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At least 703 records · Page 39

RAG for FLAG: AI Assistance for a Physics Code

Artificial intelligence (AI) has quickly become an important tool in scientific research, where significant efforts are underway to develop tools that will expedite the research process. One area of particular impact is scientific software, which can be particularly complex, and therefore time consuming to learn and use effectively. AI assistants are increasingly helping to streamline the process by performing tasks such as interactively answering user questions or suggesting solutions. Los Alamos National Laboratory (LANL) develops several advanced scientific codes, such as FLAG, which can be used to run multiphysics simulations. With this study, our goal was to develop an AI assistant for FLAG that could help make the process of understanding the software and running physics simulations more efficient. To develop an AI assistant for FLAG, we used a method called retrieval-augmented generation (RAG), which is a technique that uses information from relevant data sources to enhance the accuracy of large language models (LLMs). We used the FLAG user manual and other FLAG documentation as the knowledge base for the RAG system. When a user provides a query, RAG retrieves relevant sections from the knowledge base in response, then uses those excerpts to generate grounded and contextually rich answers. We found that our AI assistant was able to provide context aware answers and source references to user queries. To evaluate performance, we developed a set of 40 benchmark questions and compared the accuracy of the responses to those of two standard LLMs without retrieval. Our AI assistant significantly outperformed the standard LLMs at answering FLAG-related questions, with an 82.5% accuracy rate, compared to 47.5% for both of the standard LLMs. This has the potential to make the process of learning and using FLAG much easier, especially for new users. Ultimately, it supports LANL’s broader mission by empowering scientists and engineers to focus more on discovery and analysis rather than on navigating complex software systems.

97 MATHEMATICS AND COMPUTING↗

Where’s Swimmy?: Mining unique color features buried in galaxies by deep anomaly detection using Subaru Hyper Suprime-Cam data

Abstract We present the Swimmy (Subaru WIde-field Machine-learning anoMalY) survey program, a deep-learning-based search for unique sources using multicolored (grizy) imaging data from the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP). This program aims to detect unexpected, novel, and rare populations and phenomena, by utilizing the deep imaging data acquired from the wide-field coverage of the HSC-SSP. This article, as the first paper in the Swimmy series, describes an anomaly detection technique to select unique populations as “outliers” from the data-set. The model was tested with known extreme emission-line galaxies (XELGs) and quasars, which consequently confirmed that the proposed method successfully selected $\sim\!\! 60\%$–$70\%$ of the quasars and $60\%$ of the XELGs without labeled training data. In reference to the spectral information of local galaxies at z = 0.05–0.2 obtained from the Sloan Digital Sky Survey, we investigated the physical properties of the selected anomalies and compared them based on the significance of their outlier values. The results revealed that XELGs constitute notable fractions of the most anomalous galaxies, and certain galaxies manifest unique morphological features. In summary, deep anomaly detection is an effective tool that can search rare objects, and, ultimately, unknown unknowns with large data-sets. Further development of the proposed model and selection process can promote the practical applications required to achieve specific scientific goals.

Astronomy & Astrophysics↗

Opportunities and Limitations of Nuclear Magnetic Resonance Spectroscopy in Astrobiology

For decades, Nuclear Magnetic Resonance (NMR) spectroscopy has been utilized as a powerful tool in various scientific disciplines, most prominently in chemistry, to determine molecular structures or monitor reactions. While well established in various fields, NMR applications in astrobiology are still unclear. This work aims to explore the potential of NMR in astrobiology, highlighting strengths but also weaknesses. We illustrate capabilities of NMR with two applications: (1) recently developed methods for position-specific carbon isotope analysis of complex organics; and (2) well-established tools for performing quantitative compositional analysis of complex organic mixtures. By utilizing samples relevant to astrobiology, specifically the amino acid valine and analogue mixtures of organics, we showcase that molecules retain a source dependent and distinct intramolecular carbon isotope fingerprint. We demonstrate that compositional sample analysis provides an independent and complementary line of evidence pointing towards the origin of a molecule or mixture. Together, these NMR tools have the potential to support life detection efforts, and aid in distinguishing between biotic and abiotic samples. Finally, we discuss sensitivity, detection limits, the portability of NMR, and propose how integration with mass-spectrometry techniques will be imperative to enable more targeted and comprehensive analyses relevant to astrobiology, including in-situ analysis but also sample return missions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Predictive Chemical Kinetic Modeling: Where We Succeed, Where We Struggle, and What Comes Next

