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At least 307 records · Page 17

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.

60 APPLIED LIFE SCIENCES↗

Machine learning bridges local static structure with multiple properties in metallic glasses

A long-standing challenge in the metallic glass (MG) community has been how to quantitatively gauge the influence of the intricate local packing environment on the response (such as the propensity for atomic rearrangement) of the atomic configuration to external stimuli. Here we establish this structure–property relation by representing the complex amorphous structure using a single, flexibility-orientated structural quantity. This structural flexibility (SF) couples to a bona fide structural representation, the pair distribution function (PDF) of individual atoms, through a weighting function that reflects what matters in the static atomic configuration to dynamic responses. Machine learning is used, employing microscopic flexibility volume as the supervisory signal, to establish via direct regression an optimized weighting vector, which is proven robust for all quenching rates, deformation conditions, and different compositions in a given (e.g., Cu x Zr 100-x ) alloy system. Additionally, the SF is evaluated solely from the particle positions (PDF), for any structure variation, from the atomic scale up to sample average. Strong correlations are demonstrated between SF and a broad range of properties, including vibrational, diffusional, as well as elastic and plastic relaxation responses.

36 MATERIALS SCIENCE↗

Challenges and Vision for Standardization of Biopolymer Data Sets for Machine Learning

Machine learning (ML) is transforming materials research, yet potential for biopolymer discovery remains constrained by fragmented data and nonstandardized reporting. Biopolymers differ significantly from synthetic polymers, requiring specialized approaches to represent their biosynthetic origins, hierarchical structures, and application-specific metrics. In this Perspective, we identify three core challenges limiting biopolymer representation: information encoding, data quality, and data sharing. We describe the most pressing issues and propose commensurate approaches to address each key challenge. Recommendations include the design and adoption of biopolymer-specific fingerprinting and representation frameworks, development of hybrid human-large language model (LLM) data extraction strategies, and expanding Findable, Accessible, Interoperable, Reusable (FAIR)-compliant repositories. We propose a robust foundation to define interoperable, high-quality data sets that capture the full context of biopolymer materials. Standardized metadata, shared ontologies, and community-driven infrastructure would enable scalable, reproducible workflows and accelerate the ML-driven development of biopolymers.

36 MATERIALS SCIENCE↗

B56$δ$ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan’s syndrome mutations

Intrinsically disordered regions (IDR) and short linear motifs (SLiMs) play pivotal roles in the intricate signaling networks governed by phosphatases and kinases. B56δ (encoded by PPP2R5D) is a regulatory subunit of protein phosphatase 2A (PP2A) with long IDRs that harbor a substrate-mimicking SLiM and multiple phosphorylation sites. De novo missense mutations in PPP2R5D cause intellectual disabilities (ID), macrocephaly, Parkinsonism, and a broad range of neurological symptoms. Our single-particle cryo-EM structures of the PP2A-B56δ holoenzyme reveal that the long, disordered arms at the B56δ termini fold against each other and the holoenzyme core. This architecture suppresses both the phosphatase active site and the substrate-binding protein groove, thereby stabilizing the enzyme in a closed latent form with dual autoinhibition. The resulting interface spans over 190 Å and harbors unfavorable contacts, activation phosphorylation sites, and nearly all residues with ID-associated mutations. Our studies suggest that this dynamic interface is coupled to an allosteric network responsive to phosphorylation and altered globally by mutations. Furthermore, we found that ID mutations increase the holoenzyme activity and perturb the phosphorylation rates, and the severe variants significantly increase the mitotic duration and error rates compared to the normal variant.

59 BASIC BIOLOGICAL SCIENCES↗

CMIP6-based Dynamically Downscaled Hydroclimate Projection over the Conterminous US

This dataset presents a suite of downscaled hydro-climate projections over the conterminous United States (CONUS) based on multiple selected Global Climate Models (GCMs) from the Coupled Models Intercomparison Project phase 6 (CMIP6). The CMIP6 GCMs are downscaled dynamically using Regional Climate Model version 4 (RegCM4). Each ensemble member covers the 1980-2019 baseline and 2020-2059 near-future periods under the high-end (SSP585) emission scenario. This dataset is formulated to support the SECURE Water Act Section 9505 Assessment for the US Department of Energy (DOE) Water Power Technologies Office (WPTO). For further details on this dataset, please refer to Kao et al. (2022) and Rastogi et al. (2022).

