Scripts for "A Global Phylogenomic Analysis of the Shiitake Genus Lentinula" v1.0
This is a repository for scripts and documents to help reproduce the results in "A Global Phylogenomic Analysis of the Shiitake Genus Lentinula".
Min, Byoungnam↗
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Results for “reproducibility of results”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Bayesian calibration of stochastic agent based model via random forest
SAND2024-11403O The Bayesian Calibration of Stochastic Agent-based Model via Random Forest is a code that was developed in concurrence with an article by the same name that was written for a journal. The code reproduces simulation results and plots from the article. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
SciDAC↗
Swap Path Network for Robust Person Search Pre-training
This code corresponds to the WACV25 conference paper, "Swap Path Network for Robust Person Search Pre-training". In that paper, we introduce a new model for the person search task called the Swap Path Net (SPNet). The person search task is a problem in computer vision, where we locate and rank matches to an image of a query person in a set of other images where we want to find them. We also introduce a novel pre-training algorithm specific to the Swap Path Net architecture. The code implements pre-training and fine-tuning of the Swap Path Net (SPNet). This includes ingesting image datasets and updating the weights of the SPNet neural network to train it for the person search task. The repository contains code, configs, and instructions to reproduce all results from the paper.
Jaffe, LucasW [Lawrence Livermore National Laborat↗
HALLUFIELD: DETECTING LLM HALLUCINATIONS VIA FIELD-THEORETIC MODELING
A research-focused Python package that implements our hallucination-detection method for large language models(LLMs). The code computes stability signals from LLM predictions across various hyperparameters sweeps and combines free-energy/entropy–style metrics to flag likely hallucinations, with tunable thresholds for batch scoring. The repo includes evaluation scripts, config files, and example notebooks to reproduce benchmark results and ablations; it depends on standard open-source libraries (PyTorch, Hugging Face) and runs on CPU/GPU. The repository examples only use public models/datasets only.
Bhattarai, Manish [Los Alamos National Labs]↗
MeshedResevoir v1.0
This is a small Modelica library and python scripts that are used to run numerical experiments for a journal paper. The software is meant to be shared so that readers can reproduce our results. The models are a highly simplified representation of a district energy system, using components from the Modelica Buildings Library (BSD-licensed, LBL owned) and new models for an expansion vessel.
Wetter, Michael [Lawrence Berkeley National Labora↗
A comprehensive guide to CAN IDS data and introduction of the ROAD dataset
Although ubiquitous in modern vehicles, Controller Area Networks (CANs) lack basic security properties and are easily exploitable. A rapidly growing field of CAN security research has emerged that seeks to detect intrusions or anomalies on CANs. Producing vehicular CAN data with a variety of intrusions is a difficult task for most researchers as it requires expensive assets and deep expertise. To illuminate this task, we introduce the first comprehensive guide to the existing open CAN intrusion detection system (IDS) datasets. We categorize attacks on CANs including fabrication (adding frames, e.g., flooding or targeting and ID), suspension (removing an ID’s frames), and masquerade attacks (spoofed frames sent in lieu of suspended ones). We provide a quality analysis of each dataset; an enumeration of each datasets’ attacks, benefits, and drawbacks; categorization as real vs. simulated CAN data and real vs. simulated attacks; whether the data is raw CAN data or signal-translated; number of vehicles/CANs; quantity in terms of time; and finally a suggested use case of each dataset. State-of-the-art public CAN IDS datasets are limited to real fabrication (simple message injection) attacks and simulated attacks often in synthetic data, lacking fidelity. In general, the physical effects of attacks on the vehicle are not verified in the available datasets. Only one dataset provides signal-translated data but is missing a corresponding “raw” binary version. This issue pigeon-holes CAN IDS research into testing on limited and often inappropriate data (usually with attacks that are too easily detectable to truly test the method). The scarcity of appropriate data has stymied comparability and reproducibility of results for researchers. As our primary contribution, we present the Real ORNL Automotive Dynamometer (ROAD) CAN IDS dataset, consisting of over 3.5 hours of one vehicle’s CAN data. ROAD contains ambient data recorded during a diverse set of activities, and attacks of increasing stealth with multiple variants and instances of real (i.e. non-simulated) fuzzing, fabrication, unique advanced attacks, and simulated masquerade attacks. To facilitate a benchmark for CAN IDS methods that require signal-translated inputs, we also provide the signal time series format for many of the CAN captures. Our contributions aim to facilitate appropriate benchmarking and needed comparability in the CAN IDS research field.
