calculations and the shifting of fuel pebble inventory through the reactor to simulate pebble movement in the core from one step to the next of a running-in scenario. In addition to the use of Serpent for the Monte Carlo neutron transport calculations, as part of this work, updates for the use of the Shift Monte Carlo code were integrated into the official pyrates GitHub repository. Comparisons of running-in simulations for a generic pebble bed reactor produced by using pyrates with Serpent and Shift are shown. Although consistent trends are shown between the use of the two Monte Carlo codes, the limiting factor in either calculation is the computation time due to the need to perform several hundred full-core neutron transport calculations before an equilibrium core is reached.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Developing Source Term Database for Advanced Reactors

A source term database is crucial to informing nuclear emergency response measures, enabling emergency responders to assess the potential severity of nuclear and radiological consequences. In recent times, various advanced reactor designs have come into operation, are under construction, or are being designed and developed. This report documents an effort carried out to develop a source term database for advanced reactors. The report covers key design features of these reactors and discusses radioactivity buildup and source term inventories of dose-significant radionuclides in the reactor core. For neutronic and depletion analyses, we used the SCALE code system, a computational suite for reactor physics, depletion, criticality, and sensitivity/uncertainty quantification. We used SCALE/TRITON to perform depletion calculations to predict cycle length and discharge burnup and to generate the ORIGEN reactor library. Subsequently, we used SCALE/ORIGAMI to calculate radioactivity buildup and, thereby, the source term inventories at the targeted discharge burnup, using the ENDF/B-VII.1 nuclear data library. This report covers several advanced reactors, including the KLT-40S, RITM-200N, VOYGR, and eVinci. However, other reactors, such as the RITM-200S and ARC-100, have yet to be investigated and will be explored in future efforts.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Experiences with SYCL on AMD GPUs with Kokkos

With the recent diversification of the hardware landscape in the high-performance computing (HPC) community, performance-portability solutions are becoming more and more important. One of the most popular choices is Kokkos, which recently became a Linux Foundation project. Most of its development is supported by the US Department of Energy and the French Alternative Energies and Atomic Energy Commission. Kokkos is implemented as a C++ library with multiple backends to support CPUs as well as various GPU architectures. These backends include OpenMP, CUDA, HIP, and also SCYL. This approach enables users to leverage the preferred vendor toolchain for the respective platform (e.g. CUDA, ROCm, OneAPI). The SYCL backend is used to target Intel GPUs, in particular to support the Aurora exascale supercomputer. However, SYCL itself also offers a large degree of portability, and in fact Kokkos’ CI for SYCL has been running on NVIDIA hardware due to a lack of access to Intel GPUs. In this report, we describe our experience with using Kokkos SYCL backend on AMD GPUs targeting the Frontier supercomputer at Oak Ridge National Laboratory. The two major SYCL implementations are DPC++ and AdaptiveCpp. While the Kokkos SYCL backend has been implemented using the former, the latter was the first implementation to target AMD GPUs. We will discuss the experience with both of these SYCL implementations in terms of functionality and performance. Using Kokkos to evaluate SYCL toolchains has a number of benefits. Kokkos’ use of SYCL is fairly complex, exercising features such as graphs, relocatable device functions, atomics – including for non-arithmetic types, as well as pinned and page migratable memory allocations. Kokkos also needs to implement capabilities such as Kokkos’ hierarchical parallelism that are not a straight-forward mapping to SYCL capabilities. Furthermore, a large number of libraries and applications that represent diverse use cases are implemented in Kokkos, providing readily available test cases for a toolchain evaluation. Preliminary results show that support for AMD GPUs in DPC++ is much less mature than for NVIDIA GPUs or Intel GPUs. While the situation has improved significantly over the last year, we still encounter many runtime failures, dispatching problems, and code generation issues. With AdaptiveCpp the challenges arise even earlier in the evaluation process. Since Kokkos’ SYCL implementation is largely focused on supporting Intel GPUs, we opted to leverage SYCL extensions which are available in DPC++ but not in AdaptiveCpp. Furthermore, AdaptiveCpp appears to be less conformant with the SYCL2020 standard which Kokkos relies on. In some cases, we are able to work around the lack of feature support, in other cases we have to disable certain Kokkos capabilities to evaluate the toolchain. Our evaluation will leverage Kokkos’ unit tests to establish basic functionality and feature completeness. We then use simple benchmarks for components of a CG implementation as a measure of usability and performance of the SYCL toolchains.

97 MATHEMATICS AND COMPUTING↗