Chemical kinetic modeling plays a foundational role in fields ranging from energy to environmental science, pharmaceuticals, and advanced materials. The past two decades have seen remarkable progress, particularly in modeling gas-phase reactions for thermochemical processes, leading to impactful industrial applications such as steam cracking and air quality management. However, new challenges are emerging. The successful development of systematic methodologies for the description of gas-phase kinetics opens the possibility to apply the same approach to the study of more challenging systems. Here, we review recent advances, including ab initio transition state theory-based master equation estimation of elementary rates, automated mechanism generation, machine-learning-assisted kinetics, and uncertainty quantification, and discuss the advances needed to apply the same methodological approach in areas such as heterogeneous catalysis, electrochemistry, liquid-phase and solid-state reactivity, and multiscale model integration. We advocate for the development of targeted tools, especially methods that go beyond empirical tuning toward first-principles-based predictions. We highlight the need for accessible software and AIaugmented workflows to democratize modeling for industry and academia alike. In this perspective, we call attention to not only what has worked but also what remains unsolved, advocating to avoid overemphasizing successes in scientific works at the expense of realism. The next decade should focus on predictive capability, physical accuracy, and community infrastructure (e.g., databases and services) to enable innovation across diverse fields. We argue that kinetic modeling, properly equipped, can accelerate discovery far beyond its traditional domains.

ab initio calculations↗

Analysis of heat transfer and AuNPs-mediated photo-thermal inactivation of E. coli at varying laser powers using single-phase CFD modeling

In the wake of the COVID-19 pandemics, the demand for innovative and effective methods of bacterial inactivation has become a critical area of research, providing the impetus for this study. The purpose of this research is to analyze the AuNPs-mediated photothermal inactivation of E. coli. Gold nanoparticles irradiated by laser represent a promising technique for combating bacterial infection that combines high-tech and scientific progress. The intermediate aim of the work was to present the calibration of the model with respect to the gold nanorods experiment. The purpose of this work is to study the effect of initial concentration of E. coli bacteria, the design of the chamber and the laser power on heat transfer and inactivation of E. coli bacteria. Using the CFD simulation, the work combines three main concepts. 1. The conversion of laser light to heat has been described by a combination of three distinctive approximations: a- Discrete particle integration to take into account every nanoparticle within the system, b- Rayleigh-Drude approximation to determine the scattering and extinction coefficients and c- Lambert–Beer–Bourger law to describe the decrease in laser intensity across the AuNPs. 2. The contribution of the presence of E. coli bacteria to the thermal and fluid-dynamic fields in the microdevice was modeled by single-phase approach by determining the effective thermophysical properties of the water-bacteria mixture. 3. An approach based on a temperature threshold attained at which bacteria will be inactivated, has been used to predict bacterial response to temperature increases. The comparison of the thermal fields and temporal temperature changes obtained by the CFD simulation with those obtained experimentally confirms the accuracy of the light-heat conversion model derived from the aforementioned approximations. The results show a linear relationship between maximum temperature and variation in laser power over the range studied, which is in line with previous experimental results. It was also found that the temperature inside the microchamber can exceed 55 °C only when a laser power higher than 0.8 W is used, so bacterial inactivation begins. The experimental data allows to determinate the concentration of nanoparticles. This parameter is introduced into the mathematical model obtaining the same number of AuNPs. However, this assumption introduces a certain simplification, as in the mathematical model the distribution of nanoparticles is uniform. This work is directly connected to the use of gold nanoparticles for energy conversion, as well as the field of bacterial inactivation in microfluidic systems such as lab-on-a-chip. Presented mathematical and numerical models can be extended to the entire spectrum of wavelengths with particular use of white light in the inactivation of bacteria. This work represents a significant advancement in the field, as to the best of the authors’ knowledge, it is the first to employ a single-phase computational fluid dynamics (CFD) approach specifically combined with the thermal inactivation of bacteria. Moreover, this research pioneers the use of a numerical simulation to analyze the temperature threshold of photothermal inactivation of E. coli mediated by gold nanorods (AuNRs). The integration of these methodologies offers a new perspective on optimizing bacterial inactivation techniques, making this study a valuable contribution to both computational modeling and biomedical applications.

