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At least 487 records · Page 27

Binary pseudo-random array standards for calibration of 3D optical surface profilers used for metrology with significantly curved x-ray optics

High-accuracy metrology is vitally important in manufacturing ultra-high-quality free-form mirrors designed to manipulate X-ray light with nanometer-scale wavelengths. The current capabilities and possibility for improvements in X-ray mirror manufacturing are limited by inherent imperfections of the integrated metrology tools. In the case of Fizeau interferometry, metrology tools are currently calibrated with super-polished flat test-standard/reference mirrors. This is acceptable for measuring slightly curved X-ray optics. However, for even moderately curved aspherical X-ray mirrors the flat-reference calibration is not sufficiently accurate and stitching Fizeau interferometer-based surface metrology is used to mitigate the problem. But still, the retrace and aberration errors, as well as the limited spatial resolution, described with the instrument transfer function (ITF), can be transferred into the optical surface topography of X-ray mirrors obtained in stitching metrology. For ITF calibration, we have developed an original technique, based on test standards structured as two-dimensional (2D) highly-randomized (HR) binary pseudo-random arrays (BPRAs). The technique employs the unique properties of the HR BPRA patterns in the spatial frequency domain., i.e. the inherent 2D power spectral density of the HR BPRA pattern has a deterministic white-noise-like character that allows direct determination of the ITF with uniform sensitivity over the entire spatial frequency range and field-of-view of an instrument. Here, we explore technological, metrological, and analytical aspects essential for calibration of the retrace and aberration errors of Fizeau interferometers using different types of tilted test samples, including a super-polished reference mirror for the re-trace calibration and the uniformly redundant array (URA) BPRA standards for the geometrical distortion (aberration) calibration. While the first method was previously demonstrated by researchers at DIAMOND Light Source, a method based on the URA BPRA is described and demonstrated here for the first time. We outline the design and fabrication process used in fabrication of URA BPRA test standards, and present the results of application of the URA BPRA standards demonstrating the high efficacy of our approach to geometrical distortion calibration of Fizeau interferometers. We also discuss the possible sources of unexpected peculiarities of the systematic errors, including an astigmatic character of the retrace error, observed with Fizeau interferometers at the Advanced Light Source X-Ray Optics Laboratory.

Munechika, Keiko↗

BRCore: an R package implementing flexible selection of core taxa using contribution to Bray-Curtis dissimilarity and neutral model fitting

Identifying core taxa in microbial ecology highlights groups likely to participate in a broad range of potential ecological interactions. Here, we present BRCore, an R package to identify core taxa using abundance-occupancy distributions and beta-diversity contributions across ecological niches, and predict stochastic and deterministic taxa.

59 BASIC BIOLOGICAL SCIENCES↗

Polynomial Chaos Surrogate Construction for Random Fields with Parametric Uncertainty

Engineering and applied science rely on computational experiments to rigorously study physical systems. The mathematical models used to probe these systems are highly complex, and sampling-intensive studies often require prohibitively many simulations for acceptable accuracy. Surrogate models provide a means of circumventing the high computational expense of sampling such complex models. In particular, polynomial chaos expansions (PCEs) have been successfully used for uncertainty quantification studies of deterministic models where the dominant source of uncertainty is parametric. We discuss an extension to conventional PCE surrogate modeling to enable surrogate construction for stochastic computational models that have intrinsic noise in addition to parametric uncertainty. We develop a PCE surrogate on a joint space of intrinsic and parametric uncertainty, enabled by Rosenblatt transformations, which are evaluated via kernel density estimation of the associated conditional cumulative distributions. Furthermore, we extend the construction to random field data via the Karhunen–Loève expansion. We then take advantage of closed-form solutions for computing PCE Sobol indices to perform a global sensitivity analysis of the model which quantifies the intrinsic noise contribution to the overall model output variance. Additionally, the resulting joint PCE is generative in the sense that it allows generating random realizations at any input parameter setting that are statistically approximately equivalent to realizations from the underlying stochastic model. The method is demonstrated on a chemical catalysis example model and a synthetic example controlled by a parameter that enables a switch from unimodal to bimodal response distributions.

