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At least 415 records · Page 23

Brochure for the DOE Office of Science Workshop on Envisioning Frontiers in AI and Computing for Biological Research

In February of 2025 a joint ASCR/BER workshop was held to identify key transformational research directions for understanding biology using artificial intelligence (AI), digital twins and high-performance (HPC) computational methods to facilitate scientific discovery and innovation in support of the Department of Energy mission. AI technologies offer exciting new groundbreaking methods to analyze large volumes of complex biological data, thereby greatly accelerating the ability to understand, predict, and design biological processes for beneficial purposes. In the laboratory, the bridging of AI-enabled automated experimental technologies, HPC and digital twins will provide potent tools for researchers to explore the fundamental nature of biology and harness its inherent metabolic potential for a variety of beneficial purposes. The focus of this workshop was on how high-performance computational methods can impact this objective by exploring digital twins, foundational models, and data-driven approaches with applications to advance automated laboratory experiments, modeling of complex living systems and engineering new functions into plants and microbial systems relevant to DOE mission. Workshop attendees with expertise in plant science, microbiology, mathematics, computer science, and AI assessed the current state of the science, trends, and AI challenges at the interface of plant and microbial systems biology and computational science to identify opportunities for high-impact research. This collaborative effort capitalized on ASCR's advancements in applied mathematics, computer science, and Exascale systems, and BER's expertise in basic genomics-enabled research on DOE relevant plant and microbial systems. The workshop culminated in four key priority research directions to guide future research and development within DOE Office of Science programs.

59 BASIC BIOLOGICAL SCIENCES↗

Quantum Annealing for Real-World Machine Learning Applications

Optimizing the training of a machine learning pipeline is important for reducing training costs and improving model performance. One such optimizing strategy is quantum annealing, which is an emerging computing paradigm that has shown potential in optimizing the training of a machine learning model. The implementation of a physical quantum annealer has been realized by D-Wave systems and is available to the research community for experiments. Recent experimental results on a variety of machine learning applications have shown interesting results especially under the conditions where the performance of classical machine learning techniques are limited such as limited training data and high dimensional features. This chapter explores the application of D-Wave’s quantum annealer for optimizing machine learning pipelines for real-world classification problems. We review the application domains on which a physical quantum annealer has been used to train machine learning classifiers. We discuss and analyze the experiments performed on the D-Wave quantum annealer for applications such as image recognition, remote sensing imagery, security, computational biology, biomedical sciences, and physics. We discuss the possible advantages and the problems for which quantum annealing is likely to be advantageous over classical computation.

Kumar nath, Rajdeep↗

ESnet-JLab FPGA Accelerated Transport (data plane) [EJFAT (udplb)] v1.0

The ESnet-JLab FPGA Accelerated Transport system is a solution for streaming high-speed scientific measurement data from Data Acquisition Systems (DAQs) to high-performance computing facilties. It is generally compatible with many science workflows, and makes no assumptions about the specifics of any particular experiment. This program (udplb) implements the data plane portion of the EJFAT system. It is an FPGA design that rewrites and forwards data packets from a UDP-based scientific workflow to high-performance compute nodes. It depends on another program (udplbd, disclosed separately) to implement the control system.

Bengough, Peter [Malleable Networks, Inc.]↗

Building and Sustaining a Community Resource for Best Practices in Scientific Software: The Story of BSSw.io

The development of scientific software—a cornerstone of long-term collaboration and scientific progress—parallels the development of other types of software but still poses distinct challenges, especially in high-performance computing. Although web searches yield numerous resources on software engineering, there is still a scarcity specifically for scientific software development. Here, this article introduces the Better Scientific Software site (https://bssw.io), a platform that hosts a community of researchers, developers, and practitioners who share their experiences and insights on scientific software development. Since 2017, this collaborative hub has gained traction within the scientific computing community, attracting a growing number of readers and contributors eager to share ideas and elevate their software development practices. In sharing the BSSw.io site’s story, we hope to encourage further growth of the BSSw.io community through both readership and contributors, with a long-term goal of fostering culture change by increasing emphasis on best practices in scientific software.

