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At least 721 records · Page 40

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DOE OSTI2021

The role of non-standard translation in Candida albicans pathogenesis

ABSTRACT Candida albicans typically resides in the human gastrointestinal tract and mucosal membranes as a commensal organism. To adapt and cope with the host immune system, it has evolved a variety of mechanisms of adaptation such as stress-induced mutagenesis and epigenetic regulation. Niche-specific patterns of gene expression also allow the fungus to fine-tune its response to specific microenvironments in the host and switch from harmless commensal to invasive pathogen. Proteome plasticity produced by CUG ambiguity, on the other hand is emerging as a new layer of complexity in C. albicans adaptation, pathogenesis, and drug resistance. Such proteome plasticity is the result of a genetic code alteration where the leucine CUG codon is translated mainly as serine (97%), but maintains some level of leucine (3%) assignment. In this review, we dissect the link between C. albicans non-standard CUG translation, proteome plasticity, host adaptation and pathogenesis. We discuss published work showing how this pathogen uses the fidelity of protein synthesis to spawn novel virulence traits.

Bezerra, Ana Rita (ORCID:0000000346131711)↗

DOE OSTI2023

Enabling Fortran Standard Parallelism in GAMESS for Accelerated Quantum Chemistry Calculations

The performance of Fortran 2008 DO CONCURRENT (DC) relative to OpenACC and OpenMP target offloading (OTO) with different compilers is studied for the GAMESS quantum chemistry application. Specifically, DC and OTO are used to offload the Fock build, which is a computational bottleneck in most quantum chemistry codes, to GPUs. The DC Fock build performance is studied on NVIDIA A100 and V100 accelerators and compared with the OTO versions compiled by the NVIDIA HPC, IBM XL, and Cray Fortran compilers. The results show that DC can speed up the Fock build by 3.0× compared with that of the OTO model. Finally, with similar offloading efforts, DC is a compelling programming model for offloading Fortran applications to GPUs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Results of Neutron Dosimetry Measurements for the Advanced Test Reactor Cycle 173-C

Results of neutron dosimetry measurements in ATR for cycle 173-C are presented. Cobalt and nickel wires were installed in numerous irradiation locations for the duration of the cycle. The specific activity of these wire segments can be used in conjunction with the presented cycle history information to determine the thermal- and fast-neutron fluence rates for each irradiation position during the cycle using the referenced standard test methods.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

maranasgroup/yeastsMFA

The parameterization of kinetic models requires measurement of fluxes and/or metabolite levels for a base strain and a few genetic perturbations thereof. Unlike stoichiometric models that are mostly invariant to the specific strain, it remains unclear whether kinetic models constructed for different strains of the same species have similar or significantly different kinetic parameters. This important question underpins the applicability range and prediction limits of kinetic reconstructions. To this end, herein we parameterize two separate large-scale kinetic models using K-FIT with genome-wide coverage corresponding to two distinct strains of Saccharomyces cerevisiae: CEN.PK 113-7D strain (model k-sacce306-CENPK), and growth-deficient BY4741 (isogenic to S288c; model k-sacce306-BY4741). The metabolic network for each model contains 306 reactions, 230 metabolites, and 119 substrate-level regulatory interactions. The two models (for CEN.PK and BY4741) recapitulate, within one standard deviation, 77% and 75% of the fitted dataset fluxes, respectively, determined by 13C metabolic flux analysis for wild-type and eight single-gene knockout mutants of each strain. Strain-specific kinetic parameterization results indicate that key enzymes in the TCA cycle, glycolysis, and arginine and proline metabolism drive the metabolic differences between these two strains of S. cerevisiae. Our results suggest that although kinetic models cannot be readily used across strains as stoichiometric models, they can capture species-specific information through the kinetic parameterization process.