97 MATHEMATICS AND COMPUTING↗

Data-Driven Closures and Assimilation for Stiff Multiscale Random Dynamics

Here, we introduce a data-driven and physics-informed framework for propagating uncertainty in stiff, multiscale random ordinary differential equations (RODEs) driven by correlated (colored) noise. Unlike systems subjected to Gaussian white noise, a deterministic equation for the joint probability density function (PDF) of RODE state variables does not exist in closed form. Moreover, such an equation would require as many phase-space variables as there are states in the RODE system. To alleviate this curse of dimensionality, we instead derive exact, albeit unclosed, reduced-order PDF (RoPDF) equations for low-dimensional observables/quantities of interest. The unclosed terms take the form of state-dependent conditional expectations, which are directly estimated from data at sparse observation times. However, for systems exhibiting stiff, multiscale dynamics, data sparsity introduces regression discrepancies that compound during RoPDF evolution. This is overcome by introducing a kinetic-like defect term to the RoPDF equation, which is learned by assimilating in sparse, low-fidelity RoPDF estimates. Two assimilation methods are considered, namely nudging and deep neural networks, which are successfully tested against Monte Carlo simulations.

97 MATHEMATICS AND COMPUTING↗

Quantum Time-Space Tradeoffs for Matrix Problems

We consider the time and space required for quantum computers to solve a wide variety of problems involving matrices, many of which have only been analyzed classically in prior work. Our main results show that for a range of linear algebra problems—including matrix-vector product, matrix inversion, matrix multiplication and powering—existing classical time-space tradeoffs, several of which are tight for every space bound, also apply to quantum algorithms with at most a constant factor loss. For example, for almost all fixed matrices 𝐴, including the discrete Fourier transform matrix, we prove that quantum circuits with at most 𝑇 input queries and 𝑆 qubits of memory require 𝑇 = Ω⁢(𝑛 2 /𝑆) to compute matrix-vector product 𝐴⁢𝑥 for 𝑥 ∈{0,1 𝑛 . We similarly prove that matrix multiplication for 𝑛 ×𝑛 binary matrices requires 𝑇 = Ω⁢(𝑛 3 /$\sqrt{𝑆}$). Because many of our lower bounds are matched by deterministic algorithms with the same time and space complexity, our results show that quantum computers cannot provide any asymptotic advantage for these problems with any space bound. We obtain matching lower bounds for the stronger notion of quantum cumulative memory complexity—the sum of the space per layer of a circuit. We also consider Boolean (i.e., AND-OR) matrix multiplication and matrix-vector products, improving the previous quantum time-space tradeoff lower bounds for 𝑛 × 𝑛 Boolean matrix multiplication to 𝑇 = Ω⁢(𝑛 2.5 /𝑆 1/4 ) from 𝑇 = Ω⁢(𝑛 2.5 /𝑆 1/2 ). Our improved lower bound for Boolean matrix multiplication is based on a new coloring argument that extracts more from the strong direct product theorem that was the basis for prior work. To obtain our tight lower bounds for linear algebra problems, we require much stronger bounds than strong direct product theorems. We obtain these bounds by adding a new bucketing method to the quantum recording-query technique of Zhandry that lets us apply classical arguments to upper bound the success probability of quantum circuits.

lower bounds↗

Integral Kernel Methods for Nonlinear Parabolic-Elliptic Systems

Nonlinear parabolic-elliptic systems arise in many physical, biological, and chemical phenomena such as chemotaxis, ion transport, self-gravitating particles, and Brownian vortices. Existing methods struggle with the strong coupling and high nonlinearity and nonlocality of some of these systems, especially the ill-conditioned, convection-dominated problems. To overcome numerical difficulties, current approaches rely on initial guesses, preconditioning, or iterative techniques with no convergence guarantees. They might suffer from poor scalability, large memory usage, and difficulty to parallelize. Inspired by the connection of parabolic-elliptic systems to stochastic processes, we introduce a novel meshless, monolithic, and fully explicit method that naturally encapsulates the elliptic and parabolic operators into a single step which updates each node deterministically with global information. By being fully quadrature-based, it avoids solving systems of discretized equations and does not utilize initial guesses or preconditioning, while requiring little memory and being easy to parallelize. We first derive the method in an integral kernel formulation with quadratic complexity in the number of integration nodes and then leverage kernel-independent fast multipole methods (FMM) to present a scalable algorithm with linear complexity. We provide numerical examples for the Poisson-Nernst-Planck equations in one, two, and three dimensions, together with the derivation of the integral kernel for each case. Furthermore, the examples demonstrate the fast convergence and scalability of the FMM-accelerated algorithm, as well as its suitability for convection-dominated problems, making it competitive against traditional PDE solvers.

