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At least 775 records · Page 43

Multimodal Approaches for Leveraging Domain Knowledge with State-of-the-Art Machine Learning to Engineer Biocatalysts

This grant aimed to accelerate the development of specialized enzymes—biological catalysts essential for sustainable manufacturing and medicine—by integrating traditional laboratory evolution with cutting-edge artificial intelligence. To achieve this, we developed a suite of high-throughput sequencing tools and a centralized database to bridge the gap between a protein’s genetic "code" and its physical function. By training machine learning models on large datasets, we also demonstrated the ability to move beyond slow, trial-and-error testing to a "generative" approach, where AI can independently design new, versatile enzymes like tryptophan synthases. Ultimately, these findings demonstrate that combining laboratory data with computer-guided design enables the engineering of highly efficient biological tools with unprecedented speed and precision.

59 BASIC BIOLOGICAL SCIENCES↗

A parallel and performance portable implementation of a full-field crystal plasticity model

We have developed a parallel implementation of an Elasto-Viscoplastic Fast Fourier Transform-based (EVPFFT) micromechanical solver to enable computationally efficient crystal plasticity modeling for polycrystalline materials. Our primary focus lies in achieving performance portability, allowing a single EVPFFT implementation to run optimally on various homogeneous architectures, including multi-core Central Processing Units (CPUs), as well as on heterogeneous computer architectures comprising multi-core CPUs and Graphics Processing Units (GPUs) from different vendors. To accomplish this goal, we have leveraged MATAR, a C++ software library that simplifies the creation and utilization of multidimensional dense or sparse matrix and array data structures. These data structures are designed to be portable across diverse architectures through the use of Kokkos, a performance-portable library. Additionally, we have employed the Message Passing Interface (MPI) to efficiently distribute the computational workload among processors. The heFFTe (Highly Efficient FFT for Exascale) library is used to facilitate the performance portability of the fast Fourier transforms (FFTs) computation. The computational performance of EVPFFT is evaluated and presented in terms of parallel scalability and simulation runtime on different high-performance computing (HPC) architectures. As a result, the utility of the developed framework to efficiently simulate the micro-mechanical fields in polycrystalline microstructures in engineering applications is discussed.

36 MATERIALS SCIENCE↗

Comprehensive Material Characterization and Simultaneous Model Calibration for Improved Computational Simulation Credibility

Computational simulation is increasingly relied upon for high-consequence engineering decisions, and a foundational element to solid mechanics simulations is a credible material model. Our ultimate vision is to interlace material characterization and model calibration in a real-time feedback loop, where the current model calibration results will drive the experiment to load regimes that add the most useful information to reduce parameter uncertainty. The current work investigated one key step to this Interlaced Characterization and Calibration (ICC) paradigm, using a finite load-path tree to incorporate history/path dependency of nonlinear material models into a network of surrogate models that replace computationally-expensive finite-element analyses. Our reference simulation was an elastoplastic material point subject to biaxial deformation with a Hill anisotropic yield criterion. Training data was generated using either a space-filling or adaptive sampling method, and surrogates were built using either Gaussian process or polynomial chaos expansion methods. Surrogate error was evaluated to be on the order of 10 ⁻5 and 10 ⁻3 percent for the space-filling and adaptive sampling training data, respectively. Direct Bayesian inference was performed with the surrogate network and with the reference material point simulator, and results agreed to within 3 significant figures for the mean parameter values, with a reduction in computational cost over 5 orders of magnitude. These results bought down risk regarding the surrogate network and facilitated a successful FY22-24 full LDRD proposal to research and develop the complete ICC paradigm.

