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At least 397 records · Page 22

iSPECTRON: a simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software

We introduce iSPECTRON, an open source (under the Educational Community License version 2.0) program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic spectra are expressed in term of the electronic eigenstates, obtained through quantum chemistry computations, and vibrational/bath effects are incorporated in the framework of the displaced harmonic oscillator model, where all required quantities are computed at the Franck-Condon point. The code capabilities are illustrated by simulating linear absorption, transient absorption and two dimensional electronic spectra of the pyrene molecule. Two levels of electronic structure theory, TDDFT (with NWChem) and RASSCF/RASPT2 (with OpenMolcas), are compared where possible. Acknowledgements: F.S., A.N., D.R.N., N.G., S.M, M.G. acknowledge support from the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division under Award Nos. DE-SC0019484, KC-030103172684. The Spectron code was developed with support from the National Science Foundation (Grant CHE- 1953045). This research benefited from computational resources provided by EMSL, a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research and located at PNNL. PNNL is operated by Battelle Memorial Institute for the United States Department of Energy under DOE Contract No. DE-AC05-76RL1830.

Segatta, Francesco↗

Integrative visualization of the molecular structure of a cellular microdomain

Abstract An integrative approach to visualization is used to create a visual snapshot of the structural biology of the polar microdomain of Caulobacter crescentus . The visualization is based on the current state of molecular and cellular knowledge of the microdomain and its cellular context. The collaborative process of researching and executing the visualization has identified aspects that are well determined and areas that require further study. The visualization is useful for dissemination, education, and outreach, and the study lays the groundwork for future 3D modeling and simulation of this well‐studied example of a cellular condensate.

59 BASIC BIOLOGICAL SCIENCES↗

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗

A Systems-Level Approach to Address Risks and Ethics in Artificial Intelligence Systems

Artificial intelligence (AI) is rapidly changing the world, from completely controlling routine or mundane tasks like text and image generation, to powering advanced algorithms that control critical systems. The recent advances in generative AI quickly overwhelmed multiple industries from education to finance as first adopters rushed (and continue to rush) to take advantage of the technology. The expanding AI ecosystem presents novel risks and ethical challenges that must be handled to ensure that technology is leveraged fairly and ethically. There are intertwined risks and ethical challenges stemming from the stochastic nature of AI (i.e., intrinsic risks), as well as from specific applications (i.e., extrinsic risks). Appropriately regulating AI requires a systems-approach to develop an integrated solution to these dependent challenges. Thus far, however, questions of risk, ethics and regulation appear to occupy separate spaces. This paper reviews the risks and ethical implications of AI and proposes a system-level approach to integrating ethics and regulation for the nascent industry.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

Parameter estimation from spontaneous imbibition into volcanic tuff

Two-phase fluid flow properties underlie quantitative prediction of water and gas movement, but constraining these properties typically requires multiple time-consuming laboratory methods. The estimation of two-phase flow properties (van Genuchten parameters, porosity, and intrinsic permeability) is illustrated in cores of vitric nonwelded volcanic tuff using Bayesian parameter estimation that fits numerical models to observations from spontaneous imbibition experiments. The uniqueness and correlation of the estimated parameters is explored using different modeling assumptions and subsets of the observed data. The resulting estimation process is sensitive to both moisture retention and relative permeability functions, thereby offering a comprehensive method for constraining both functions. The data collected during this relatively simple laboratory experiment, used in conjunction with a numerical model and a global optimizer, result in a viable approach for augmenting more traditional capillary pressure data obtained from hanging water column, membrane plate extractor, or mercury intrusion methods. This method may be useful when imbibition rather than drainage parameters are sought, when larger samples (e.g., including heterogeneity or fractures) need to be tested that cannot be accommodated in more traditional methods, or when in educational laboratory settings.