Dinh, Hoang↗

DOE OSTI2023

maranasgroup/k-sacce306

Dinh, Hoang↗

DOE OSTI2024

eCC++ : A Compiler Construction Framework for Embedded Domain-Specific Languages

eCC++ is a new compiler construction framework for embedding domain-specific programming languages within C++. That is, the host language is C++, the guest language is the DSL to be embedded in C++, and eCC++ is the tool that enables the embedding. The eCC++ framework is composed of three main components: a front-end, an API for program verification based on a functional and declarative intermediate representation (IR), and a Multi-Level Intermediate Representation (MLIR) code generator. The eCC++ front-end consists of a library of C++ classes and operators that can be used to define the guest language. Guest sources are compiled with any standard C++ compiler, and when run, the resulting executable generates an eCC++ IR representation of the program, which can be verified within the eCC++ framework. Finally, eCC++ allows for high-level and domain-specific optimizations before generating MLIR. In summary, eCC++ aims to act as a generic front-end that enables embedding guest languages into C++, and provides necessary compiler technology for program verification, targeting the existing capabilities in the MLIR infrastructure. The paper evaluates the eCC++ expressiveness and usability describing the process of embedding GraphIt, a high-performance graph language in C++.

Gonzalez Tallada, Marc↗

DOE OSTI2023

Simulating noise on a quantum processor: interactions between a qubit and resonant two-level system bath

Material defects fundamentally limit the coherence times of superconducting qubits, and manufacturing completely defect-free devices is not yet possible. Therefore, understanding the interactions between defects and a qubit in a real quantum processor design is essential. We build a model that incorporates the standard tunneling model, the electric field distributions in the qubit, and open quantum system dynamics, and draws from the current understanding of two-level system (TLS) theory. Specifically, we start with one million TLSs distributed on the surface of a qubit and pick the 200 systems that are most strongly coupled to the qubit. We then perform a full Lindbladian simulation that explicitly includes the coherent coupling between the qubit and the TLS bath to model the time dependent density matrix of resonant TLS defects and the qubit. We find that the 200 most strongly coupled TLSs can accurately describe the qubit energy relaxation time. This work confirms that resonant TLSs located in areas where the electric field is strong can significantly affect the qubit relaxation time, even if they are located far from the Josephson junction (JJ). Similarly, a strongly-coupled resonant TLS located in the JJ does not guarantee a reduced qubit relaxation time if a more strongly coupled TLS is far from the JJ. In addition to the coupling strengths between TLSs and the qubit, the model predicts that the geometry of the device and the TLS relaxation time play a significant role in qubit dynamics. Our work can provide guidance for future quantum processor designs with improved qubit coherence times.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Evanescent operators in one-loop matching computations

Effective Field Theory calculations used in countless phenomenological analyses employ dimensional regularization, and at intermediate stages of computations, the operator bases extend beyond the four-dimensional ones. The extra pieces — the evanescent operators — can ultimately be removed with a suitable renormalization scheme, resulting in a finite shift of the physical operators. Modern Effective Field Theory matching techniques relying on the method of expansion by regions have to be extended to account for this. After illustrating the importance of these shifts in two specific examples, we compute the finite shifts required to remove all evanescent operators appearing in the one-loop matching of generic ultraviolet theories to the Standard Model Effective Field Theory and elucidate the formalism for generic Effective Field Theory calculations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Defining an industrial heat pump: A review & synthesis

Clear and understandable definitions of advanced energy technologies are not common and often confuse those who are not experts. This review paper addresses a critical issue in the field of heat pumps: the ambiguity surrounding the term “industrial heat pump.” The term, as discussed in various literature and media, often leads to misconceptions about the capabilities and applications of heat pumps, particularly in industrial contexts. This review paper seeks to refine and unify the definition of industrial heat pumps by analyzing existing academic and commercial literature, industry reports, and classifications. Unique identifiers explored for the definition of an industrial heat pump include the use of waste heat, operating temperature ranges, size specifications, and specific end-use applications. The study reveals differences in how industrial heat pumps are defined in academic and commercial contexts, highlighting the need for a standardized definition to facilitate better communication among manufacturers, policymakers, and end users. This is especially important considering recent legislative efforts such as the HEAT Act, which seeks to promote industrial heat pump adoption. The proposed definition aims to provide clarity while supporting the effective deployment of industrial heat pumps. With proper adoption, the definition will help promote the role of industrial heat pumps in achieving energy efficiency goals in the industrial sector. The intended impact is for the definition to serve as a foundational reference for future research and policy development.