13 HYDRO ENERGY↗

Evaluation of the Lawrence Livermore Microbal Detection Array at the Statens Serum Institut

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Statens Serum Institut to evaluate and transition the Lawrence Livermore Microarray Detection Array (LLMDA) analysis software package, the Composite Likelihood Maximization method (CLiMax) to the SSI. The SSI is a public enterprise under the Danish Ministry of Health that operates a microbiology reference laboratory for the Danish population and analyzes tens to thousands of human clinical samples annually. SSI has been collaborating with the LLNL team for several years to use the LLMDA to analyze viral and bacterial infections from human clinical samples. The collaboration has resulted in two joint publications thus far, describing improvements to LLMDA sample preparation, and the utility of the LLMDA for detecting emerging viruses in clinical samples.

59 BASIC BIOLOGICAL SCIENCES↗

Science and Technology Review June 2021

When the COVID-19 pandemic hit, Lawrence Livermore National Laboratory scientists came together, leveraging many different disciplines and technologies to address this global challenge. Livermore focused on three areas of research: creating alternatives for medical equipment in short supply, such as ventilators and nasal swabs; developing methods to help detect the SARS-CoV-2 virus responsible for COVID-19; and designing medical countermeasures such as antibodies and antivirals to combat the disease.

36 MATERIALS SCIENCE↗

WiDS Livermore Datathon 2025

The WiDS Datathon 2025 requires participants to build a model to predict both an individual’s sex and their ADHD diagnosis using functional brain imaging data of children and adolescents and their socio-demographic, emotions, and parenting information. The task is to create a multi-outcome model to predict two target variables: 1) ADHD (1=yes or 0=no) and 2) female (1=yes or 0=no).

59 BASIC BIOLOGICAL SCIENCES↗

FY24 LLNL Laboratory Directed Research and Development (LDRD) Project Accomplishments

Large duration energy storage is the key to couple renewable energy generation with power supply. This project aimed to advance the durability of a low-cost and eco-friendly flow battery technology based on iron chemistry to speed up the technology readiness level rapidly and radically. A novel device which is called “an artificial kidney” was innovated through disruptive research to integrate with the flow battery for rebalancing capacity. Key results at 50 cm2 scale demonstrates that artificial kidney enabled retaining the storage capacity of the flow battery over 100 cycles. Comparison of outcome of this work showing 0% capacity degradation to the state-of-the-art technology corroborates that this novel system is a game changing innovation.

99 GENERAL AND MISCELLANEOUS↗

Deep learning symmetries and their Lie groups, algebras, and subalgebras from first principles

Abstract We design a deep-learning algorithm for the discovery and identification of the continuous group of symmetries present in a labeled dataset. We use fully connected neural networks to model the symmetry transformations and the corresponding generators. The constructed loss functions ensure that the applied transformations are symmetries and the corresponding set of generators forms a closed (sub)algebra. Our procedure is validated with several examples illustrating different types of conserved quantities preserved by symmetry. In the process of deriving the full set of symmetries, we analyze the complete subgroup structure of the rotation groups SO (2), SO (3), and SO (4), and of the Lorentz group S O ( 1 , 3 ) . Other examples include squeeze mapping, piecewise discontinuous labels, and SO (10), demonstrating that our method is completely general, with many possible applications in physics and data science. Our study also opens the door for using a machine learning approach in the mathematical study of Lie groups and their properties.

97 MATHEMATICS AND COMPUTING↗

Optimizing the hypre solver for manycore and GPU architectures

The solution of large-scale combustion problems with codes such as Uintah on modern computer architectures requires the use of multithreading and GPUs to achieve performance. Uintah uses a low-Mach number approximation that requires iteratively solving a large system of linear equations. The Hypre iterative solver has solved such systems in a scalable way for Uintah, but the use of OpenMP with Hypre leads to at least slowdown due to OpenMP overheads. The proposed solution uses the MPI Endpoints within Hypre, where each team of threads acts as a different MPI rank. This approach minimizes OpenMP synchronization overhead and performs as fast or (up to 1.44) faster than Hypre's MPI-only version, and allows the rest of Uintah to be optimized using OpenMP. The profiling of the GPU version of Hypre shows the bottleneck to be the launch overhead of thousands of micro-kernels. The GPU performance was improved by fusing these micro-kernels and was further optimized by using Cuda-aware MPI, resulting in an overall speedup of 1.16—1.44 compared to the baseline GPU implementation. The above optimization strategies were published in the International Conference on Computational Science 2020 [1]. This work extends the previously published research by carrying out the second phase of communication-centered optimizations in Hypre to improve its scalability on large-scale supercomputers. Additionally, this includes an efficient non-blocking inter-thread communication scheme, communication-reducing patch assignment, and expression of logical communication parallelism to a new version of the MPICH library that utilizes the underlying network parallelism [2]. The above optimizations avoid communication bottlenecks previously observed during strong scaling and improve performance by up to 2 on 256 nodes of Intel Knight's Landing processor.