36 MATERIALS SCIENCE↗

Distributed Cross-Channel Hierarchical Aggregation for Foundation Models

Vision-based scientific foundation models hold significant promise for advancing scientific discovery and innovation. This potential stems from their ability to aggregate images from diverse sources—such as varying physical groundings or data acquisition systems—and to learn spatio-temporal correlations using transformer architectures. However, tokenizing and aggregating images can be compute-intensive, a challenge not fully addressed by current distributed methods. In this work, we introduce the Distributed Cross-Channel Hierarchical Aggregation (D-CHAG) approach designed for datasets with a large number of channels across image modalities. Our method is compatible with any model-parallel strategy and any type of vision transformer architecture, significantly improving computational efficiency. We evaluated D-CHAG on hyperspectral imaging and weather forecasting tasks. When integrated with tensor parallelism and model sharding, our approach achieved up to a 75% reduction in memory usage and more than doubled sustained throughput on up to 1,024 AMD GPUs on the Frontier Supercomputer.

Tsaris, Aristeidis (aris) [ORNL] (ORCID:0000000277↗

Feasibility of a Novel Density Functional Method Outside the Kohn-Sham Framework for Modeling Global Potential Energy Surfaces of Molecular Chemical Reactions (Final Technical Report)

The project aimed towards the construction of computational methods capable of modeling the global potential energy surface (PES) of small molecules, molecular ions, and radicals — including the parts of the PES which correspond to chemical reactions, and the reaction paths connecting reactants, intermediates, and reaction products. This goal may seem humble at first glance, but for chemical systems with more than about six atoms in total, at the time the project was proposed, there were no established theoretical methods capable of simulating such systems reliably, not even for small molecules in the gas phase which are electronically benign. This restriction severely hampers our ability to model and control chemical processes under harsh conditions. With the goal of constructing a method capable of modeling such chemical systems, we proposed to pursue a novel approach towards a Multi-Configuration (MC) DFT outside the traditional frameworks of Kohn-Sham theory and other methods of coupling wave function theory with DFT. Rather than being a complete active space (CAS) method, the proposed DOCI-DFT would employ a special restricted form of the active space wave function, called Doubly-Occupied CI (DOCI)—this wave function form is sufficient to describe not only heterolytic, but also homolytic bond dissociation processes at the zeroth order (i.e., as active space wave function). There are no other standard mean field methods which can do so. In the original proposal, we also outlined strong formal and practical arguments speaking for this method. The project proposal was accepted by the Department of Energy and provided two years of seed funding for one graduate student, as well as two years of two weeks PI summer-salary for the PI. However, ultimately the project could not be effectively pursued due to severe interferences outside the context scientific problems and was cancelled. Apart from two weeks of PI salary (and associated fringe & overhead costs issues by the performing institution), no costs were charged against the award, with the entire rest of funding returned to the Department of Energy. This report reiterates the primary background information regarding the project, its original goals, and outlines the preliminary work performed during the two weeks of DOE funding charged.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-phenomenology Yield Characterization