97 MATHEMATICS AND COMPUTING↗

Integrating Machine-learning-assisted Computer Vision with RICH System

Developments in artificial intelligence have vastly expanded the capabilities of robots. Currently, the Spallation Neutron Source (SNS) beamlines at Oak Ridge National Lab (ORNL) have robotic sample loaders to increase the efficiency of running experiments. However, they require retraining if anything about the situation changes, e.g., where the samples are, and cannot notice if errors occur. So, the viability of using computer vision and machine learning to enhance these sample loaders’ functionality was investigated. In this project, the RICH system with a Dobot CR3 6-axis robot present at the VULCAN beamline assisted by an Intel Realsense D435i camera, a unique camera that enables convenient translation of 2D pixel coordinates to 3D world points, was programmed to load ceramic crucibles into a thermogravimetric analyzer (TGA) furnace. An algorithm was constructed in Python with three major phases planned: (1) obtaining a sample, (2) moving it to the target location, and then (3) bringing the sample back to its original location once the experiment finished. In the first phase, the algorithm would dynamically detect sample locations using ArUco markers to recognize the samples’ general location and a custom-trained yolov5 object detection model to locate the crucibles’ centers. Afterward, the robot would be directed to pick up samples based on the crucibles’ calculated positions. In the second phase, the robot would move the sample to a secondary point, reorient its grip, and place the sample at the target location. In the final phase, the robot would determine whether the sample was intact and would bring it back to its original place if it was or raise an alarm. Using this algorithm, the robot was able to pick up different types of crucibles at varying positions. These results indicate that integrating machine-learning-assisted computer vision with robotic sample loaders can result in effective autonomous detection of samples.

97 MATHEMATICS AND COMPUTING↗

Intelligent experiments through real-time AI: Fast Data Processing and Autonomous Detector Control for sPHENIX and future EIC detectors (Phase-I)

With an ever increasing demand for high precision data from modern detectors for discovery science and precision measurements, all major high energy nuclear and particle experiments, current and future, are facing the challenge on how to deal with the large volume of raw data generated from sophisticated state-of-the-art detectors in high rate collisions. These goals need to be balanced with available hardware and cost limits on DAQ (Data AcQuisition system) bandwidth and offline computing resources to capture, store and process the signal events. Two prototypical examples are the upcoming sPHENIX experiment, the DOE next generation heavy ion physics experiment at the Relativistic Heavy Ion Collider at BNL, and the future EIC experiments that are planned to be online circa 2030.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Intrusive Uncertainty Quantification and Optimal Experiment Design in the Open-Source Pyomo Ecosystem

This contribution describes ParmEst and Pyomo.DoE, two pillars of the open-source Python-based Pyomo ecosystem for computational optimization with (partial differential) algebraic equation mathematical models. Specifically, ParmEst facilitates intrusive frequentist parameter estimation (PE) and uncertainty quantification (UQ) through built-in features, such as covariance matrix estimation, bootstrapping, and likelihood ratio tests. Complementary, Pyomo.DoE enables optimal experiment design by maximizing various metrics of the Fisher information matrix, such as A-optimality (trace), D-optimality (determinant), E-optimality (minimum eigenvalue), and ME-optimality (condition number). ParmEst and Pyomo.DoE can solve high-dimensional optimization problems by leveraging the model structure and exact derivative information. Finally, we will discuss future opportunities to integrate PE and UQ capabilities with optimization under uncertainty, including robust optimization with non-convex models via PyROS.

97 MATHEMATICS AND COMPUTING↗

Structure-preserving neural networks for the regularized entropy-based closure of a linear, kinetic, radiative transport equation

The main challenge of large-scale numerical simulation of radiation transport is the high memory and computation time requirements of discretization methods for kinetic equations. In this work, we derive and investigate a neural network-based approximation to the entropy-based closure method to accurately compute the solution of the multi-dimensional moment system with a low memory footprint and competitive computational time. We extend methods developed for the standard entropy-based closure to the regularized entropy-based closures. The main idea is to interpret structure-preserving neural network approximations of the regularized entropy-based closure as a two-stage approximation to the original entropy-based closure. We conduct a numerical analysis of this approximation and investigate optimal parameter choices. Our numerical experiments demonstrate that the method has a much lower memory footprint than traditional methods with competitive computation times and simulation accuracy. The code and all trained networks are provided on GitHub.