PDE systems↗

Algorithm 1049: The Delaunay Density Diagnostic

Accurate approximation of a real-valued function depends on two aspects of the available data: the density of inputs within the domain of interest and the variation of the outputs over that domain. There are few methods for assessing whether the density of inputs is sufficient to identify the relevant variations in outputs—i.e., the “geometric scale” of the function—despite the fact that sampling density is closely tied to the success or failure of an approximation method. In this article, we introduce a general purpose, computational approach to detecting the geometric scale of real-valued functions over a fixed domain using a deterministic interpolation technique from computational geometry. The algorithm is intended to work on scalar data in moderate dimensions (2–10). Our algorithm is based on the observation that a sequence of piecewise linear interpolants will converge to a continuous function at a quadratic rate (in L 2 norm) if and only if the data are sampled densely enough to distinguish the feature from noise (assuming sufficiently regular sampling). We present numerical experiments demonstrating how our method can identify feature scale, estimate uncertainty in feature scale, and assess the sampling density for fixed (i.e., static) datasets of input–output pairs. Finally, we include analytical results in support of our numerical findings and have released lightweight code that can be adapted for use in a variety of data science settings.

97 MATHEMATICS AND COMPUTING↗

EVI-EnSitePy (Electric Vehicle Infrastructure – Energy Estimation and Site Optimization Tool in Python) [EVI-X Modeling Suite] [SWR-25-07]

EVI-EnSitePy is a comprehensive agent-based tool designed for the analysis and design of high-power charging sites, encompassing a wide array of site agents including Electric Vehicles (EVs), chargers, energy storage units (ESS), renewable energy resources (DER), and loads. This versatile tool offers diverse functionalities and a modular modeling approach, allowing detailed configuration of agents based on power ratings, port numbers, energy capacities, demand requirements, charger interfaces, and flexibility to customize the tool for project specific goals. By simulating agent interactions and employing various metrics, EVI-EnSitePy enables the assessment of site performance, exploration of energy management systems (EMS), and implementation of innovative EV charging policies. Utilizing EV charge schedules and arrival states, the tool performs thorough charging site simulations, with outputs consisting of agent and site-level power profiles and statistical metrics. Employing a tree graph structure, EVI-EnSitePy supports nested site structures and power distribution modeling. The tool's ability to generate charging schedules deterministically or via stochastic analysis further enhances its versatility. Through its features and capabilities, EVI-EnSitePy offers a powerful platform for informed decision-making in the realm of high-power charging site design and operation.

Jackson, Derek [National Renewable Energy Laborato↗

RFSoC based digital low level RF control firmware and software suite (mimo_llrf) v1.0

It features a framework of a firmware and software architecture in support of building a digital low-level RF control system for accelerators, where precised digital RF generation and measurement are needed across many RF channels. It primarily supports the Xilinx RFSoC chips (xczu48dr, xczu47dr, xczu29dr) and their evaluation boards (zcu208, zcu216), for a highly integrated solution enabling the need for synchronous low-level RF systems, including: multi-tile synchronization, external reference for sampling clocks, deterministic delay, aligned NCO phase for digital mixers, and built-in EPICS IOC.

Du, Qiang [Lawrence Berkeley National Laboratory (↗

fortfmt-fix

SF-25-126 **fortfmt‑fix** is a small, deterministic codemod that rewrites these descriptors to explicit, standard‑conforming forms (e.g., `I12`, `F25.16`), enabling clean builds on modern compilers without vendor‑specific options. The tool is designed to be idempotent and conservative, preserving semantics while reducing maintenance burden in research codebases.