This report serves as the first delivery of a four-year applied science effort to transform and advance the error bounds for the yield estimate of an explosion. Each year’s delivery will be in this form, culminating in the submission of this work for peer review to a scientific journal. Importantly, the yearly progress reports can then also be viewed as expanding drafts working towards a formal journal article submission. For the first tranche of funding, we collaborated with Air Force Technical Applications Center (AFTAC) scientists to identify unclassified real-world data that demonstrate and validate our advanced error propagation methods. Collaboration includes visits to AFTAC and telecons. For this development, we illustrate the fusion of seismic, acoustic, optical, and surface effect signatures from an explosion. The mathematics and code being adapted to this specific application (Williams et al., 2021) involves physics models of multiple sensor signatures. We have also identified related physics models and have integrated them into code. Current methods of underground explosion yield estimation for the Threshold Test Ban Treaty (TTBT) have served the US treaty monitoring mission well for decades. A research objective of the Defense Nuclear Nonproliferation Research and Development (DNN R&D) office of the National Nuclear Security Administration (NNSA) has always been to provide new technical capabilities for monitoring lower thresholds. The general model and error propagation code to be developed in this project is based on significant advances in error modeling and propagation needed to analyze data at lower detection thresholds. The second tranche of funding for this project began on May 1, 2022, and planned work for the second tranche includes: i) completing the integration of physical model code into the general error model framework; this code accommodates a wide range of linear/nonlinear source models, fixed/ random effects, and frequentist/Bayesian analyses (the purpose of which is not to dictate to users how to analyze data, but instead to allow users the maximum flexibility in their work); ii) illustrative application of code to identified data, and; iii) initial planning with AFTAC researchers on delivery of code to the Common Development Environment at AFTAC, and continued writing of the planned final journal article submission (year two of this progress report), with particular emphasis on descriptions of data identified for this effort.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Tokamak Disruption Simulation (Final Technical Report)

The Tokamak Disruption Simulation collaboration was a SciDAC (Scientific Discovery through Advanced Computing) program led by Xianzhu Tang of the Los Alamos National Laboratory but with separate grants to each institution. I was the PI for Columbia University and the only person at Columbia directly funded by this SciDAC. Disruptions are a sudden loss of confinement in tokamaks, and a reliable method of preventing disruptions must be developed before tokamak fusion power plants become feasible. A related plasma confinement concept, the stellarator, is the only way known way of preventing disruptions with the required reliability. The largest devices, both existing and under construction, for confining plasmas for fusion using magnetic fields are tokamaks, so it is important to solve their disruption issues. The sudden loss of confinement in tokamaks can be from a bit of material falling into the plasma, which causes the plasma energy to be quickly lost by radiation, or by an instability causing a breakup of the confining surfaces formed by the magnetic field. This breakup can occur more than a million times faster than one would naively think possible. The sudden breakup of surfaces is called a fast magnetic reconnection and also results in a sudden cooling of the plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Operator inference for non-intrusive model reduction of systems with non-polynomial nonlinear terms

Here in this work we present a non-intrusive model reduction method to learn low-dimensional models of dynamical systems with non-polynomial nonlinear terms that are spatially local and that are given in analytic form. In contrast to state-of-the-art model reduction methods that are intrusive and thus require full knowledge of the governing equations and the operators of a full model of the discretized dynamical system, the proposed approach requires only the non-polynomial terms in analytic form and learns the rest of the dynamics from snapshots computed with a potentially black-box full-model solver. The proposed method learns operators for the linear and polynomially nonlinear dynamics via a least-squares problem, where the given non-polynomial terms are incorporated on the right-hand side. The least-squares problem is linear and thus can be solved efficiently in practice. The proposed method is demonstrated on three problems governed by partial differential equations, namely the diffusion–reaction Chafee–Infante model, a tubular reactor model for reactive flows, and a batch-chromatography model that describes a chemical separation process. The numerical results provide evidence that the proposed approach learns reduced models that achieve comparable accuracy as models constructed with state-of-the-art intrusive model reduction methods that require full knowledge of the governing equations.

42 ENGINEERING↗

Autonomous alloy composition optimization using molecular dynamics guided by a large language model

Here, we present an autonomous materials discovery framework that couples a large language model (LLM) with molecular dynamics (MD) simulations to optimize Fe–Cr–Mn alloy compositions for tensile strength. Starting from six distinct compositions, the LLM operated as an intelligent agent, iteratively proposing changes based on prior simulation results and constraints. Over 50 iterations per case, the LLM adaptively explored the composition space, identifying high-strength regions, not easily accessible by conventional methods. The highest strength, 18.7 GPa, was achieved with Fe 71 Cr 25 Mn 4 composition, identified from a Fe 75 Cr 20 Mn 5 starting point. The LLM autonomously adjusted its strategy in real time, demonstrating closed-loop decision-making using commodity hardware. This approach showcases the potential of LLMs as scientific co-pilots, capable of accelerating materials discovery and generalizable to other domains like biology and drug design.