entropy closure↗

Design and evaluation of alphabetic and numeric input methods for virtual reality

In today’s virtual reality (VR), users have various ways to influence their VR experience, including alphanumeric input. While typing characters and numbers is straightforward on desktop computers, it presents challenges and opportunities in head-mounted display VR due to specific interaction methods and a lack of real-world visual stimuli. Addressing these open questions, our work implements and evaluates ten approaches to alphabetic and numeric inputs in VR. Here, we describe the design motivation behind these input methods and evaluate them in a user study with 40 participants divided into groups for alphabetic and numeric keyboards. This comparison investigates each method’s performance and user interactions. Our findings suggest that different input methods significantly impact words per minute and error rates, and that certain keyboard designs may receive better subjective evaluations despite poorer objective performance.

97 MATHEMATICS AND COMPUTING↗

Magnetosynthesis Effect on the Structure and Ground State of Cu 2+ -Based Antiferromagnets

Synthetic variables can have an outsized influence on the crystal structure and magnetic properties of a material, particularly those of quantum materials. In this work, we investigate the impact of synthesis under a magnetic field (magnetosynthesis) on the crystal structure and magnetic properties of several Cu 2+ (S = 1/2)-based materials with antiferromagnetic interactions and varying levels of magnetic frustration, from simple antiferromagnets to a quantum spin liquid. Here, we develop methods to apply small (0.09–0.37 T) magnetic fields during low-temperature hydrothermal, evaporative, and rehydration syntheses of the simple antiferromagnet CuCl 2 ·2H 2 O, the canted antiferromagnet (Cu,Zn) 3 Cl 4 (OH) 2 ·2H 2 O, the frustrated and canted antiferromagnet atacamite Cu 2 (OH) 3 Cl, and the highly frustrated quantum spin liquid herbertsmithite Cu 3 Zn(OH) 6 Cl 2 . We report the first single-crystal X-ray structural determination of the Cu 3 Cl 4 (OH) 2 ·2H 2 O structure type and probe the stability of this phase both experimentally and computationally. Atacamite Cu 2 (OH) 3 Cl synthesized under a 0.19 T field experiences a 0.15 K (∼3%) decrease in its Néel transition temperature. This result suggests that magnetosynthesis with small applied fields may have a very subtle influence upon the magnetic properties of moderately magnetically frustrated 3 d materials.

36 MATERIALS SCIENCE↗

Multi-Fidelity Bayesian Optimization with Gaussian Processes for Double Shell Inertial Confinement Fusion Target Design

Reliable, secure access to energy is a major focus for national security efforts. One potential route to such energy is through fusion reactions in inertial confinement fusion (ICF) experiments. Such experiments are carried out at facilities such as the National Ignition Facility (NIF) in Livermore, California, where high powered lasers are used to compress a DT fuel-containing target to the necessary high temperature, high pressure conditions. These experiments are limited in number, which creates a heavy dependence on high fidelity predictive physics simulations and analysis performed “pre shot,” or before the experiment occurs. Many of these simulations in higher dimensions (2D and 3D) are computationally expensive, so finding optimal simulation-based designs presents its own challenges. In this work, we present our multi-fidelity Bayesian optimization with Gaussian processes (GPs) for ICF double shell targets, where a 1D surrogate model is used to help find a 2D surrogate model, enabling us to find optimal targets in the higher fidelity (2D), while saving computational cost.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Application of Portable Parallelization Strategies for GPUs on track reconstruction kernels

Utilizing the computational power of GPUs is one of the key ingredients to meet the computing challenges presented to the next generation of High-Energy Physics (HEP) experiments. Unlike CPUs, developing software for GPUs often involves using architecturespecific programming languages promoted by the GPU vendors and hence limits the platform that the code can run on. Various portability solutions have been developed to achieve portable, performant software across different GPU vendors. Given the rapid evolution of these portability solutions, an early adoption of them in simple HEP testbed applications will help us understand the strengths and weaknesses of respective approaches.We apply several portability solutions, including Alpaka, Kokkos, SYCL and std::execution::par, on kernels for track propagation extracted from the mkFit project. We report on the development experience of the same application with different portability solutions, as well as their performance on GPUs, measured as the throughput of the kernels, from different manufacturers such as NVIDIA, AMD and Intel.