97 MATHEMATICS AND COMPUTING↗
GOOML Big Kahuna Forecast Modeling and Genetic Optimization Files
This submission includes example files associated with the Geothermal Operational Optimization using Machine Learning (GOOML) Big Kahuna fictional power plant, which uses synthetic data to model a fictional power plant. A forecast was produced using the GOOML data model framework and fictional input data, and a genetic optimization is included which determines optimal flash plant parameters. The inputs and outputs associated with the forecast and genetic optimization are included. The input and output files consist of data, configuration files, and plots. A link to the Physics-Guided Neural Networks (phygnn) GitHub repository is also included, which augments a traditional neural network loss function with a generic loss term that can be used to guide the neural network to learn physical or theoretical constraints. phygnn is used by the GOOML framework to help integrate its machine learning models into the relevant physics and engineering applications. Note that the data included in this submission are intended to provide a demonstration of GOOML's capabilities. Additional files that have not been released to the public are needed for users to run these models and reproduce these results. Units can be found in the readme data resource.
15 GEOTHERMAL ENERGY↗
Role of physics in physics-informed machine learning
Physical systems are characterized by inherent symmetries, one of which is encapsulated in the units of their parameters and system states. These symmetries enable a lossless order-reduction, e.g., via dimensional analysis based on the Buckingham theorem. Despite the latter's benefits, machine learning (ML) strategies for the discovery of constitutive laws seldom subject experimental and/or numerical data to dimensional analysis. We demonstrate the potential of dimensional analysis to significantly enhance the interpretability and generalizability of ML-discovered secondary laws. Our numerical experiments with creeping fluid flow past solid ellipsoids show how dimensional analysis enable both deep neural networks and sparse regression reproduce old results, e.g., Stokes law for a sphere, and generate new ones, e.g., an expression for an ellipsoid misaligned with the flow direction. Furthermore, our results suggest the need to incorporate other physics-based symmetries and invariances into ML-based techniques for equation discovery.
97 MATHEMATICS AND COMPUTING↗
D-branes and orbit average
We study correlation functions of D-branes and a supergravity mode in AdS, which are dual to structure constants of two sub-determinant operators with large charge and a BPS single-trace operator. Our approach is inspired by the large charge expansion of CFT and resolves puzzles and confusions in the literature on the holographic computation of correlation functions of heavy operators. In particular, we point out two important effects which are often missed in the literature; the first one is an average over classical configurations of the heavy state, which physically amounts to projecting the state to an eigenstate of quantum numbers. The second one is the contribution from wave functions of the heavy state. To demonstrate the power of the method, we first analyze the three-point functions in N=4 super Yang-Mills and reproduce the results in field theory from holography, including the cases for which the previous holographic computation gives incorrect answers. We then apply it to ABJM theory and make solid predictions at strong coupling. Finally we comment on possible applications to states dual to black holes and fuzzballs.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Zero-bias conductance peaks at zero applied magnetic field due to stray fields from integrated micromagnets in hybrid nanowire quantum dots
Many recipes for realizing topological superconductivity rely on broken time-reversal symmetry, which is often attained by applying a substantial external magnetic field. Alternatively, using magnetic materials can offer advantages through low-field operation and design flexibility on the nanoscale. Mechanisms for lifting spin degeneracy include exchange coupling, spin-dependent scattering, spin injection – all requiring direct contact between the bulk or induced superconductor and a magnetic material. Here, we implement locally broken time-reversal symmetry through dipolar coupling from nearby micromagnets to superconductor-semiconductor hybrid nanowire devices. Josephson supercurrent is hysteretic due to micromagnets switching. At or around zero external magnetic field, we observe an extended presence of Andreev bound states near zero voltage bias. We also show a zero-bias peak plateau of a non-quantized value. Our findings largely reproduce earlier results where similar effects were presented in the context of topological superconductivity in a homogeneous wire, and attributed to more exotic time-reversal breaking mechanisms [Nat. Phys. 17, 43 (2020)]. In contrast, our stray field profiles are not designed to create Majorana modes, and our data are compatible with a straightforward interpretation in terms of trivial states in quantum dots. At the same time, the use of micromagnets in hybrid superconductor-semiconductor devices shows promise for future experiments on topological superconductivity.