Heat pump characteristics↗

DOE OSTI2024

Efficient generation of grids and traversal graphs in compositional spaces towards exploration and path planning

Abstract Diverse disciplines across science and engineering deal with problems related to compositions, which exist in non-Euclidean simplex spaces, rendering many standard tools inaccurate or inefficient. This work explores such spaces conceptually in the context of materials discovery, quantifies their computational feasibility, and implements several essential methods specific to simplex spaces through a new high-performance open-source library . Most significantly, we derive and implement an algorithm for constructing a novel n-dimensional simplex graph data structure, containing all discretized compositions and possible neighbor-to-neighbor transitions. Critically, no distance or neighborhood calculations are performed, instead leveraging pure combinatorics and order in procedurally generated simplex grids, keeping the algorithm $${\mathcal{O}}(N)$$ O ( N ) , with minimal memory, enabling rapid construction of graphs with billions of transitions in seconds. Additionally, we demonstrate how such graph representations can be combined to homogeneously express complex path-planning problems, while facilitating efficient deployment of existing high-performance gradient descent, graph traversal, and other optimization algorithms.

Krajewski, Adam M. (ORCID:0000000222660099)↗

DOE OSTI2020

Early retirement of power plants in climate mitigation scenarios

International efforts to avoid dangerous climate change aim for large and rapid reductions of fossil fuel CO 2 emissions worldwide, including nearly complete decarbonization of the electric power sector. However, achieving such rapid reductions may depend on early retirement of coal- and natural gas-fired power plants. Here, we analyze future fossil fuel electricity demand in 171 energy-emissions scenarios from Integrated Assessment Models (IAMs), evaluating the implicit retirements and/or reduced operation of generating infrastructure. Although IAMs calculate retirements endogenously, the structure and methods of each model differ; we use a standard approach to infer retirements in outputs from all six major IAMs and—unlike the IAMs themselves—we begin with the age distribution and region-specific operating capacities of the existing power fleet. We find that coal-fired power plants in scenarios consistent with international climate targets (i.e. keeping global warming well-below 2 °C or 1.5 °C) retire one to three decades earlier than historically has been the case. If plants are built to meet projected fossil electricity demand and instead allowed to operate at the level and over the lifetimes they have historically, the roughly 200 Gt CO 2 of additional emissions this century would be incompatible with keeping global warming well-below 2 °C. Thus, ambitious climate mitigation scenarios entail drastic, and perhaps un-appreciated, changes in the operating and/or retirement schedules of power infrastructure.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2020

Interplay between fractional quantum Hall liquid and crystal phases at low filling

The nature of the state at low Landau-level filling factors has been a long-standing puzzle in the field of the fractional quantum Hall effect (FQHE). While theoretical calculations suggest that a crystal is favored at filling factors $\nu$≲1/6, experiments show, at somewhat elevated temperatures, minima in the longitudinal resistance that are associated with fractional quantum Hall effect at $\nu$ 1/7, 2/11, 2/13, 3/19, 1/9, 2/15, and 2/17, which belong to the standard sequences $\nu$ =n/(6n ± 1) and $\nu$=n/(8n ± 1). To address this paradox, we investigate the nature of some of the low-$\nu$ states, specifically $\nu$= 1/7, 2/13, and 1/9, by variational Monte Carlo, density matrix renormalization group, and exact diagonalization methods. We conclude that in the thermodynamic limit, these are likely to be incompressible fractional quantum Hall liquids, albeit with strong short-range crystalline correlations. Finally, this suggests a natural explanation for the experimentally observed behavior and a rich phase diagram that admits, in the low-disorder limit, a multitude of crystal-FQHE liquid transitions as the filling factor is reduced.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Phonon Screening of Excitons in Atomically Thin Semiconductors