36 MATERIALS SCIENCE↗

ElasTool v3.0: Efficient computational and visualization toolkit for elastic and mechanical properties of materials

Efficient computation and visualization of elastic and mechanical properties are crucial in the selection of materials and the design of new materials. Here, the ElasTool v3.0 toolkit marks a significant advancement in the computational analysis and visualization of elastic and mechanical properties of materials, essential in material selection and design. This enhanced version extends beyond standard calculations like elastic tensor, Young's modulus, bulk modulus, and Poisson's ratio. It introduces capabilities for computing minimum thermal conductivity, linear compressibility, rendering the Christoffel equation, and elastic energy density. Notably, it integrates advanced visualization tools, including compatibility with Plotly and Elate web platforms for interactive web-based property exploration. A key feature of ElasTool v3.0 is the implementation of second-order elastic constants (SOECs) for tubular 2D-based nanostructures and nanotubes. Leveraging high-efficiency strain-matrix sets (OHESS), the toolkit now facilitates efficient computation of elastic constants and mechanical properties at both zero and finite temperatures for 1D, 2D, and 3D dimensions. ElasTool is openly accessible on GitHub: https://github.com/gmp007/elastool.

1D, 2D, 3D, and tubular 2D nanostructure and nanot↗

Online Machine Learning for Accelerating Molecular Dynamics Modeling of Cells

We developed a biomechanics-informed online learning framework to learn the dynamics with ground truth generated with multiscale modeling simulation. It was built on Summit-like supercomputers, which were also used to benchmark and validate our framework on one physiologically significant modeling of deformable biological cells. We generalized the century-old equation of Jeffery orbits to a new equation of motion with additional parameters to account for the flow conditions and the cell deformability. Using simulation data at particle-based resolutions for flowing cells and the learned parameters from our framework, we validated the new equation by the motions, mostly rotations, of a human platelet in shear blood flow at various shear stresses and platelet deformability. Our online framework, which surrogates redundant computations in the conventional multiscale modeling by solutions of our learned equation, accelerates the conventional modeling by three orders of magnitude without visible loss of accuracy.

multiscale modeling↗

Predicting metabolic modules in incomplete bacterial genomes with MetaPathPredict

The reconstruction of complete microbial metabolic pathways using ‘omics data from environmental samples remains challenging. Computational pipelines for pathway reconstruction that utilize machine learning methods to predict the presence or absence of KEGG modules in incomplete genomes are lacking. Here, we present MetaPathPredict, a software tool that incorporates machine learning models to predict the presence of complete KEGG modules within bacterial genomic datasets. Using gene annotation data and information from the KEGG module database, MetaPathPredict employs deep learning models to predict the presence of KEGG modules in a genome. MetaPathPredict can be used as a command line tool or as a Python module, and both options are designed to be run locally or on a compute cluster. Benchmarks show that MetaPathPredict makes robust predictions of KEGG module presence within highly incomplete genomes.

59 BASIC BIOLOGICAL SCIENCES↗

Hypernetwork Science: From Multidimensional Networks to Computational Topology

As data structures and mathematical objects used for complex systems modeling, hypergraphs sit nicely poised between on the one hand the world of network models, and on the other that of higher-order mathematical abstractions from algebra, lattice theory, and topology. They are able to represent complex systems interactions more faithfully than graphs and networks, while also being some of the simplest classes of systems representing topological structures as collections of multidimensional objects connected in a particular pattern. In this paper we discuss the role of (undirected) hypergraphs in the science of complex networks, and provide a mathematical overview of the core concepts needed for hypernetwork modeling, including duality and the relationship to bicolored graphs, quantitative adjacency and incidence, the nature of walks in hypergraphs, and available topological relationships and properties. We close with a brief discussion of two example applications: biomedical databases for disease analysis, and domain-name system (DNS) analysis of cyber data.

Joslyn, Cliff A.↗

A Co-Registered In-Situ and Ex-Situ Dataset from an Electron Beam Powder Bed Fusion Additive Manufacturing Process (Peregrine v2023-09)

This release contains a co-registered in-situ and ex-situ Peregrine dataset from a single Arcam Q10 Electron Beam Powder Bed Fusion (EB-PBF) Inconel 738 build. These data were collected at the Manufacturing Demonstration Facility (MDF) located at Oak Ridge National Laboratory (ORNL). The dataset includes layer-wise Near Infrared (NIR) in-situ imaging data, in-situ temporal sensor data, ex-situ X-Ray Computed Tomography (X-CT) scans, and the target part geometries. Additionally, anomaly detections produced by a trained Dynamic Segmentation Convolutional Neural Network (DSCNN) are provided.