97 MATHEMATICS AND COMPUTING↗

Metastable Materials Discovery in the Age of Large-Scale Computation

Computational materials discovery has been successful in predicting novel, technologically relevant materials. However, it has remained focused almost exclusively on finding ground-state structures. Now that the lower-hanging fruit has been found in many fields of application, materials exploration is moving toward metastable materials: higher energy phases that are stable at practical time scales. Because of the challenges associated with predicting which phases are realistic, this class of materials has remained relatively unexplored, despite numerous examples of metastable structures with unmatched properties (e.g., diamond). This article highlights recent advances in developing computational and theoretical methods for predicting useful and realizable metastable materials. Topics discussed cover (1) the latest strategies for identifying potential metastable phases, (2) methodologies for assessing which phases can be realized experimentally, and (3) current approaches to estimate the lifetime of metastable materials.

amorphous materials↗

Solving the Bernstein-Vazirani problem using Majorana-based topological quantum algorithms

Executing quantum algorithms using Majorana zero modes—a major milestone for the field of topological quantum computing—requires a platform that can be scaled to large quantum registers, can be controlled in real time and space, and a braiding protocol that uses the unique properties of these exotic particles. Here, we demonstrate the first successful simulation of a Majorana-based, fault-tolerant quantum algorithm to solve the Bernstein-Vazirani problem in two-dimensional magnet-superconductor hybrid structures from initialization to read-out of the final many-body state. Utilizing the Majorana zero modes’ topological properties, we introduce an optimized braiding protocol for the algorithm and a scalable architecture for its implementation with an arbitrary number of qubits. We visualize the algorithm protocol in real time and space by computing the non-equilibrium density of states, which is proportional to the time-dependent differential conductance, and the non-equilibrium charge density, which assigns a unique signature to each final state of the algorithm.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quantum Computing Market Report

The quantum computing market is entering a rapid growth phase. Growth was originally driven by private investment interest in high value applications such as drug discovery, materials science, and finance. Currently the main market drivers include technical advances, continued private investment, and rising public funding. The quantum computing market is poised for explosive growth — with its market size estimated at $1.42 billion USD in 2024, and an expected compound annual growth rate of 20.5% from 2025 to 2030 [4]. Superconducting qubits are the largest qubit type by revenue. However, alternative approaches such as trapped ion, neutral atom, spin based, and photonic qubits are also attracting investment.

97 MATHEMATICS AND COMPUTING↗

Fast and Accurate Intersections on a Sphere

We introduce a fast, high-precision algorithm for calculating intersections between great circle arcs and lines of constant latitude on the unit sphere. We first propose a simplified intersection point formula with improved speed and numerical robustness over the ones traditionally implemented in geoscience software. We then show how algorithms based on the concept of error-free transformations (EFT) can be applied to evaluate this formula within a relative error bound that is on the order of machine precision. Here, we demonstrate that, with a vectorized and parallelized implementation, this enhanced accuracy is achieved with no compute time overhead compared to a direct calculation in hardware floating point, making our algorithm suitable for performance-sensitive applications like regridding of high-resolution climate data. In contrast, evaluating our formula using high-precision data types like quadruple precision and arbitrary precision, or using the robust intersection computation routines from the Computational Geometry Algorithms Library, leads to significant computational overhead, especially since these alternatives inhibit vectorization. More generally, our work demonstrates how EFT techniques can be combined and extended to implement nontrivial geometric calculations with high accuracy and speed.

Environmental sciences↗

UMap: An application-oriented user level memory mapping library

Exploiting the prominent role of complex memories in exascale node architecture, the UMap page fault handler offers new capabilities to access large memory-mapped data sets directly. UMap provides flexible configuration options to customize page handling to each application, including analysis of massive observational and simulation data sets. The high-performance design features I/O decoupling, dynamic load balancing, and application-level controls. Page faults triggered by application threads and processes accessing data mapped to a UMapp’ed region are handled via the Linux userfaultfd protocol, an asynchronous message-oriented kernel-user communication mechanism that avoids the context switch penalty of traditional signal fault handlers. UMap is fully open source. In this paper, we give an overview of the UMap library architecture, its extensible plugin architecture, and the use/performance of UMap in emerging heterogeneous memory hierarchies such as near-node Non-volatile Memory (NVM) and network attached memories. We highlight new capabilities in two pagefault management plugins, the NetworkStore and SparseStore. We demonstrate the integration between UMap and multiple ECP products including Caliper, Metall, ZFP, Mochi, and Ripples.

97 MATHEMATICS AND COMPUTING↗