Jiang, Luyao [Univ. of Pittsburgh, PA (United Stat↗
Measurements of the Antiquark Flavor Asymmetry in the Proton by the Drell-Yan Experiment SeaQuest
The antiquark flavor asymmetry \bar{d}/\bar{u} d ‾ / u ‾ in the proton gives an insight on the non-perturbative structure of the proton. The SeaQuest experiment measured the Drell–Yan cross section ratio of proton-deuterium to proton-proton to determine the antiquark flavor asymmetry \bar{d}/\bar{u} d ‾ / u ‾ precisely in the range of 0.13 0.13 < x < 0.45 . SeaQuest provides the evidence of \bar{d}/\bar{u} > 1.0 d ‾ / u ‾ > 1.0 over a wide range of momenta. Some theoretical models reproduce this result.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
HED Hydrodynamics in the Common Modeling Framework
Within the Common Modeling Framework (CMF), the HED Hydrodynamics Project has implemented a common methodology, or "Authority", for modeling high energy density (HED) experiments by extending development of the Eulerian Applications Project code Authority, "EAPA," to include relevant physics models, customization tools and templates, and in situ and post-processing capabilities. Additionally, several models for small-scale HED experiments were successfully added to the CMF and simulations reproduce the results of preexisting, benchmarked input decks. We expect use of the CMF to improve our effectiveness in developing predictive capabilities for experiments ranging from small-scale planar single-interface, single-shock to multi-interface, multi-shock configurations and up through multi-shell inertial confinement fusion (ICF) implosions. Additionally, this will strengthen our ability to design future targeted experiments. Using the CMF infrastructure and Authorities for HED modeling has three key impacts. First, it enables a version-controlled, pedigreed and archived base model for each experiment with tools that allow easy setup, execution and analysis of simulations to assess and/or expose sensitivities to various parameters. Second, having a common base set of inputs and physics definitions helps identify systematic differences between models in the codes and experimental data to support code validation, and build confidence in our predictive capabilities. Finally, designed to work in concert with multiple programs and projects including PEM, IC, OES, V&V and DSW, the CMF supports improved collaboration and integration through shared model definitions, data, simulations and results, enhancing the workflow required to underwrite the knowledge base and capabilities ultimately required for stockpile stewardship
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Advanced Thin Film Core Technology: CIGS Final Technical Report (FTR)
Cu(In,Ga)Se 2 (CIGS) thin-film photovoltaics are a high-efficiency and reliable technology. This project completed research in two important areas and was designed to work collaboratively with industrial partners. Task 1: Alkali Science focused on alkali post-deposition treatments (PDT). PDTs have been instrumental in the dramatic voltage improvements that have moved CIGS device efficiencies from 20% to 23.35% [1]. Based on a survey of CIGS companies at the beginning of the project, the single biggest breakthrough for the CIGS community would be a mechanistic understanding of the role of alkalis in the material system. Significant accomplishments of Task 1: Alkali Science: 1) KF post-deposition treatments were shown to improve lifetime, open-circuit voltage (VOC), and efficiency of industrial partner samples, even when done as a later step, separate from the original CIGS deposition. 2) KF boosted efficiency when incorporated at the end of the third stage of NREL CIGS growth. 3) XPS characterization of CIGS surfaces with and without PDTs led to a proposed mechanism whereby K drives structural transformation at 350 degrees C that is locked in at room temperature even after K is rinsed away. 4) Published recipes for KF and RbF PDTs. Literature to date did not provide enough detail to quickly reproduce experimental results. 