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At least 289 records · Page 16

Ecosystems for Scientific Computing in the Age of AI

Scientific computing is at an inflection point. Artificial intelligence (AI) is reshaping how scientific software is developed, how teams collaborate, how projects are governed, and how the next generation is trained. Drawing on insights from a 2025 workshop report, this article argues that the future of discovery will depend on agile, robust ecosystems built through socio-technical co-design—the intentional integration of technical and human systems. This perspective is essential for ensuring that future scientific computing remains trustworthy, sustainable, and scalable. It combines advances in AI, high-performance computing, and software with new models for cross-disciplinary collaboration, education, and workforce development. Key recommendations include building modular, trustworthy AI-enabled software ecosystems; enabling teams to integrate AI into scientific workflows while preserving human creativity, integrity, and rigor; and developing adaptive training pathways that keep pace with rapid technological change. By sharing these perspectives, we hope to stimulate broader community dialogue and encourage coordinated action.

AI↗

Analysis-Software for Hyperspectral Algal Reflectance Probes v. 1.0

This software provides onsite analysis of the hyperspectral reflectance data acquired on an outdoor algal pond by a multichannel, fiber-coupled spectroradiometer. The analysis algorithm is based on numerical inversion of a reflectance model, in which the above-water reflectance is expressed as a function of the single backscattering albedo, which is dependent on the backscatter and absorption coefficients of the algal culture, which are in turn related to the algal biomass and pigment optical activity, respectively. Prior to the development of this software, while raw multichannel data were displayed in real time, analysis required a post-processing procedure to extract the relevant parameters. This software provides the capability to track the temporal variation of such culture parameters in real time, as raw data are being acquired, or can be run in a post processing mode. The software allows the user to select between different algal species, incorporate the appropriate calibration data, and observe the quality of the resulting model inversions.

Timlin, Jerilyn A.↗

New Method to Estimate the Permittivity of Dielectric Materials Using MSPS

A new method to estimate the relative dielectric permittivity of material’s sheet is presented. In this method, a conventional microstrip patch sensor (MSPS) is utilized to resonate at 2.45 GHz. An unknown material, considered as a superstrate layer of 5 mm thickness, is located in the near-field region of the MSPS, at a distance of 5 mm above the sensor. From the changes in the MSPS’s parameters, the dielectric property of the unknown material can be deduced. Based on the conformal map theory, theoretical analyses were performed, and hence, simulation analyses were done using the CST-MW software package. This proposed method was validated through measurements. From the theoretical, simulation, and measurement results, it was shown that depending on the frequency response, the relative permittivity can be estimated.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Nature of Electronically Excited States of Furocoumarins

A comprehensive study of spectral-luminescent and photophysical properties of coumarin sensitizers is performed using the methods of quantum chemistry, electron spectroscopy, and fluorescence. A comparative study of photophysical processes occurring in 8-methoxypsoralen (8-MOP) and 4,9-dimethoxy-7-methylfuro [3,2-g][1] benzofuran-5-1 (khellin) is performed using the quantum-chemical software package based on the semi-empirical method of intermediate neglect of differential overlap with original spectroscopic parameterization. The dependences of the fluorescent properties and reactivity of the compounds on the geometry and composition of the solvation shell of molecules are established. It is shown that incorporation of additional methoxy groups in the structure of molecules has the strongest effect on the spectral-luminescent characteristics of khellin compared with 8-MOP.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Role of microstructure on twin nucleation and growth in HCP titanium: A statistical study

In this study, a detailed statistical analysis is performed using Electron Back Scatter Diffraction (EBSD) to establish the effect of microstructure on twin nucleation and growth in deformed commercial purity hexagonal close packed (HCP) titanium. Rolled titanium samples are compressed along rolling, transverse and normal directions to establish statistical correlations for {10–12}, {11–21}, and {11–22} twins. A recently developed automated EBSD-twinning analysis software is employed for the statistical analysis. Finally, the analysis provides the following key findings: (I) grain size and strain dependence is different for twin nucleation and growth; (II) twinning statistics can be generalized for the HCP metals magnesium, zirconium and titanium; and (III) complex microstructure, where grain shape and size distribution is heterogeneous, requires multi-point statistical correlations.

