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At least 847 records · Page 47

Π4U: A high performance computing framework for Bayesian uncertainty quantification of complex models

We present Π4U,{sup 1} an extensible framework, for non-intrusive Bayesian Uncertainty Quantification and Propagation (UQ+P) of complex and computationally demanding physical models, that can exploit massively parallel computer architectures. The framework incorporates Laplace asymptotic approximations as well as stochastic algorithms, along with distributed numerical differentiation and task-based parallelism for heterogeneous clusters. Sampling is based on the Transitional Markov Chain Monte Carlo (TMCMC) algorithm and its variants. The optimization tasks associated with the asymptotic approximations are treated via the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). A modified subset simulation method is used for posterior reliability measurements of rare events. The framework accommodates scheduling of multiple physical model evaluations based on an adaptive load balancing library and shows excellent scalability. In addition to the software framework, we also provide guidelines as to the applicability and efficiency of Bayesian tools when applied to computationally demanding physical models. Theoretical and computational developments are demonstrated with applications drawn from molecular dynamics, structural dynamics and granular flow.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of the stoichiometry, affinity and cooperativity of multi-site interactions. The principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT are reviewed, their complementarity in GMMA is described and a new GMMA simulation tool set in SEDPHAT is presented. Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysical techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

SERIIUS-MAGEEP Visiting Scholars Program

Recent studies have assessed closed-loop supercritical carbon dioxide (s-CO 2 ) Brayton cycles to be a higher energy-density system in comparison to equivalent superheated steam Rankine systems. At turbine inlet conditions of 700°C and 20 MPa, a cycle thermal efficiency of ~50% can be achieved. Achieving these high efficiencies will help concentrating solar power (CSP) technologies to become a competitive alternative to current power generation methods. To incorporate an s-CO 2 Brayton power cycle in a solar power tower system, the development of a solar receiver capable of providing an outlet temperature of 700°C (at 20 MPa) is necessary. To satisfy the temperature requirements of an s-CO 2 Brayton cycle with recuperation and recompression, the s-CO 2 must undergo a temperature rise of ~200°C as it flows through the solar receiver. The main objective is to develop an optical-thermal-fluid and structural model to validate a tubular receiver that will receive a heat input ~0.33 MWth from the heliostat field at the National Solar Thermal Test Facility (NSTTF), Albuquerque, NM, USA. We also commenced the development of computational models and testing of air receivers being developed by the Indian Institute of Science (IISc) and the Indian Institute of Technology in Bombay (IIT-B). The helical tubular receiver is expected to counteract the effect of thermal expansion while using a cavity to reduce the radiative and convective losses. Initially, this receiver will be tested for a temperature range of 100-300°C under 1 MPa of pressurized air. The helical air receiver will be exposed to 10kWth to achieve a temperature rise of ~200°C. Preliminary tests to validate the modeling will be performed before the design and construction of a larger scale receiver. Lastly, I focused on the development of a new computational tool that would allow us to perform a nodal creep-fatigue analysis on the receivers and heat exchangers being developed. This tool was developed using MATLAB and is capable of processing the results obtained from ANSYS Fluent and Structural combined, which was limited when using commercial software. The main advantage of this code is that it can be modified to run in parallel making it more affordable and faster compared to commercial codes available. The code is in the process of validation and is currently being compared to nCode Design Life.

25 ENERGY STORAGE↗

TEAM Project Review, Year 2

This report summarizes our research activities within the TEAM project between December 2020 and December 2021, funded by the ASCR Advanced Research in Quantum Computing program. During the reporting period the LLNL-MSU team has made progress on several fronts. An overarching goal of the team is to provide a comprehensive suite of software tools that can be used for the Characterize-Optimize-Compute loop needed to implement and execute algorithms on quantum devices. We are concurrently developing lightweight solvers that can be used on desktop computers to find optimal control pulses and to characterize small quantum systems (consisting of a few transmons and cavities). However, desktop computers are insufficient for simulating and characterizing larger quantum systems. We have therefore also developed parallel, distributed memory, simulators and optimization solvers, both for open and closed quantum systems. These parallel solvers have, for example, been used to study quantum optimal control for pure-state preparation, utilizing 1000’s of cores on a modern high-performance computing (HPC) platform.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Development of Updated ABsorption SIMulation Software (ABSIM)