Kwok, Martin [Fermilab] (ORCID:0000000286936146)↗

PvaPy streaming framework for real-time data processing

User facility upgrades, new measurement techniques, advances in data analysis algorithms as well as advances in detector capabilities result in an increasing amount of data collected at X-ray beamlines. Some of these data must be analyzed and reconstructed on demand to help execute experiments dynamically and modify them in real time. In turn, this requires a computing framework for real-time processing capable of moving data quickly from the detector to local or remote computing resources, processing data, and returning results to users. In this paper, we discuss the streaming framework built on top of PvaPy, a Python API for the EPICS pvAccess protocol. We describe the framework architecture and capabilities, and discuss scientific use cases and applications that benefit from streaming workflows implemented on top of this framework. We also illustrate the framework's performance in terms of achievable data-processing rates for various detector image sizes.

EPICS pvAccess↗

Tunable Few-Layer van der Waals Crystals and Heterostructures as Emerging Energy and Quantum Materials (Final Technical Report)

2D and layered (van der Waals) semiconductors offer extraordinary opportunities for manipulating optically excited charge carriers, many-body excitations, and non-charge based quantum numbers. To date, research has focused on a limited group of materials, mostly transition metal dichalcogenides in the monolayer limit. Other van der Waals semiconductors, and especially few-layer to multilayer crystals and their heterostructures, carry large potential for the discovery of phenomena of interest for future energy and information technologies. But they remain largely unexplored, often due to a lack of access to high-quality materials and approaches for measuring their properties at the relevant scales. The goal of this project was to develop an EPSCoR-State/National Laboratory Partnership that addresses the challenges of preparing high-quality van der Waals semiconductors and of probing their structure, composition, and especially their optoelectronic and photonic properties, near the atomic scale using electron microscopy techniques. A central component of the project was the development of advanced methods for electron microscopy and electron-excited spectroscopy, taking advantage of unique samples as well as leading capabilities and expertise at the partner institutions. Efforts to advance leading-edge techniques was supported by ancillary developments, such as precision sample preparation for electron microscopy/spectroscopy, coordinated chemical imaging, and analytical electron microscopy. Experiments in materials synthesis and technique development were closely linked to theory and computation. The results obtained under this project yielded multifaceted benefits to the involved partners and their institutions, DOE-BES, the wider scientific community, and society at large, particularly in the State of Nebraska through dividends from knowledge and human capital generated under the project.

36 MATERIALS SCIENCE↗

DetSuM: Detector Surrogate Model for LArTPC

In large neutrino experiments such as the Deep Underground Neutrino Experiment (DUNE), estimating detector response uncertainties typically requires simulation samples that consume substantial computing resources and time. To mitigate this challenge, we present DetSuM, an uncertainty-aware surrogate model designed to capture the detector response variations with reduced computing load compared to full simulations. This poster describes the construction and evaluation of DetSuM using simulation and reconstruction datasets in a rare-event search at DUNE. We assess DetSuM's ability to predict key detector-response variations and their associated uncertainties, discuss current limitations, and outline improvements to extend its validity in systematics studies of DUNE physics.

Li, Aobo [UC, San Diego]↗

Characterizing Supernovae Neutrinos in MARLEY

This summer I worked on characterizing the uncertainties in neutrino-argon interactions due to the optical model potential. Functionally, this was a great deal of new experience coding in C++. I wrote a script using MARLEY(Gardiner 2019) to compute both the branching ratios and exclusive cross sections for a whole host of different decay processes from the unstable Potassium nucleus created by a v+Ar charged current interaction. These decays were computed through MARLEY, governed by a global parametrization of the Optical Model potential(Koning-Delaroche 2003). Helpfully, Pruitt+ 2023 provided public supplemental material outlining 400 separate "universes" for the optical model potential parameters. These "universes" represent uncertainties on the optical potential itself, and I wrote code to incorporate them into the MARLEY framework and quantify their impact on the predictions of neutrino-argon cross sections. This stands as the first computation of nuclear de-excitation systematic errors on cross sections in this energy band for v+Ar interactions, a critical step to understanding the science we can do with DUNE in the tens-of-MeV band.