Autonomy↗

Robust estimation of charge carrier diffusivity using transient photoluminescence microscopy

Transient microscopy has emerged as a powerful tool for imaging the diffusion of excitons and free charge carriers in optoelectronic materials. In many excitonic materials, extraction of diffusion coefficients can be simplified because of the linear relationship between signal intensity and local excited state population. However, in materials where transport is dominated by free charge carriers, extracting diffusivities accurately from multidimensional data is complicated by the nonlinear dependence of the measured signal on the local charge carrier density. To obtain accurate estimates of charge carrier diffusivity from transient microscopy data, statistically robust fitting algorithms coupled to efficient 3D numerical solvers that faithfully relate local carrier dynamics to raw experimental measurables are sometimes needed. Here, we provide a detailed numerical framework for modeling the spatiotemporal dynamics of free charge carriers in bulk semiconductors with significant solving speed reduction and for simulating the corresponding transient photoluminescence microscopy data. To demonstrate the utility of this approach, we apply a fitting algorithm using a Markov chain Monte Carlo sampler to experimental data on bulk CdS and methylammonium lead bromide (MAPbBr 3 ) crystals. Parameter analyses reveal that transient photoluminescence microscopy can be used to obtain robust estimates of charge carrier diffusivities in optoelectronic materials of interest, but that other experimental approaches should be used for obtaining carrier recombination constants. Additionally, simplifications can be made to the fitting model depending on the experimental conditions and material systems studied. Our open-source simulation code and fitting algorithm are made freely available to the scientific community.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On Transfer Learning Of Neural Networks Using Bi-Fidelity Data For Uncertainty Propagation

Due to their high degree of expressiveness, neural networks have recently been used as surrogate models for mapping inputs of an engineering system to outputs of interest. Once trained, neural networks are computationally inexpensive to evaluate and remove the need for repeated evaluations of computationally expensive models in uncertainty quantification applications. However, given the highly parameterized construction of neural networks, especially deep neural networks, accurate training often requires large amounts of simulation data that may not be available in the case of computationally expensive systems. In this paper, to alleviate this issue for uncertainty propagation, we explore the application of transfer learning techniques using training data generated from both high- and low-fidelity models. We explore two strategies for coupling these two datasets during the training procedure, namely, the standard transfer learning and the bi-fidelity-weighted learning. In the former approach, a neural network model mapping the inputs to the outputs of interest is trained based on the low-fidelity data. The high-fidelity data are then used to adapt the parameters of the upper layer(s) of the low-fidelity network, or train a simpler neural network to map the output of the low-fidelity network to that of the high-fidelity model. In the latter approach, the entire low-fidelity network parameters are updated using data generated via a Gaussian process model trained with a small high-fidelity dataset. The parameter updates are performed via a variant of stochastic gradient descent with learning rates given by the Gaussian process model. Using three numerical examples, we illustrate the utility of these bi-fidelity transfer learning methods where we focus on accuracy improvement achieved by transfer learning over standard training approaches.

97 MATHEMATICS AND COMPUTING↗

Lost in transduction: Critical considerations when using viral vectors

The application of retroviral vectors in the laboratory requires considerations that often go overlooked but are often easy to circumvent. Here, we discuss the relationship between the observed transduction efficiency of a cell population and per-cell viral insertions—and describe how differential cell-type susceptibilities can confound results. We consider the math underlying this problem and review an alternative approach to the commonly used “multiplicity of infection” (MOI) method of titering and using viral vectors in the biomedical research laboratory.