ABsorption SIMulation, ABSIM, was developed for the simulation of absorption systems by The Oak Ridge National Laboratory during 1980s and 1990s. ABSIM provides a platform for users to investigate various cycle configurations and working fluids, to calculate their operating parameters, to predict their performance, and to compare them with each other on a uniform basis. ABSIM is indeed a very useful and accurate tool for researchers to investigate various absorption systems. However, it has not been well maintained: it is incompatible with recent operating systems; the interface needs improved user-friendliness, and the system needs better parameter setting and debugging tools to help achieve convergence. Therefore, it is highly needed to update and improve ABSIM. The paper presents recent efforts to improve ABSIM s compatibility with current operating systems, user interface, and analysis capabilities. The paper details the features and functions of the newly updated ABSIM software. The new ABSIM still uses the previously validated calculation engine of the old ABSIM. The new graphic user interfaces (GUI) were developed in Qt, which is an open source license GUI software based on C++. XML was used as the database for data storage in the new ABSIM. The new ABSIM has been designed to be easily learned and used. It has enhanced editing and construction functions, plus enhanced analysis features including parametric tables, plotting, property plots, and master panels for debugging. A single effect water/LiBr absorption system is used as a case study in this paper to illustrate the features, capabilities, and functions of the new ABSIM. This case study was actually an example system available in the old ABSIM. The new version of ABSIM will be continuously developed to include additional subroutines for the components in liquid desiccant systems. The new ABSIM will be available to public for free. The ultimate goal of the new ABSIM is to allow it to become a simulation platform for both absorption heat pump and liquid desiccant systems.

ABSIM↗

A Program Analysis Tool to Query Static and Dynamic Characteristics of HPC Applications

Emerging HPC platforms are becoming extraordinarily difficult to program as a result of complex, deep and heterogeneous memory hierarchies, heterogeneous cores, and the need to divide work and data among them. New programming models and libraries are being developed to aid in porting efforts of application developers, but substantial code restructuring is still necessary to fully make use of these new technologies. To do this effectively, these developers need information about their source code characteristics, including static and dynamic (e.g. performance) information to direct their optimisation efforts and make key decisions. On the other hand, system administrators need to understand how users are using the software stack and resources on their systems to understand what software they need to provide to improve the productivity of the users on a platform.In this paper we describe a tool that combines compiler and profiler information to query performance characteristics within an application or across multiple applications on a given platform. Static and dynamic data about applications are collected and stored together in an SQL database that can be queried by either a developer or a system administrator. We will demonstrate the capabilities of this tool via a real-world example from application-driven case studies that aims at understanding the use of scientific libraries on a routine from the molecular simulation application CP2K.

Welch, Aaron↗

Demonstration of a modeling toolkit for the design of building electrical distribution systems

The deployment of building equipment (e.g., lighting, security) and miscellaneous electrical loads that fundamentally require DC power for operation is increasing. Powering these DC loads has traditionally required an AC/DC converter, but the installation of photovoltaic (PV) and battery energy storage systems that primarily produce DC power eliminates the need for AC/DC converters at each end-device. However, analyzing system energy efficiency and cost for different electrical distribution architectures can be challenging as software tools that support this are not readily available. This paper presents preliminary results from a laboratory verification of the Building Electrical Efficiency Analysis Model (BEEAM) toolkit that was developed to address this gap. Three different eight-luminaire lighting systems comprised of market-available products were designed and modeled: one that used traditional AC distribution, a second that used a hybrid AC -to- centralized DC electrical distribution architecture, and a third that used a hybrid AC -to- distributed DC architecture. Notably, AC/DC conversions are required in all three systems. BEEAM models for LED drivers as well as Power-over-Ethernet (PoE) switches were created using laboratory characterization data. The lighting systems were simulated in Modelica, and the results were compared with each other and physics-based expectations. Simulation results show that PoE system energy efficiency is highly dependent on both device specification (e.g., LED driver and PoE switch efficiency) and system architecture (e.g., PoE switch loading) choices, as expected. For the products and system architectures selected for this study, the two DC systems were found to be less efficient than the AC system over the course of typical operation. In future work, simulation results will be compared with laboratory measurements to validate the usefulness of this software for design, and lighting systems with integrated PV and battery energy storage will be simulated to quantify the energy performance improvements that result from the elimination of some AC/DC converters.