58 GEOSCIENCES↗

Decision-making Framework to Support the End-of-Life Management of High-Activity Radioactive Sources

Sealed radioactive sources are used for an extremely wide range of purposes, including as radiation sources in various nuclear facilities, universities, hospitals, biomedical and industrial applications, as well as for geological prospecting and exploration. The proper management of these sealed radioactive sources once they have reached their end-of-life is still a global challenge. Very few field-tested Mobile Hot Cells (MHC) exist in the world to support the end-of-life management of disused high-activity radioactive sources. One of the critical challenges that a source recovery team encounters on each site is to find adequate space, and access to that space to complete the staging and recapture process with a MHC; this process is tedious, uncertain, and time-consuming. Therefore, it is essential to understand the planning and management of the MHC setup and takedown. Currently, there isn't an single capable planning tool that will provide an effective medium to plan, inform, educate, and communicate knowledge about the environment where the MHC will be deployed. We present a novel approach for the planning and management of the deployment of the MHC to several different sites that relies on technology. Furthermore, this planning tool will support collaboration, promote information sharing, and foster better decision making processes, resulting in a more efficient, and reliable setup and source recovery with the MHC.

61 RADIATION PROTECTION AND DOSIMETRY↗

Research Connections: Career and Research Journeys from the SMP Community. Association for Women in Mathematics Series

This book aims to provide perspectives on important questions that undergraduate and graduate students in mathematics ask themselves. Each chapter gives readers a taste of a different mathematician’s work, presented with enough background material that an advanced undergraduate or early graduate student can understand the key ideas of the research. Each mathematical contribution is prefaced by a short biography of the mathematician who wrote the chapter, to give the reader a connection to the author and provide examples of paths from undergraduate education, through graduate school and beyond.

mathematics, research, biographies↗

A2SD: Accelerating Scientific Innovation Through Autonomous Discovery Systems

The 2025 Advancing Autonomous Scientific Discovery (A2SD) workshop convened researchers from academia, national laboratories, and industry to explore the transformative role of autonomy in scientific discovery. The workshop highlighted a convergence of artificial intelligence, robotics, and computational workflows into autonomous systems capable of accelerating the scientific process. Presentations and discussions spanned autonomous experimentation, intelligent workflow orchestration, digital twins, and agent-based systems for managing complex research ecosystems. Key challenges discussed included interoperability across heterogeneous infrastructures, near real-time data management under FAIR principles, reproducibility, and the integration of human oversight. The workshop also emphasized the need for modular software interfaces, federated learning models, and education initiatives to support a next-generation scientific workforce.

Taufer, Michela [University of Tennessee, Knoxvill↗

CubeSats for Gamma-Ray Astronomy [Book Chapter]

After many years of flying in space primarily for educational purposes, CubeSats – tiny satellites with form factors corresponding to arrangements of “1U” units, or cubes, each 10 cm on a side – have come into their own as valuable platforms for technology advancement and scientific investigations. CubeSats offer comparatively rapid, low-cost access to space for payloads that can be built, tested, and operated by relatively small teams, with substantial contributions from students and early career researchers. Continuing advances in compact, low-power detectors, readout electronics, and flight computers have now enabled X-ray and gamma-ray sensing payloads that can fit within the constraints of CubeSat missions, permitting in-orbit demonstrations of new techniques and innovative high-energy astronomy observations. Gamma-ray-sensing CubeSats are certain to make an important contribution in the new era of multi-messenger, time-domain astronomy by detecting and localizing bright transients such as gamma-ray bursts, solar flares, and terrestrial gamma-ray flashes; however, other astrophysical science areas requiring long observations in a low-background environment, including gamma-ray polarimetry, studies of nuclear lines, and measurement of diffuse backgrounds, will likely benefit as well. Here we present the primary benefits of CubeSats for high-energy astronomy, highlight the scientific areas currently or soon to be studied, and review the missions that are currently operating, under development, or proposed. A rich portfolio of CubeSats for gamma-ray astronomy already exists, and the potential for a broad range of creative and scientifically productive missions in the near future is very high.

79 ASTRONOMY AND ASTROPHYSICS↗

Workforce Development Survey Results: Industry, Government Laboratories, Academia, and Recent Graduates

Herein, we describe the results of the survey from the TMS Education committee. The committee designated a subcommittee on Workforce Development to survey professionals in industry/government laboratories (I/G), academia (A), and recent graduates (RG) to gain insights into the alignment of materials science curricula with workforce needs. The survey project began with a charter to explore any disconnects that might exist between university materials curriculum and workforce knowledge, skill, and ability needs for MSE-related careers, and also highlight critical areas of excellence that should be preserved. Focused surveys for each category were developed and received over 150 responses, including 83 responses from industry/government, 40 responses from recent graduates, 29 responses from academia.