Atomically thin semiconductors, encompassing both 2D materials and quantum wells, exhibit a pronounced enhancement of excitonic effects due to geometric confinement. Consequently, these materials have become foundational platforms for the exploration and utilization of excitons. Recent ab initio studies have demonstrated that phonons can substantially screen electron-hole interactions in bulk semiconductors and strongly modify the properties of excitons. While excitonic properties of atomically thin semiconductors have been the subject of extensive theoretical investigations, the role of phonon screening on excitons in atomically thin structures remains unexplored. In this Letter, we demonstrate via ab initio GW-Bethe-Salpeter equation calculations that phonon screening can have a significant impact on optical excitations in atomically thin semiconductors. We further show that the degree of phonon screening can be tuned by structural engineering. We focus on atomically thin GaN quantum wells embedded in AlN and identify specific phonons in the surrounding material, AlN, that dramatically alter the lowest-lying exciton in monolayer GaN via screening. Our studies provide new intuition beyond standard models into the interplay among structural properties, phonon characteristics, and exciton properties in atomically thin semiconductors, and have implications for future experiments.

2-dimensional systems↗

DOE OSTI2023

Assessment of the Distributed Ledger Technology for Energy Sector Industrial and Operational Applications Using the MITRE ATT&CK® ICS Matrix

In recent times, Distributed Ledger Technology (DLT) has gained significant attention for its potential application in the energy sector. Utilizing blockchain and DLT has demonstrated the ability to enhance the resilience of the electric infrastructure, which will support a more flexible infrastructure and advance grid modernization. However, the deployment of these technologies increases the overall attack surface. The MITRE ATT&CK® matrices have been developed to document an adversary’s tactics and techniques based on real-world observations. The MITRE ATT&CK® matrices provide a common taxonomy for offense and defense and have become a valuable conceptual tool across multiple cybersecurity disciplines for conveying threat intelligence, performing testing through red teaming or adversary emulation, and enhancing network and system defenses against intrusions. The MITRE ATT&CK® for Industrial Control Systems (ICS) matrix was created to provide knowledge about adversary behavior in the ICS technology domain. This study analyzes the relevance of various tactics and techniques across a seven-layer DLT engineering and cybersecurity stack, known as the DLT stack, designed by the Cybersecurity Taskforce under IEEE P2418.5 - Standard for Blockchain in Energy working group sponsored by Power and Energy Systems - Smart Buildings, Loads and Customer Systems (PES/SBLC) Technical Committee. Additionally, this paper identifies specific mitigation strategies tailored to the energy ICS environment

42 ENGINEERING↗

DOE OSTI2025

Towards Automatically Matching Security Advisories to CPEs: String Similarity-based Vendor Matching

When a vulnerability is reported by the National Vulnerability Database (NVD), affected products are listed in the structured Common Platform Enumeration (CPE) format. Unfortunately, if the vulnerability is in a software library (e.g., Log4j), it will not include CPEs for each product containing that library. In these cases, security operators need to manually read the vendor's or third-party security advisories to see if their product is affected. However, these advisories do not report affected products in a structured format, which prevents automated processing, This paper makes the first effort towards automatically constructing structured CPEs for the vulnerable products in a non-NVD security advisory from the unstructured data in the advisory. Since this is a very challenging problem, this paper specifically focuses on the initial but key step of matching the un-structured vendor names in security advisories to the structured vendor representations in the standard CPE format. We explore the feasibility of using string similarity to solve the problem. The basic idea is to compare a vendor name from the non-NVD advisory with each vendor in the official CPE dictionary. The CPE vendor with the highest similarity score to the advisory's vendor will be considered as the match. We first conduct an experimental, comparative study of multiple mainstream string similarity metrics for this matching problem. To improve the performance, we then design a new string similarity metric that is adapted from an existing metric by weighing different tokens in the advisory's vendor name differently.