Waghale, Anay S.↗

RetroTide v1.0

RetroTide is a retrobiosynthesis software tool, designed to guide the design of biological pathways to make valuable small molecules. It takes as input a desired small molecule chemical structure, and outputs a design for a polyketide synthase enzyme (PKS) that has the closest possible chemical structure, as accessible by PKS chemistry. It is developed as a Python software library, and internally performs a search of the PKS design space, while simulating the chemicals produced by each design.

Backman, Tyler↗

Building Efficiency Targeting Tool for Energy Retrofits (BETTER) Application Programing Interface (API) (BETTER API) v1.0

The BETTER API allows advanced users and developers to access BETTER's analytical functionalities via HTTP requests from their own software platform without using the BETTER web-interface. API users prepare the input data and analysis configurations in a JSON format and send it to the web application via an HTTP request. The web application runs the analytical workflow on the back end and returns an HTTP response in JSON format. The user can then decide to render the results or further process it.

Szum, Carolyn↗

The HUNTER Dynamic Human Reliability Analysis Tool: Coupling an External Plant Code

The Human Unimodel for Nuclear Technology to Enhance Reliability (HUNTER) is a framework to support dynamic human reliability analysis (HRA) with the aim to develop standalone software to perform the dynamic HRA calculations. Within the HRA, human actions in nuclear power plants (NPPs) are predicated by plant states, and human actions influence the plant. In other words, plant operations are necessarily recursive, and it becomes challenging to model complex human-plant interactions. Consequently, we have linked two software simulations that complement those shortcomings. RELAP5-3D—the Reactor Excursion and Leak Analysis Program (RELAP; Aumiller, Tomlinson, and Bauer 2001) is the foundational thermal-hydraulic software used to model nuclear systems. Using RELAP5-3D, we have simulated the plant operations proceeding according to procedures developed to address emergent situations in NPPs. Plant operations include various actions such as the operator checking plant parameters, as well as actions that are continuously performed over time until a specific parameter reaches certain criteria. That means that HUNTER and RELAP5-3D exchange information with each other and should be carried out simultaneously over time. To simulate plant operations, which represent the actual operator checks of plant parameters and corresponding manual control actions, changes in plant status are identified through simulation and performed according to the criteria and order of the procedure. Thus, the goal of coupling HUNTER with RELAP5-3D is to facilitate synchronous coupling, where human and plant models provide iterative feedback loops that drive the course of actions. The advantage of coupling with RELAP5-3D to serve as the external environment module in HUNTER is the ability to customize the plant model and streamline for particular model applications. In this paper, we will address the key features of the coupling and the coupling structure built to perform the feedback loops.

99 GENERAL AND MISCELLANEOUS↗

Device Scale Modeling of Solvent Absorption using MFIX-TFM

Recent climate change is largely attributed to greenhouse gases (e.g., carbon dioxide, methane) and fossil fuels account for a large majority of global CO 2 emissions. That said, fossil fuels will continue to play a significant role in the generation of power for the foreseeable future. The extent to which CO 2 is emitted needs to be reduced, however, carbon capture and sequestration are also necessary actions to tackle climate change. Different approaches exist for CO 2 capture including both post-combustion and pre-combustion technologies, oxy-fuel combustion and/or chemical looping combustion. The focus of this effort is on post-combustion solvent-absorption technology. To apply CO 2 technologies at commercial scale, the availability and maturity and the potential for scalability of that technology need to be considered. Solvent absorption is a proven technology but not at the scale needed by typical power plant. The scale up and down and design of laboratory and commercial packed bed reactors depends heavily on the specific knowledge of two-phase pressure drop, liquid holdup, the wetting efficiency and mass transfer efficiency as a function of operating conditions. Simple scaling rules often fail to provide proper design. Conventional reactor design modeling approaches will generally characterize complex non-ideal flow and mixing patterns using simplified and/or mechanistic flow assumptions. While there are varying levels of complexity used within these approaches, none of these models resolve the local velocity fields. Consequently, they are unable to account for important design factors such as flow maldistribution and channeling from a fundamental perspective. Ideally design would be aided by development of predictive models based on truer representation of the physical and chemical processes that occur at different scales. Computational fluid dynamic (CFD) models are based on multidimensional flow equations with first principle foundations. CFD models can include a more accurate physical description of flow processes and be modified to include more complex behavior. Wetting performance and spatial liquid distribution inside the absorber are recognized as weak areas of knowledge requiring further investigation. CFD tools offer a possible method to investigating such topics and gaining a better understanding of their influence on reactor performance. This report focuses first on describing a hydrodynamic model for countercurrent gas-liquid flow through a packed column and then on the chemistry, heat and mass transfer specific to CO 2 absorption using monoethanolamine (MEA). The indicated model is implemented in MFIX, a CFD open source software package. The user defined functions needed to build this model are described in detail along with the keywords for the corresponding input file. A test case is outlined along with a few results. The example serves to briefly illustrate the developed CFD tool and its potential capability to investigate solvent absorption.