36 MATERIALS SCIENCE↗

User defined elements in ANSYS for 2D multiphysics modeling of superconducting magnets

Dynamic simulation of superconducting magnets is critical for the design of quench protection systems to prevent potentially damaging temperatures and high voltage from developing after magnet quench. Modeling these scenarios is challenging due to the many multiscale phenomena which impact magnet behavior. These range from conductor scale effects of quench and interfilament coupling currents up to the behavior of the magnet in its powering and protection circuit. In addition, a strong coupling between electromagnetic and thermal domains is required to capture temperature and field dependent material properties and quench behavior. We present a finite element approach which integrates the various effects into the commercial software ANSYS by means of programming new element types. This is shown capable of simulating the strongly coupled transient electromagnetic, thermal, and circuit behavior of superconducting magnets required for quench protection studies. A benchmarking study is presented which shows close agreement between the new ANSYS elements and a COMSOL Multiphysics implementation developed at CERN for dump resistor and coupling loss induced quench based magnet protection of a Nb 3 Sn block dipole. Following this, the ANSYS implementation is shown reproducing strongly coupled quench back behavior observed during the test of a Nb 3 Sn superconducting undulator prototype at Lawrence Berkeley National Laboratory.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies

Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking and dependency management. To manage these processes, a diverse set of tools is required, from command-line utilities to powerful ontology-engineering environmentsr. Particularly in the biomedical domain, which has developed a set of highly diverse yet inter-dependent ontologies, standardizing release practices and metadata and establishing shared quality standards are crucial to enable interoperability. The Ontology Development Kit (ODK) provides a set of standardized, customizable and automatically executable workflows, and packages all required tooling in a single Docker image. In this paper, we provide an overview of how the ODK works, show how it is used in practice and describe how we envision it driving standardization efforts in our community.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

LBNL_DIATOMICS v1

LBNL_DIATOMICS is a software package developed by P. Zarzycki (Lawrence Berkeley National Laboratory) for computing isotopic effects in diatomic molecules using mass-dependent spectroscopic parameters obtained experimentally or from first principles. The package provides a streamlined pipeline from the potential energy surface to the equilibrium constant of an isotopic exchange reaction.

Zarzycki, Piotr [Lawrence Berkeley National Labora↗

ROBOT: A Tool for Automating Ontology Workflows

BACKGROUND:Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extracting dependencies and application-specific subsets, generating standard reports, and generating release files in multiple formats. Similar to more general software development, automation is the key to executing and managing these tasks effectively and to releasing more robust products in standard forms. For ontologies using the Web Ontology Language (OWL), the OWL API Java library is the foundation for a range of software tools, including the Protégé ontology editor. In the Open Biological and Biomedical Ontologies (OBO) community, we recognized the need to package a wide range of low-level OWL API functionality into a library of common higher-level operations and to make those operations available as a command-line tool. RESULTS:ROBOT (a recursive acronym for "ROBOT is an OBO Tool") is an open source library and command-line tool for automating ontology development tasks. The library can be called from any programming language that runs on the Java Virtual Machine (JVM). Most usage is through the command-line tool, which runs on macOS, Linux, and Windows. ROBOT provides ontology processing commands for a variety of tasks, including commands for converting formats, running a reasoner, creating import modules, running reports, and various other tasks. These commands can be combined into larger workflows using a separate task execution system such as GNU Make, and workflows can be automatically executed within continuous integration systems. CONCLUSIONS:ROBOT supports automation of a wide range of ontology development tasks, focusing on OBO conventions. It packages common high-level ontology development functionality into a convenient library, and makes it easy to configure, combine, and execute individual tasks in comprehensive, automated workflows. This helps ontology developers to efficiently create, maintain, and release high-quality ontologies, so that they can spend more time focusing on development tasks. It also helps guarantee that released ontologies are free of certain types of logical errors and conform to standard quality control checks, increasing the overall robustness and efficiency of the ontology development lifecycle.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DRACO: An Overview [Slides]

DRACO (Diffusion ReACtiOn) is a diffusion and chemistry code designed to: 1) Operate on 3D with an unstructured grid defining an arbitrary geometry of interacting parts. 2) Generate its own meshes and use meshes created by other software. 3)Model the transport of any number of diffusing quantities: Concentrations, pressures, temperature, etc. 4) Allow diffusion coefficients to depend in an arbitrary way on concentration, temperature, position, time, etc. 5) Model general chemistry between concentrations with arbitrary reaction rates. 6) Allow arbitrary initial conditions, boundary conditions, and sources/sinks. 7) Allow all of the above to be specified by the user.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Multireference Approach to Electron and Electron–Nuclear Dynamics in Nanomaterials (Final Report)

Many important chemical and physical phenomena involve dynamics on large number of electronic states. Thus, there is a critical need to develop methods to simulate dynamics in dense manifolds of states. Towards this end, we have: a) developed the multiple cloning in dense manifolds of states (MCDMS) method, which is capable of accurately modeling the quantum mechanical coherence between populations on a large number of electronic states, b) implemented MCDMS into the free, open-source PySpawn software package, c) developed graphics processing unit-accelerated algorithms modeling electron dynamics in light fields via Floquet time-dependent configuration interaction (F-TDCI), and d) critically compared different orbital bases in order to achieve an accurate and efficient F-TDCI expansion. This grant ended in August 2020, when our group moved to from Michigan State University to Stony Brook University, where this project continues under grant number DE-SC0021643.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NGEE Arctic Leaf Spectral Absorptance, Utqiagvik (Barrow), Alaska, 2015-2016