59 BASIC BIOLOGICAL SCIENCES↗

Computational Math Problems for a Clean Energy Future

Cutting edge computational mathematics are ubiquitous in renewable energy research. Problems in resilient and reliable electric grid operations, infrastructure planning, wind farm yaw control, and more demand sophisticated and scalable computational tools that enable the transition of renewable energy technologies from proof of concept to deployment into our energy system. The mission of the Computational Science Center at NREL is to lead the lab's efforts to solve energy challenges using high-performance computing (HPC), computational science, applied mathematics, scientific data management, visualization, and informatics. In this poster, we provide a short overview of three areas of computational mathematics research at NREL: wind power scenario generation for stochastic grid operations and infrastructure planning, improved rational function approximations for electromagnetic transients codes, and wind farm yaw control using a combination of the Alternating Direction Method of Multipliers (ADMM) and reinforcement learning (RL). Increasing penetrations of renewable energy into power grids motivate the investigation of new approaches to characterizing uncertainty for five-minute economic dispatch problems. Similarly, as the penetration of distributed energy resources on power grids increases, it becomes important to revisit our methods of modelling transient phenomena, i.e. electromagnetic transients programs. Finally, the combination of ADMM and RL for wind farm yaw control presented here can potentially increase the efficiency of the deployed distributed controllers by orders of magnitude.

ADMM↗

Prescreening-Based Subset Selection for Improving Predictions of Earth System Models With Application to Regional Prediction of Red Tide

We present the ensemble method of prescreening-based subset selection to improve ensemble predictions of Earth system models (ESMs). In the prescreening step, the independent ensemble members are categorized based on their ability to reproduce physically-interpretable features of interest that are regional and problem-specific. The ensemble size is then updated by selecting the subsets that improve the performance of the ensemble prediction using decision relevant metrics. We apply the method to improve the prediction of red tide along the West Florida Shelf in the Gulf of Mexico, which affects coastal water quality and has substantial environmental and socioeconomic impacts on the State of Florida. Red tide is a common name for harmful algal blooms that occur worldwide, which result from large concentrations of aquatic microorganisms, such as dinoflagellate Karenia brevis, a toxic single celled protist. We present ensemble method for improving red tide prediction using the high resolution ESMs of the Coupled Model Intercomparison Project Phase 6 (CMIP6) and reanalysis data. The study results highlight the importance of prescreening-based subset selection with decision relevant metrics in identifying non-representative models, understanding their impact on ensemble prediction, and improving the ensemble prediction. These findings are pertinent to other regional environmental management applications and climate services. Additionally, our analysis follows the FAIR Guiding Principles for scientific data management and stewardship such that data and analysis tools are findable, accessible, interoperable, and reusable. As such, the interactive Colab notebooks developed for data analysis are annotated in the paper. This allows for efficient and transparent testing of the results’ sensitivity to different modeling assumptions. Moreover, this research serves as a starting point to build upon for red tide management, using the publicly available CMIP, Coordinated Regional Downscaling Experiment (CORDEX), and reanalysis data.

54 ENVIRONMENTAL SCIENCES↗

Forte: A suite of advanced multireference quantum chemistry methods

Software development plays a critical role in advancing quantum chemistry, enabling the exploration of new fundamental theoretical ideas and modeling systems of ever-increasing complexity. In the past decade, the availability of quantum chemistry packages that use modular designs and provide application programming interfaces (APIs) has enabled the creation of specialized software plugins, enhancing the capabilities of the original codes. Here, the availability of well-documented APIs is particularly beneficial in the context of academic scientific software development because it reduces the entry barrier for new developers and shields them from the complexities of large software projects.

74 ATOMIC AND MOLECULAR PHYSICS↗

Optimal Transport as a Tool for Scientific Discovery in Radiation Biology

This report summarizes findings from research conducted for the “Exploration of the Poten tial for Artificial Intelligence and Machine Learning to Advance Low-Dose Radiation Biology Re search” (RadBio-AI) program, supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, under Awards KP1601011/FWP CC121 and KP1601017/FWP CC121. The research reported here was undertaken in an effort to assess the potential of optimal measure transport methods as components within the larger scope of a com putational framework envisioned to support research in the radiation biology domain. Within this effort, our interest centered on enabling a unified generic framework where probabilistic modeling, inference, and statistical learning can be carried out for a wide range of data distributions. As described next in Section 1 (and in more detail in our original publication), optimal measure transport offers the possibility of such unified approach.

97 MATHEMATICS AND COMPUTING↗