36 MATERIALS SCIENCE↗

Modeling Tree Foliage for Microwave Radar Transparency Study

The motivation for this report is to discuss and present some realistic tree models employed in computational electromagnetics (EM) simulations to study foliage penetration (FOPEN) at Ku-band. The detail obtained in these trees is unprecedented in FOPEN modeling since many studies in this area focus on lower frequencies where precise tree parameters are not required due to the associated large wavelengths relative to the tree dimensions. The focus of this study is in the Ku-band range where the wavelength is notably smaller and the details of the trees have more of an influence on EM waves (i.e. scattering, attenuating, reflecting, diffracting etc.). Therefore, explicit tree parameters are modeled. Also, moderate foliage is of most interest because with less dense foliage t here is a higher percentage of Ku-band transmission. The EM wave and foliage interaction s are simulated with the computational electromagnetics (CEM) Altair FEKO software. The realistic tree model s implemented for simulations are created in the computer-aided design (CAD) software Arbaro and the module CADFEKO that is offered in FEKO. Details of these tree models are provided, and EM simulation results will be discussed in a follow-on report

59 BASIC BIOLOGICAL SCIENCES↗

FAIR Data and Interpretable AI Framework for Architectured Metamaterials

Our interdisciplinary effort successfully generated FAIR (Findable, Accessible, Interoperable, and Reusable) benchmark datasets for mechanical metamaterials while introducing a novel Artificial Intelligence (AI) framework known as Learning Refined Compositional Rules (LRCR). This framework was specifically designed to bridge the gap across varying computational length scales and extract the underlying physical mechanisms that connect a material's structural geometry to its bulk acoustic properties. Historically, the discovery of such structured materials relied heavily on human intuition or opaque, black-box optimization algorithms that were difficult to generalize. By combining interpretable machine learning techniques with rigorous experimental validation, this project established clear, generalizable design guidelines for tuning wave dispersion and controlling vibrations. Ultimately, the public availability of these structured datasets and algorithms will significantly reduce computational costs and accelerate the design of advanced multi-functional acoustic devices, offering broad societal impacts across fields like aerospace engineering, telecommunications, and biomedical implant design.

36 MATERIALS SCIENCE↗

Cooperative Research and Development Agreement With Georgetown University Report: National Institutes of Health, National Center for Advancing Translational Sciences Clinical and Translational Science Award

Oak Ridge National Laboratory (ORNL) is participating with Georgetown University (GU) as a subrecipient in response to the National Institutes of Health (NIH), National Center for Advancing Translational Sciences (NCATS) Clinical and Translational Science Award (CTSA) (U54 Clinical Trial Optional) funding opportunity announcement. This Cooperative Research and Development Agreement is put in to place to facilitate the development and implementation of clinical interventions that demonstrably improve human health is currently a complex, recursive, and inefficient process that leads to delays of years or decades before discoveries in biomedical research result in health benefits for patients and communities. NCATS conducts and supports research in the science of translation, to discover the mechanistic and operational principles of the intervention development and dissemination process, thereby providing the scientific foundation for improvements in translational efficiency that will accelerate the realization of interventions that improve human health. Under NCATS’ leadership, the CTSA Program supports a national network of medical research institutions called hubs. GU is the lead institution in one of the NIH hubs that was created as a result of a previous NIH CTSA. The missions of the GU have historically included the advancement of health through research in the clinical and biomedical sciences, the education of future leaders in medical and nursing practice and academia, and the provision of compassionate and scientifically competent patient care and service to the Washington, DC community and the nation. GU is the lead institution for the Georgetown-Howard Universities Center for Clinical and Translational Science (GHUCCTS), a multi-institutional partnership of medical research institutions forged from a desire to promote clinical research and translational science. Through multiple collaborations among these institutions, GHUCCTS is transforming clinical research and translational science in order to bring new scientific advances to health care. Oak Ridge National Laboratory is the Department of Energy's (DOE) largest science and energy laboratory. Managed since April 2000 by a partnership of the University of Tennessee and Battelle, ORNL was established in 1943 as a part of the secret Manhattan Project to pioneer a method for producing and separating plutonium. During the 1950s and 1960s, ORNL became an international center for the study of nuclear energy and related research in the physical and life sciences. With the creation of DOE in the 1970s, ORNL's mission broadened to include a variety of energy technologies and strategies. Today the laboratory supports the nation with a peacetime science and technology mission that is just as important as, but very different from, its role during the Manhattan Project. ORNL is home to the world's premier center for high performance supercomputing to enable scientific discovery. ORNL has extensive expertise in various areas of computer science that are uniquely situated to support GU. Additionally, ORNL’s leading computational user facilities present a unique opportunity to leverage the largest scale machines for open science in support of the stated mission of the NCATS CTSA. ORNL's partnership with GU will offer unparalleled opportunity in data analytics, deep-learning, artificial intelligence, and urban dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