Leaf level reflectance on each sample leaf was measured using a portable, full range (i.e. 0.35 to 2.5 microns) Spectra Vista Corporation (SVC) HR-1024i spectroradiometer, together with a leaf clip assembly with an internal, calibrated light source (SVC, Poughkeepsie, NY, USA). Each measurement was referenced against a LabSphere Spectralon (R) standard (LabSphere, Inc., North Sutton, NH, USA) to calculate leaf reflectance from the ratio of target and standard calibrated radiance measurements for each leaf. For each leaf, we collected two to five measurements over the leaf adaxial surface to calculate an average, depending on the leaf size and morphology. Spectral discontinuities in the detector overlap areas were corrected using the SVC instrument software prior to sample averaging and other quality control steps, as described previously (Serbin et al., 2014) using the R-FieldSpectra package (https://github.com/serbinsh/R-FieldSpectra). Refer to Serbin et al (2017) for the complete spectral reflectance dataset. We then calculated leaf spectral absorptance using the measured leaf reflectance following the approach of Wu et al., (2018), based on the original method derived by Shiklomanov et al., (2016) using the PEcAnRTM package (https://github.com/PecanProject/pecan/tree/develop/modules/rtm). This dataset contains one xlsx file, one csv file, and one pdf file.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Failure Mechanism Traceability and Application in Human System Interface of Nuclear Power Plants using RESHA

In recent years, there has been considerable effort to modernize existing and new nuclear power plants with digital instrumentation and control systems (DI&C). However, there has also been considerable concern both by industry and regulatory bodies for the risk and consequence analysis of these systems. Of particular concern are digital common cause failures (CCFs) specifically related to software defects. These “misbehaviors” by the software can occur in both the control and monitoring of a system. While many new methods have been proposed to identify potential software failure modes, such as Systems-theoretic Process Analysis (STPA), Hazard and Consequence Analysis for Digital Systems (HAZCADS), etc., these methods are focused primarily on the control action pathway of a system. In contrast, the information feedback pathway lacks unsafe control actions (UCAs), which are typically related to software basic events; thus, assessment of software basic events in such systems is unclear. In this work, we present the idea of intermediate processors and unsafe information flow (UIF) to help safety analysts trace failure mechanisms in the feedback pathway and how they can be integrated into a fault tree for improved assessment capability. The concepts presented are demonstrated in two comprehensive case studies, a smart sensor integrated platform for unmanned autonomous vehicles and another on a representative advanced human system interface (HSI) for safety critical plant monitoring. The qualitative software basic events are identified, and a fault tree analysis is conducted based on a modified Redundancy-guided Systems-theoretic Hazard Analysis (RESHA) methodology. The case studies demonstrate the use of UIF and intermediate processors in the fault tree to improve traceability of software failures in highly complex digital instrumentation feedback. The improved method can also clarify fault tree construction when multiple component dependencies are present in the system.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Failure Mechanism Traceability and Application in Human System Interface of Nuclear Power Plants using RESHA

In recent years, there has been considerable effort to modernize existing and new nuclear power plants with digital instrumentation and control systems (DI&C). However, there has also been considerable concern both by industry and regulatory bodies for the risk and consequence analysis of these systems. Of particular concern are digital common cause failures (CCFs) specifically related to software defects. These “misbehaviors” by the software can occur in both the control and monitoring of a system. While many new methods have been proposed to identify potential software failure modes, such as Systems-theoretic Process Analysis (STPA), Hazard and Consequence Analysis for Digital Systems (HAZCADS), etc., these methods are focused primarily on the control action pathway of a system. In contrast, the information feedback pathway lacks unsafe control actions (UCAs), which are typically related to software basic events; thus, assessment of software basic events in such systems is unclear. In this work, we present the idea of intermediate processors and unsafe information flow (UIF) to help safety analysts trace failure mechanisms in the feedback pathway and how they can be integrated into a fault tree for improved assessment capability. The concepts presented are demonstrated in two comprehensive case studies, a smart sensor integrated platform for unmanned autonomous vehicles and another on a representative advanced human system interface (HSI) for safety critical plant monitoring. The qualitative software basic events are identified, and a fault tree analysis is conducted based on a modified Redundancy-guided Systems-theoretic Hazard Analysis (RESHA) methodology. The case studies demonstrate the use of UIF and intermediate processors in the fault tree to improve traceability of software failures in highly complex digital instrumentation feedback. The improved method can also clarify fault tree construction when multiple component dependencies are present in the system.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