99 GENERAL AND MISCELLANEOUS↗

PDMATLAB2D: A Peridynamics MATLAB Two-dimensional Code

PDMATLAB2D is a meshfree peridynamics implementation in MATLAB suitable for simulation of two-dimensional fracture problems. The purpose of this code is twofold. First, it provides an entry-level peridynamics computational tool for educational and training purposes. Second, it serves as an accessible and easily modifiable computational tool for peridynamics researchers who would like to adapt the code for a multitude of peridynamics simulation scenarios. The current version of the code implements a bond-based brittle elastic peridynamic model and a critical stretch criterion for bond breaking. However, the code is designed to be extendable for other peridynamic models and computational features. In this paper, we provide an overview of the code structure and functions with illustrative examples. In conclusion, due to the integrated computation and postprocessing MATLAB capabilities, PDMATLAB2D can serve as an effective testbed for testing new constitutive models and advanced numerical features for peridynamics computations.

97 MATHEMATICS AND COMPUTING↗

Razorback – A reactor transient analysis code for large rapid reactivity additions in a natural circulation research reactor

Research reactors play an important role in higher education, scientific research, and medical radioisotope production around the world. It is thus important to ensure the safety of facility workers and the public. This work presents a new reactor transient analysis code referred to as Razorback. The code has been developed for the evaluation of large rapid reactivity addition in research reactors. Its initial focus is the Annular Core Research Reactor (ACRR) at Sandia National Laboratories. Results have been validated against ACRR pulse operations. Razorback models the reactor kinetics, fuel element heat transfer, fuel element thermal expansion, and natural circulation coolant channel thermal-hydraulic response. Simulation results for ACRR pulse operations are shown to agree very well with operational data obtained from the ACRR. Finally, Razorback is expected to be a valuable tool for ACRR pulse performance prediction and ACRR reactor safety analyses.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

The role of social support on midwestern farmers’ willingness to grow perennial bioenergy crops

The lack of farmers' willingness to grow perennial bioenergy crops (PBCs) presents a critical barrier to the emergence of cellulosic biofuel production. The willingness relies on a complex network of economic, environmental, and social drivers, among which the influence of social factors (e.g., the influence of neighborhood, community, and communication) is less understood. This study addresses this knowledge gap via a survey analysis of midwestern farmers. The survey data are analyzed through ordinary least square regression and structural equation model, which together investigate the individual and interactive impacts of multiple factors on farmers' decisions to adopt PBCs. Based on a farm-scale analysis, six statistically significant predictors of farmer willingness to grow PBCs are identified: perception of PBCs' environment benefits, education level, willingness to take risks, familiarity with PBCs, portion of peers already growing PBCs, and support of biorefineries locating in the local community. Among these, the latter three predictors are social support variables. It is found that familiarity with the crops is the most significant predictor of willingness; familiarity is also an important intermediate variable that mediates the influence of many other predictors. In addition, peer adoption can both directly and indirectly affect willingness via its influence on familiarity. Furthermore, these findings suggest that it is a pressing need to improve farmers’ knowledge of PBCs to promote the adoption of such crops.

09 BIOMASS FUELS↗

Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors

Suicide is a leading cause of death worldwide, and non-fatal suicide attempts, which occur far more frequently, are a major source of disability and social and economic burden. Both have substantial genetic etiology, which is partially shared and partially distinct from that of related psychiatric disorders. Methods: We conducted a genome-wide association study (GWAS) of 29,782 suicide attempt (SA) cases and 519,961 controls in the International Suicide Genetics Consortium. The GWAS of SA was conditioned on psychiatric disorders using GWAS summary statistics via mtCOJO, to remove genetic effects on SA mediated by psychiatric disorders. We investigated the shared and divergent genetic architectures of SA, psychiatric disorders and other known risk factors. Results: Two loci reached genome-wide significance for SA: the major histocompatibility complex and an intergenic locus on chromosome 7, which remained associated with SA after conditioning on psychiatric disorders and replicated in an independent cohort from the Million Veteran Program. This locus has been implicated in risk-taking, smoking, and insomnia. SA showed strong genetic correlation with psychiatric disorders, particularly major depression, and also with smoking, pain, risk-taking, sleep disturbances, lower educational attainment, reproductive traits, lower socioeconomic status and poorer general health. After conditioning on psychiatric disorders, the genetic correlations between SA and psychiatric disorders decreased, whereas those with non-psychiatric traits remained largely unchanged. Conclusions: Our results identify a risk locus that contributes more strongly to SA than other phenotypes and suggest a shared underlying biology between SA and known risk factors that is not mediated by psychiatric disorders.