Bross, David [Argonne National Laboratory (ANL), A↗

Consist v0.1.0

A Python library for provenance tracking, intelligent caching, and data virtualization in scientific simulation workflows. It automatically records code, configuration, and input data to skip redundant computations and enables querying results across many runs without manual bookkeeping. Designed to support multi-model simulation workflows like the BEAM CORE toolset at LBL, but designed to be extensible to a wide range of research workflows. Combines lineage tracking features as provided by OpenLineage with deterministic hashing like SnakeMake, and adds powerful analysis tools on model outputs.

Needell, Zachary [Lawrence Berkeley National Labor↗

allium

High-performance library for deterministic thermal radiative transfer

Olivier, Sam↗

PRISMA: PARALLEL REFINEMENT AND INTEGRATION SYSTEM FOR MULTI-AZIMUTHAL ANALYSIS

The Parallel Refinement and Integration System for Multi-azimuthal Analysis (PRISMA, version 1.1.0) is a Python application for processing X-ray diffraction (XRD) image data. PRISMA wraps GSAS-II to perform azimuthally-binned peak refinement, computes per-frame strain and d-spacing from those fits, and provides three PyQt5 graphical interfaces: (1) a Recipe Builder for selecting GSAS-II control (.imctrl) files, optional mask (.immask) files or threshold-ased masking, reference and experiment image sets, peaks, zimuthal range and bin size, and an optional ceria-based auto-calibration; (2) a Batch Processor that uses Dask on local workstations and pure MPI (mpi4py.futures.MPICommExecutor) on HPC to distribute GSAS-II refinement across cores or compute nodes and write results to a 4-dimensional (peaks x frames x azimuths x measurements) Zarr dataset; and (3) a Data Analyzer that renders heatmaps of fit parameters, strain, frame-to-frame deltas, and percent-change-vs-reference, and exports user-defined subsections to CSV or Excel. The peak-refinement algorithm is deterministic. Benchmark on ALCF Crux: a 20,000-image set, single-peak fit in frame mode with 44 azimuthal bins on 128 nodes x 128 workers, 48 seconds total wall time.

Lorenzo Martin, Maria De La Cinta [Argonne Nationa↗

Scientific Core Library Stack (SCLS) v2026

SCLS (Scientific Core Library Stack) is an opinionated build and packaging system for scientific computing libraries developed at Lawrence Berkeley National Laboratory. It produces a coherent, reproducible stack of numerical libraries — including BLAS/LAPACK, MPI, sparse direct and iterative solvers, graph partitioners, and parallel I/O libraries (e.g., PETSc, SLEPc, HDF5, NetCDF, MUMPS, OpenBLAS) — that work together without manual repair by downstream scientific software. From a single recipe-and-flavor model, SCLS produces native RPM packages for RHEL-family Linux, DEB packages for Debian/Ubuntu, direct Unix-style prefix installs for HPC and locked-down environments, and native macOS builds. Multiple build "flavors" (e.g., GCC+OpenBLAS, GCC+MKL, Intel+MKL, debug) coexist in distinct prefixes on the same host. Compared to general-purpose meta-build frameworks, SCLS is deliberately curated rather than infinitely configurable. It enforces deterministic, audit-friendly behavior: explicit build dependencies, no silent feature autodetection, a clear open-source license policy, and rpath-based runtime linkage so installs integrate cleanly with standard package-manager workflows.

Messe, Christian [Lawrence Berkeley National Labor↗

Analyzing and Exploring Training Recipes for Large-Scale Transformer-Based Weather Prediction