An in-situ conductometric apparatus for physicochemical characterization of solutions and in-line monitoring of separation processes at elevated temperatures and pressures

Specific conductance and frequency-dependent resistance (impedance) data are widely utilized for understanding the physicochemical characteristics of aqueous and non-aqueous fluids and for evaluating the performance of chemical processes. However, the implementation of such an in-situ probe in high-temperature and high-pressure environments is not trivial. This work provides a description of both the hardware and software associated with implementing a parallel-type in-situ electrochemical sensor. The sensor can be used for in-line monitoring of thermal desalination processes and for impedance measurements in fluids at high temperature and pressure. Further, a comparison between the experimental measurements on the specific conductance in aqueous sodium chloride solutions and the conductance model demonstrate that the methodology yields reasonable agreement with both the model and literature data. A combination of hardware components, a software-based correction for experimental artifacts, and computational fluid dynamics (CFD) calculations used in this work provide a sound basis for implementing such in-situ electrochemical sensors to measure frequency-dependent resistance spectra.

47 OTHER INSTRUMENTATION↗

Optical analysis of nanoparticle packing after drying in microdroplets

The optical spectra of nanostructured patterns with different degrees of order, obtained by dehydration self-assembly of nanoparticles in solution microdroplets placed on a planar substrate, have been analyzed. The reflectance spectrum of the best-ordered pattern contains a characteristic peak, the position of which is determined by the average lattice period in the layer. It is shown that the height of this peak depends on the degree of order of the pattern structure. Patterns with different degrees of order have been simulated using a software for modeling the self-assembly process, which takes into account the properties of particles, substrate, and solvent, as well as the contact line dynamics during solvent evaporation. A peak occurs in the reflectance spectrum due to the resonance Rayleigh scattering in the ordered layer. The described technique for optical diagnostics can be used to analyze the degree of particle order in a pattern.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Workflows Community Summit: Tightening the Integration between Computing Facilities and Scientific Workflows

Scientific workflows are used almost universally across science domains for solving complex and largescale computing and data analysis problems. The importance of workflows is highlighted by the fact that they have underpinned some of the most significant discoveries of the past decades. Many of these workflows have significant computational, storage, and communication demands, and thus must execute on a range of large-scale computer systems, from local clusters to public clouds and upcoming exascale HPC platforms. Managing these executions is often a significant undertaking, requiring a sophisticated and versatile software infrastructure. Historically, infrastructures for workflow execution consisted of complex, integrated systems, developed in-house by workflow practitioners with strong dependencies on a range of legacy technologies—even including sets of ad hoc scripts. Due to the increasing need to support workflows, dedicated workflow systems were developed to provide abstractions for creating, executing, and adapting workflows conveniently and efficiently while ensuring portability. While these efforts are all worthwhile individually, there are now hundreds of independent workflow systems. These workflow systems are created and used by thousands of researchers and developers, leading to a rapidly growing corpus of workflows research publications. The resulting workflow system technology landscape is fragmented, which may present significant barriers for future workflow users due to many seemingly comparable, yet usually mutually incompatible, systems that exist. In order to tackle some of the challenges described above, the DOE-funded ExaWorks and NSF-funded WorkflowsRI projects have organized in 2021 a series of events entitled the “Workflows Community Summit”. The third edition of the “Workflows Community Summit” explored workflows challenges and opportunities from the perspective of computing centers and facilities. This third summit builds on two prior summits (https://workflowsri.org/summits) that (i) established a high level vision for workflows research; and (ii) explored technical approaches for realizing that vision. The third summit brought together a small group of facilities representatives with the aim to understand how workflows are currently being used at each facility, how facilities would like to interact with workflow developers and users, how workflows fit with facility roadmaps, and what opportunities there are for tighter integration between facilities and workflows. This report documents and organizes the wealth of information provided by the participants before, during, and after the summit.

97 MATHEMATICS AND COMPUTING↗

Determination of particle-dependent light response for defining detector response functions

This study comprehensively characterizes two scintillation detectors, an organic deuterated liquid and a stilbene crystal, concerning their response to charged particles such as electrons, protons, alphas, and carbon nuclei. The Birks function was used to determine the detectors’ response to charged particles, enabling the determination of particle-dependent light responses. The particle-dependent light characterization was used to determine detector response functions (DRF) using Geant in combination with Gamma Detector Response and Analysis Software (GADRAS). These DRFs enhance GADRAS by enabling full spectral analysis functionality for previously underrepresented detector materials. Additionally, neutron-specific DRFs are determined for neutron energy spectrum unfolding applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