Abu El-Haj, Luca↗

Unraveling the Heterogeneous but Ordered Microstructure of the Nonionic Deep Eutectic Solvent Formed by Lauric Acid and N -Methylacetamide

The nonionic deep eutectic solvent, formed by lauric acid (LA) and N-methylacetamide (NMA), has been shown to have a heterogeneous molecular structure in which the LA and NMA form nonpolar and polar domains, respectively. Previous vibrational spectroscopy experiments demonstrated that the ability of the LA domains to solvate compounds was limited to long carbon chains, whereas other nonpolar molecules, such as W(CO) 6 , were found to be solvated by both LA and NMA. These experiments were not fully compatible with the previously proposed micelle-like structure of the nonpolar domains of the LA-NMA DES. In this work, the modeling of the DES molecular structure is pursued using classical molecular dynamics simulations. The new classical model reproduces both the SAXS structural factors and the previously experimentally derived interaction map for these LA-NMA DESs. In addition, the simulation also shows that LA-NMA DESs form highly organized LA aggregates that are difficult to disorganize. Further evidence of the correct description provided by the newly derived model is obtained using a moderately polar probe: chloroform-d. Computations using the classical model have a good agreement with the solvation behavior of the probe derived from experiments, in which the location of the probe is found to be mostly within the polar domain of the DES. The computational model also demonstrates that the probe solvation is a consequence of the tightly packed LA structure, which causes nonpolar molecules to be located at the interphase of the DES nonpolar domains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Experiences with SYCL on AMD GPUs with Kokkos

With the recent diversification of the hardware landscape in the high-performance computing (HPC) community, performance-portability solutions are becoming more and more important. One of the most popular choices is Kokkos, which recently became a Linux Foundation project. Most of its development is supported by the US Department of Energy and the French Alternative Energies and Atomic Energy Commission. Kokkos is implemented as a C++ library with multiple backends to support CPUs as well as various GPU architectures. These backends include OpenMP, CUDA, HIP, and also SCYL. This approach enables users to leverage the preferred vendor toolchain for the respective platform (e.g. CUDA, ROCm, OneAPI). The SYCL backend is used to target Intel GPUs, in particular to support the Aurora exascale supercomputer. However, SYCL itself also offers a large degree of portability, and in fact Kokkos’ CI for SYCL has been running on NVIDIA hardware due to a lack of access to Intel GPUs. In this report, we describe our experience with using Kokkos SYCL backend on AMD GPUs targeting the Frontier supercomputer at Oak Ridge National Laboratory. The two major SYCL implementations are DPC++ and AdaptiveCpp. While the Kokkos SYCL backend has been implemented using the former, the latter was the first implementation to target AMD GPUs. We will discuss the experience with both of these SYCL implementations in terms of functionality and performance. Using Kokkos to evaluate SYCL toolchains has a number of benefits. Kokkos’ use of SYCL is fairly complex, exercising features such as graphs, relocatable device functions, atomics – including for non-arithmetic types, as well as pinned and page migratable memory allocations. Kokkos also needs to implement capabilities such as Kokkos’ hierarchical parallelism that are not a straight-forward mapping to SYCL capabilities. Furthermore, a large number of libraries and applications that represent diverse use cases are implemented in Kokkos, providing readily available test cases for a toolchain evaluation. Preliminary results show that support for AMD GPUs in DPC++ is much less mature than for NVIDIA GPUs or Intel GPUs. While the situation has improved significantly over the last year, we still encounter many runtime failures, dispatching problems, and code generation issues. With AdaptiveCpp the challenges arise even earlier in the evaluation process. Since Kokkos’ SYCL implementation is largely focused on supporting Intel GPUs, we opted to leverage SYCL extensions which are available in DPC++ but not in AdaptiveCpp. Furthermore, AdaptiveCpp appears to be less conformant with the SYCL2020 standard which Kokkos relies on. In some cases, we are able to work around the lack of feature support, in other cases we have to disable certain Kokkos capabilities to evaluate the toolchain. Our evaluation will leverage Kokkos’ unit tests to establish basic functionality and feature completeness. We then use simple benchmarks for components of a CG implementation as a measure of usability and performance of the SYCL toolchains.

97 MATHEMATICS AND COMPUTING↗