McClanahan, Kylie↗

DOE OSTI2021

Code Artifact for: Clustering Analysis of Commercial Vehicles Using Automatically Extracted Features from Time Series Data [SWR-21-96]

This repository contains data ingestion, feature extraction, and analysis code used in NREL Technical report "Clustering Analysis of Commercial Vehicles Using Automatically Extracted Features from Time Series Data." The code is written in Python. The ETL and feature extraction code must be run in a Spark context. The analysis code can be run without Spark, provided you have pre-computed features in a CSV file. Analysis code related to the NREL Technical Report NREL/TP-2C00-74212. Includes PySpark functions to perform trip segmentation and feature extraction over big time series data in Apache Spark. Includes "domain specific" features such as Aerodynamic Speed (ft/s), Characteristic Acceleration (ft/s2), Percent Below 55 (%), Percent Zero (%), Stops Per Mile, Average Speed (mph), Maximum Speed (mph), and Speed Standard Deviation (mph). Includes Pyspark UDF to compute "domain agnostic" features using the TSFresh library. This software record also includes the analysis notebooks and code to generate the results in the previously mentioned technical report.

Perr-Sauer, Jordan↗

DOE OSTI2023

Recent Code Developments/Improvements to SAM Multi-dimensional Flow Model

The System Analysis Module (SAM) is under development at Argonne National Laboratory as a modern system-level modeling and simulation tool for advanced non-light water reactor safety analyses. In addition to its conventional one-dimensional flow network module, the multi-dimensional flow model of SAM offers significant benefits to its end-users, including the U.S. NRC, who uses it to develop reference models for advanced reactor concepts. This report provides a summary of the recent progress achieved under DOE-NE’s Nuclear Energy Advanced Modeling and Simulation program in the continuous code development and improvements of the SAM code, specifically its multi-dimensional flow model. The improvements include enhancements to the physical model, code usability, addressing user feedback, and compliance with the SQA program standards that aim to enhance and maintain the quality of the software.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Leveraging Large Language Models for Real-World Data Evidence: A Framework for Automated Treatment Extraction and Data Harmonization

Background: The ability to comprehensively collect treatment information from cancer patient medical records would enable studies to evaluate real-world benefits and risks tied to specific treatments. Currently, it is difficult to system- atically collect high-quality treatment information because it is often stored in unstructured text. Manually extracting and standardizing drug and regimen data is time-intensive. Recent advances in large language models (LLMs) offer a potential solution for automated extraction of structured treatment information from clinical text. Objective: This study systematically evaluates the utility of four LLMs from the Llama family for automated extraction of oncology treatment information from clinical text. This information can guide researchers using cancer registry data to provide insights into cancer care and outcomes beyond clinical trials. Methods: Four instruction-tuned Llama models with varying parameter counts (1B, 3B, 8B, and 70B) were evaluated for their ability to extract treatment information from clinical documents. A unified oncology knowledge base integrating seven major public data sources was developed to standardize and normalize extracted entities—a critical step for harmonizing data from diverse sources. Extracted treatment data were compared against expert-annotated ground truth. Model performance was assessed using accuracy metrics (Precision, Recall, F1-Score) and opera- tional feasibility metrics, including processing speed and structural compliance of the output. Results: A strong positive correlation was observed between model size and extraction accuracy. F1-score improved from 0.609 for the 1B model to 0.710 (3B), 0.807 (8B), and 0.828 (70B). While larger models demonstrated superior accuracy and compliance, they incurred higher computational costs. The modest performance difference between 8B and 70B suggests diminishing returns with increasing model size. Conclusions: LLMs represent a viable technology for automating oncology treatment extraction. The 8B-parameter model emerged as a highly effective option, balancing high accuracy and computational efficiency. Selecting an appropriate LLM for deployment in cancer registries involves a trade-off between desired accuracy and available operational resources. Harmonizing extracted entities with the oncology knowledge base facilitates standardized integration into common data models, enhancing data quality for real-world evidence analyses.

artificial intelligence↗