09 BIOMASS FUELS↗

SAM Co-Development to Support Fluoride-salt-cooled High-temperature Reactor Design and Licensing (CRADA 2018-18177 Final Report)

This project aims to raise the SAM code's technical and commercial maturity level to enable the Kairos Power ("Kairos") to use SAM to support its KP-FHR design analysis and licensing application. Argonne National Laboratory ("Argonne") has actively developed and maintained SAM, a modern system-level analysis tool for advanced nonlight water reactors safety analysis. Kairos is currently actively pursuing development of an FHR design and associated technology, and consequently requires a pedigreed safety analysis tool. The purpose of this project is to increase the maturity of the SAM code for the modeling and simulation of the KP-FHR design, thus enabling its use in safety analyses that support licensing application. Argonne will primarily be responsible for software design, development, and testing; while Kairos will be responsible for software requirements, assessment of software capabilities, needs, gaps, and priorities, and development of proprietary models. The research and development activities for the joint SAM development project include: a series of identification and prioritization studies on design characteristics, event sequences, relevant phenomena, and software capabilities; SAM capability enhancements for specific KP-FHR systems and components; performing code verification and validations; integrating uncertainty quantification (UQ), model calibration, and sensitivity analysis (SA) techniques in safety analyses; and raising the software quality rigor level for commercial-grade applications.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Secure Route: Roadway Risk Mapping for Transportation Planners

The secure transport of sensitive materials across U.S. road networks pose unique challenges for local, state, and federal agencies. Threats range from random events (e.g., accidents, medical emergencies, mechanical failures) to opportunistic or organized tactical assaults. Although the probability of such attacks is very low, the consequences of material loss to foreign states or terrorists can be catastrophic, qualifying these scenarios as “grey swan” events—low-probability, high-impact occurrences that are predictable but difficult to quantify. Traditional risk assessments struggle in these contexts, necessitating a shift toward subjective risk perception to inform planning. Risk perception in transport planning is shaped by various factors, including knowledge of adversarial capabilities, vehicle defenses, manifest details, and geographic features along the route. Geographic features such as bridges, tunnels, roadside elevation, and gaps in cellular coverage introduce vulnerabilities, while mitigative features include safe havens, police stations, and medical services. Temporal variables such as congestion, accidents, and weather further complicate route planning. Despite their importance, existing routing tools like Google Maps and commercial software do not explicitly account for geographic risk features, requiring planners to rely on personal familiarity with routes—a time-intensive, non-scalable approach. This work addresses these gaps by: (1) developing datasets that catalog geographic risk features along U.S. roadways, (2) eliciting risk perceptions from experienced transportation security experts, and (3) linking these perceptions to roadway conditions and geographic data. We implement these capabilities within Secure Route a novel mapping tool for classifying route segment risks associated with roadway conditions. This system provides transportation planners with an intuitive interface to assess and contextualize risk along potential routes, improving decision-making for secure transport. We present current progress in this effort and identify next steps.