PNNL OS3300 Alpha/Beta Monitoring System Software and Hardware Operations Manual (Rev.2)

The Pacific Northwest National Laboratory (PNNL) OS3300 Alpha/Beta Monitoring System Software and Hardware Operations Manual describes how to operate the software and hardware on a personal computer in conjunction with the Berthold Technologies LB150D continuous air monitor. Included are operational details for the software functions and information about how to read and use the dropdown menus and how to understand readings and calculations.

54 ENVIRONMENTAL SCIENCES↗

Exascale applications: skin in the game

As noted in Wikipedia, skin in the game refers to having ‘incurred risk by being involved in achieving a goal’, where ‘ skin is a synecdoche for the person involved, and game is the metaphor for actions on the field of play under discussion’. For exascale applications under development in the US Department of Energy Exascale Computing Project, nothing could be more apt, with the skin being exascale applications and the game being delivering comprehensive science-based computational applications that effectively exploit exascale high-performance computing technologies to provide breakthrough modelling and simulation and data science solutions. These solutions will yield high-confidence insights and answers to the most critical problems and challenges for the USA in scientific discovery, national security, energy assurance, economic competitiveness and advanced healthcare. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.

97 MATHEMATICS AND COMPUTING↗

A Finite Difference informed Random Walk solver for simulating radiation defect evolution in polycrystalline structures with strongly inhomogeneous diffusivity

Diffusivity of species and defects on grain boundaries is usually several orders of magnitude larger than that inside grains. Such strongly inhomogeneous diffusivity requires prohibitively high computational demands for modeling microstructural evolution. Here, this paper presents a highly-efficient numerical solver, combining the Finite Difference method and Random Walk model, designed for accurately modeling strongly inhomogeneous diffusion within polycrystalline structures. The proposed solver, termed Finite Difference informed Random Walk (FDiRW), integrates a customized Finite Difference (cFD) scheme tailored for fast diffusion along thin grain boundaries represented by a single-layer of nodes. Numerical experiments demonstrate that the FDiRW solver achieves an impressive efficiency gain of 1560x compared to traditional Finite Difference methods while maintaining accuracy, making it feasible for personal computer machines to handle diffusional systems with strongly inhomogeneous diffusivity across static polycrystalline microstructures. The model has been successfully applied to simulate radiation defect evolution, showcasing its scalability to engineering scales in both length and time dimensions.

36 MATERIALS SCIENCE↗

UT Austin's 2022 Sandia Day (Summary Report)

On March 30th and 31st, 2022, the University of Texas at Austin (UT) Office of the Vice President for Research (OVPR) hosted Sandia National Laboratories (Sandia) for “Sandia Day at UT Austin” to understand the status of the strategic partnership and explore opportunities for partnership growth. The event brought together more than 115 UT and Sandia participants including executive leadership, researchers, faculty, staff, and students. Sandia Day primarily consisted of a half-day leadership meeting, a research poster session and networking event, and three break-out sessions focused on strategic priority areas: Microelectronics, Energy and Climate Security, and High-Performance and Edge Computing. Appendix A contains the full Sandia Day agenda. Additional meetings and workshops (adjunct meetings) were held in conjunction with Sandia Day to maximize partnership exploration. Adjunct meetings were Hypersonics, Decarbonization, Disinformation, and Battery Workshops. A summary of Sandia Day events, sessions, and meetings follows.

42 ENGINEERING↗