Abstract The rapid rise of deep learning (DL) in numerical weather prediction (NWP) has led to a proliferation of models which forecast atmospheric variables with comparable or superior skill than traditional physics-based NWP. However, among these leading DL models, there is a wide variance in both the training settings and architecture used. Further, the lack of thorough ablation studies makes it hard to discern which components are most critical to success. In this work, we show that it is possible to attain high forecast skill even with relatively off-the-shelf architectures, simple training procedures, and moderate compute budgets. Specifically, we train a minimally modified Swin Transformer V2 (SwinV2) on ERA5 data and find that it attains superior skill in terms of mean-square errors of deterministic forecasts when compared against the European Centre for Medium-Range Weather Forecasts’ Integrated Forecasting System (IFS). Almost all DL–NWP systems share a core set of hyperparameters and design decisions. To aid and expedite future DL–NWP research, we present an in-depth, systematic exploration of different loss functions, model sizes and depths, patch sizes, and multistep training objectives. We also examine the model performance with metrics beyond the typical accuracy (ACC) and RMSE and investigate how the performance scales with model size. Through our open-source code, scoring pipelines, and models, we share our findings on key aspects of the training pipeline. These ablations reduce the necessity for expensive hyperparameter tuning and lower the barrier to entry for future DL–NWP research. Significance Statement This study investigates the potential of using large-scale transformer-based models for weather prediction, showing that it is possible to achieve high forecast accuracy with simpler, off-the-shelf architectures. By training a minimally modified SwinV2 transformer on ERA5 data, we show that the model achieves competitive forecast skill in terms of mean-square error for key variables, outperforming the European Centre for Medium-Range Weather Forecasts’ Integrated Forecasting System (IFS) at all lead times. Our findings suggest that effective training strategies, such as multistep fine-tuning and channel-weighted losses, significantly enhance the model’s performance. However, we also highlight that these improvements come with trade-offs in other areas, such as ensemble spread and high-frequency spatial detail. This work highlights the promise of deep learning in improving weather forecasts, which could lead to better preparedness and response to weather events, ultimately benefiting society by providing more reliable weather predictions.

Willard, Jared D. [Lawrence Berkeley National Labo↗

Automated Operational Forecasting of Monsoon Low Pressure Systems

Monsoon low pressure systems (LPSs) are the dominant rain-bearing weather system of South Asia, often producing extreme precipitation and hydrological disasters in a region inhabited by nearly two billion people. Despite the importance of these storms, no operational system has automatically identified and tracked LPS in real time in numerical weather prediction model output; many commonly used vortex-tracking algorithms are ill suited for monsoon LPS because of the weak winds and cold cores of these systems. Here, we describe a new system that uses optimized algorithms to identify monsoon LPS in short- to medium-range forecasts from the U.S. Global Ensemble Forecast System (GEFS) and a version of the deterministic Global Forecast System (GFS) adapted and used operationally by the Indian Institute of Tropical Meteorology (IITM). We also assess the historical performance of these models in forecasting South Asian monsoon LPS, comparing this with the performance of the Integrated Forecasting System of the ECMWF. We assess the accuracy of model predictions of LPS genesis, position, intensity, and precipitation rates for forecast lead times of 1–5 days, yielding quantitative information on model biases to guide operational forecasters and disaster managers. The system we introduce here could be extended to other low-latitude regions affected by dynamically weak, heavily precipitating atmospheric vortices that are often not included in tropical cyclone inventories.

54 ENVIRONMENTAL SCIENCES↗

Chemical classification program synthesis using generative artificial intelligence

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or are deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against deep learning models and a naive SMARTS pattern based classifier. C3PO outperforms the naive classifier, but does not reach the performance of state of the art deep learning methods. However, C3PO has a number of strengths that complement deep learning methods, including explainability and reduced data dependence. C3PO can be used alongside deep learning classifiers to provide an explanation of the classification, where both methods agree. The programs can be used as part of the ontology development process, and iteratively refined by expert human curators.

Artificial Intelligence↗

Binary Quantum Control Optimization with Uncertain Hamiltonians

Optimizing the controls of quantum systems plays a crucial role in advancing quantum technologies. The time-varying noises in quantum systems and the widespread use of inhomogeneous quantum ensembles raise the need for high-quality quantum controls under uncertainties. In this paper, we consider a stochastic discrete optimization formulation of a discretized binary optimal quantum control problem involving Hamiltonians with predictable uncertainties. We propose a sample-based reformulation that optimizes both risk-neutral and risk-averse measurements of control policies, and solve these with two gradient-based algorithms using sum-up-rounding approaches. Furthermore, we discuss the differentiability of the objective function and prove upper bounds of the gaps between the optimal solutions to binary control problems and their continuous relaxations. We conduct numerical simulations on various sized problem instances based on two applications of quantum pulse optimization; we evaluate different strategies to mitigate the impact of uncertainties in quantum systems. In conclusion, we demonstrate that the controls of our stochastic optimization model achieve significantly higher quality and robustness compared with the controls of a deterministic model.

conditional value-at-risk (CVaR)↗