5) Identified most important parameters (RbF cell temperature and lamp setpoint temperature) and set boundaries for successful RbF PDTs. The purpose of Task 2: Cell-level Reliability was to overcome the largest challenges to investor confidence and long product lifetime in CIGS-based photovoltaic products: metastability, shading-induced hot spots, and potential-induced degradation (PID). Key findings were made in each of these areas by studying CIGS reliability at the cell level: 1) Published NREL's cell-level reliability testing procedures along with challenges that were encountered while developing them. These were also distributed to the community through an MRS conference presentation. 2) Decreased metastability by adding a CdS hole-injection layer between the CIGS and Zn(O,S) in the device stack. It also improved device performance. Materials other than CdS can be used for the same purpose. 3) Reduced front-glass PID by replacing soda-lime glass with low-Na borosilicate glass. 4) Found that PID depends on leakage current and light/electrical bias. This will help labs avoid test-specific degradation. 5) Discovered that CIGS can suffer from two different types of PID with different mechanisms. Front is slower and leads to shunting ZnO. Back is faster and degrades the p-n junction. 6) Holding cells at open circuit slows PID compared to short circuit. This affects testing protocols for glass/glass modules.
14 SOLAR ENERGY↗
Development of a creep model informed by lower-length scale simulations to simulate creep in doped UO 2
Using molecular dynamics, we predict information at the atomistic scale used to develop a mechanistic UO 2 creep model for use in higher length-scale fuel performance codes. The ultimate objective of the model is to better describe the grain size dependence and therefore impact of doping on creep rates in UO 2 . In a previous NEAMS milestone, we found that Nabarro-Herring (bulk diffusional) creep was too low to capture the experimentally observed creep rates in standard UO 2 . Moreover, in that milestone, other mechanisms were explored, such as Coble (grain boundary) creep and dislocation climb, with each mechanism exhibiting different grain size dependencies. Again, these were orders of magnitude too low to describe the experimental creep rates. In this work, we address the previous assumptions made for the Coble creep mechanism by investigating the diffusivity of various defects at grain boundaries in UO 2 and, critically, to determine if enhanced grain boundary diffusivity allows the model to better reproduce experimental results. The diffusivity as a function of temperature for different concentrations of uranium vacancies and interstitials for bulk UO 2 have also been examined using cluster dynamics. Furthermore, using a concentration dependent segregation model, the concentration of defects at the grain boundary were predicted. This atomistic data was then input into the various creep mechanisms and the creep rates compared to the empirical MATPRO correlation (used in BISON) and experiment.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
A Data Processing Pipeline for Socio-Technical Network Analysis [Slides]
With the rapid adoption of emerging technologies, there is a need to catalog and model sociotechnical interdependencies that have been historically used to influence the operation of Critical Infrastructure networks including the impacts of mergers and acquisitions, hostile takeovers, and foreign investment. Our research intends to address this need with two primary contributions. First, we have developed a data curation and processing pipeline to generate sociotechnical networks extracted from a variety of data sources including SEC filings and infrastructure asset databases. The pipeline, implemented in Apache Airflow, extracts and normalizes the representation of entities and relations, specified within ontologies. Second, networks produced by our pipeline enable the development of graph-theoretic metrics that consider the properties of network components in addition to its topology. Measures of network complexity, such as degree distribution, reachability analyses, temporal analysis, and community detection may be adapted to indicate adversarial organizational influence. Our intent is to provide an extensible, machine-actionable approach to quickly communicate such models, reproduce previous results, and adapt them to new, unanticipated situations.