60 APPLIED LIFE SCIENCES↗

The future low-temperature geochemical data-scape as envisioned by the U.S. geochemical community

Data sharing benefits the researcher, the scientific community, and the public by allowing the impact of data to be generalized beyond one project and by making science more transparent. However, many scientific communities have not developed protocols or standards for publishing, citing, and versioning datasets. One community that lags in data management is that of low-temperature geochemistry (LTG). This paper resulted from an initiative from 2018 through 2020 to convene LTG and data scientists in the U.S. to strategize future management of LTG data. Through webinars, a workshop, a preprint, a townhall, and a community survey, the group of U.S. scientists discussed the landscape of data management for LTG – the data-scape. Currently this data-scape includes a “street bazaar” of data repositories. This was deemed appropriate in the same way that LTG scientists publish articles in many journals. The variety of data repositories and journals reflect that LTG scientists target many different scientific questions, produce data with extremely different structures and volumes, and utilize copious and complex metadata. Nonetheless, the group agreed that publication of LTG science must be accompanied by sharing of data in publicly accessible repositories, and, for sample-based data, registration of samples with globally unique persistent identifiers. LTG scientists should use certified data repositories that are either highly structured databases designed for specialized types of data, or unstructured generalized data systems. Recognizing the need for tools to enable search and cross-referencing across the proliferating data repositories, the group proposed that the overall data informatics paradigm in LTG should shift from “build data repository, data will come” to “publish data online, cybertools will find”. Funding agencies could also provide portals for LTG scientists to register funded projects and datasets, and forge approaches that cross national boundaries. Finally, the needed transformation of the LTG data culture requires emphasis in student education on science and management of data.

58 GEOSCIENCES↗

The DEAL.II finite element library: Design, features, and insights

DEAL.II is a state-of-the-art finite element library focused on generality, dimension-independent programming, parallelism, and extensibility. In this paper, we outline its primary design considerations and its sophisticated features such as distributed meshes, h p -adaptivity, support for complex geometries, and matrix-free algorithms. But DEAL.II is more than just a software library: It is also a diverse and worldwide community of developers and users, as well as an educational platform. We therefore also discuss some of the technical and social challenges and lessons learned in running a large community software project over the course of two decades.

97 MATHEMATICS AND COMPUTING↗

Cross-domain digital twin architecture for predictive maintenance via machine learning and Large Language Models

This research introduces a comprehensive framework for creating and deploying a digital twin platform for continuous monitoring and predictive maintenance within industrial settings. Through utilizing advanced technologies, including Unreal Engine 5, Unity 3D, the Message Queue Telemetry Transport protocol, Random Forest machine learning algorithms, and Large Language Models (LLMs), we establish a platform that digitally reproduces physical equipment and translates digital controls into real-world actions. This facilitates preventive maintenance approaches and improves operational effectiveness. The digital twin platform gathers sensor data from operational equipment, analyzes it using machine learning, and delivers practical insights to prevent potential malfunctions and enhance equipment performance. Furthermore, the incorporation of a web portal enables efficient monitoring and access to historical data, educational materials, and equipment status information. Preliminary findings indicate that digital twins can transform industrial equipment management and maintenance methodologies.

97 MATHEMATICS AND COMPUTING↗

ADAM: A web platform for graph-based modeling and optimization of supply chains

Modeling and optimization are essential tasks that arise in the analysis and design of supply chains (SCs). SC models are essential for understanding emergent behavior such as transactions between participants, inherent value of products exchanged, as well as impact of externalities (e.g., policy and climate) and of constraints. Unfortunately, most users of SC models have limited expertise in mathematical optimization, and this hinders the adoption of advanced decision-making tools. Here, in this work, we present ADAM, a web platform that enables the modeling and optimization of SCs. ADAM facilitates modeling by leveraging intuitive and compact graph-based abstractions that allow the user to express dependencies between locations, products, and participants. ADAM model objects serve as repositories of experimental, technology, and socio-economic data; moreover, the graph abstractions facilitate the organization and exchange of models and provides a natural framework for education and outreach. Here, we discuss the graph abstractions and software design principles behind ADAM, its key functional features and workflows, and application examples.

97 MATHEMATICS AND COMPUTING↗