97 MATHEMATICS AND COMPUTING↗
Modeling and Optimization of Zeolites for Contaminant Removal from Coal Combustion Impoundment Leachates
Coal Combustion Residual (CCR) landfills in the U.S. can lead to elevated contaminant concentrations in groundwater and runoff, particularly of arsenic, boron, and selenium. Zeolites can be readily synthesized from materials contained within the coal combustion ash impoundments and can be cation-exchanged to enhance adsorption capacity, selectivity, and reactivity. However, the optimization of zeolites becomes a daunting task when accounting for the variety of Si:Al ratios, the species of extra-framework cations present, and the zeolite pore structure. Molecular simulations provide methods to study and guide the design of zeolites for the sorption of contaminants from aqueous solution. In this work, models that predict the sorption of arsenic, boron, and selenium from water using cation-exchanged zeolites. Because of the lack of experimental adsorption data for these species of contaminants, models were parametrized to reproduce the results of first-principles calculations and then used to predict sorption for zeolites for a dataset containing 6000 combinations of zeolites and sorption conditions. Machine learning was used to train a model to predict sorption for materials in this database based on the results of the molecular simulations. Next, a genetic algorithm was used to optimize zeolites for the removal of each contaminant from aqueous solution for individual impoundment sites based on contaminant concentrations reported by the Electric Power Research Institute.
Findley, John↗
Docker Containers for MCNP ® Development
Containers are a revolutionary technology in software development and deployment that provides a lightweight, portable environment for ensuring consistency across multiple computing environments. In anticipation of the MCNP 6.3.1 release, two Docker container images have been released on DockerHub for general use. The MCNP source code is not included in the images, and users are still required to obtain it through RSICC. The images produced by Docker are compliant with the OCI (Open Container Initiative) standards, ensuring compatibility with other container engines such as Podman or Kubernetes’ CRI-O. Initially, the images are stored under the author’s personal space on DockerHub (docker.io/azukaitis), but they will be relocated to a dedicated MCNP group space once approved. In the future, they will also be available through the registry feature of the https://github.com/lanl/mcnp-containers project. The use of Docker provides a pre-configured environment for building and running MCNP, ensuring reproducibility of results across various host architectures. This significantly improves consistency when running MCNP on different systems. Notably, executables and installers from the Docker images have successfully passed the MCNP development branch testing suite on x86-64 architectures, including Windows, macOS, and Linux operating systems. Furthermore, testing has demonstrated compatibility with macOS Docker in emulation mode on the latest Apple Mac M2 Ultra hardware, ensuring robust support even on the latest platforms. In this document, we will provide a step-by-step guide to using the Docker images across multiple platforms. Additionally, we will present performance numbers for building and running the MCNP test suite.
97 MATHEMATICS AND COMPUTING↗
Pulse-level noisy quantum circuits with QuTiP
The study of the impact of noise on quantum circuits is especially relevant to guide the progress of Noisy Intermediate-Scale Quantum (NISQ) computing. In this paper, we address the pulse-level simulation of noisy quantum circuits with the Quantum Toolbox in Python (QuTiP). We introduce new tools in qutip-qip, QuTiP's quantum information processing package. These tools simulate quantum circuits at the pulse level, leveraging QuTiP's quantum dynamics solvers and control optimization features. We show how quantum circuits can be compiled on simulated processors, with control pulses acting on a target Hamiltonian that describes the unitary evolution of the physical qubits. Various types of noise can be introduced based on the physical model, e.g., by simulating the Lindblad density-matrix dynamics or Monte Carlo quantum trajectories. In particular, the user can define environment-induced decoherence at the processor level and include noise simulation at the level of control pulses. We illustrate how the Deutsch-Jozsa algorithm is compiled and executed on a superconducting-qubit-based processor, on a spin-chain-based processor and using control optimization algorithms. We also show how to easily reproduce experimental results on cross-talk noise in an ion-based processor, and how a Ramsey experiment can be modeled with Lindblad dynamics. Finally, we illustrate how to integrate these features with other software frameworks.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