Stewart, Robert [ORNL] (ORCID:0000000281867559)↗

Sustainability and Reproducibility via Containerized Computing

Recent developments in the commercial open source community have catalysed the use of Linux containers for scalable deployment of web-based applications to the cloud. Scientific software can be containerized with dependencies, configuration files, post-processing tools and even simulation results, referred to as containerized computing. This new approach promises to significantly improve sustainability, productivity and reproducibility. In this article, we present our experiences, technology, and future plans for open source containerization of software used to model particle and radiation beams. Vagrant is central to our approach, using Docker for cloud deployment and VirtualBox virtual machines for deployment to Mac OS and Windows computers. Our technology enables seamless switching between the desktop and the cloud to simplify simulation development and execution.

97 MATHEMATICS AND COMPUTING↗

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 software package for plasma facing component analysis and design: the Heat flux Engineering Analysis Toolkit (HEAT)

The engineering limits of plasma facing components (PFCs) constrain the allowable operational space of tokamaks. Poorly managed heat fluxes that push the PFCs beyond their limits not only degrade core plasma performance via elevated impurities, but can also result in PFC failure due to thermal stresses or melting. Simple axisymmetric assumptions fail to capture the complex interaction between 3D PFC geometry and 2D or 3D plasmas. This results in fusion systems that must either operate with increased risk or reduce PFC loads, potentially through lower core plasma performance, to maintain a nominal safety factor. High precision 3D heat flux predictions are necessary to accurately ascertain the state of a PFC given the evolution of the magnetic equilibrium. A new code, the Heat flux Engineering Analysis Toolkit (HEAT), has been developed to provide high precision 3D predictions and analysis for PFCs. HEAT couples many otherwise disparate computational tools together into a single open source python package. Magnetic equilibrium, engineering CAD, finite volume solvers, scrape off layer plasma physics, visualization, high performace computing, and more, are connected in a single web-based user interface. Linux users may use HEAT without any software prerequisites via an appImage. This manuscript introduces HEAT, discusses the software architecture, presents first HEAT results, and outlines physics modules in development.

divertor physics↗

SU-E-T-103: Development and Implementation of Web Based Quality Control Software

Purpose: Historically many radiation medicine programs have maintained their Quality Control (QC) test results in paper records or Microsoft Excel worksheets. Both these approaches represent significant logistical challenges, and are not predisposed to data review and approval. It has been our group's aim to develop and implement web based software designed not just to record and store QC data in a centralized database, but to provide scheduling and data review tools to help manage a radiation therapy clinics Equipment Quality control program. Methods: The software was written in the Python programming language using the Django web framework. In order to promote collaboration and validation from other centres the code was made open source and is freely available to the public via an online source code repository. The code was written to provide a common user interface for data entry, formalize the review and approval process, and offer automated data trending and process control analysis of test results. Results: As of February 2014, our installation of QAtrack+ has 180 tests defined in its database and has collected ∼22 000 test results, all of which have been reviewed and approved by a physicist via QATrack+'s review tools. These results include records for quality control of Elekta accelerators, CT simulators, our brachytherapy programme, TomoTherapy and Cyberknife units. Currently at least 5 other centres are known to be running QAtrack+ clinically, forming the start of an international user community. Conclusion: QAtrack+ has proven to be an effective tool for collecting radiation therapy QC data, allowing for rapid review and trending of data for a wide variety of treatment units. As free and open source software, all source code, documentation and a bug tracker are available to the public at https://bitbucket.org/tohccmedphys/qatrackplus/.

07 ISOTOPE AND RADIATION SOURCES↗

SU-F-E-03: PET/CT Guided Dose Boost to Hypoxic Sub-Volume in Nasopharyngeal Carcinomas Using Self-Optimizing Non-Uniform VMAT

Purpose: This study is to evaluate the feasibility of simultaneously integrated boost (SIB) to hypoxic subvolume (HTV) in nasopharyngeal carcinomas under the guidance of 18F-Fluoromisonidazole (FMISO) PET/CT using a novel non-uniform volumetric modulated arc therapy (VMAT)technique. Methods: Eight nasopharyngeal carcinoma patients treated with conventional uniform VMAT were retrospectively analyzed. For each treatment, actual conventional uniform VMAT plan with two or more arcs (2–2.5 arcs, totally rotating angle < 1000o) was designed with dose boost to hopxic subvolume (total dose, 84Gy) in the gross tumor volme (GTV) under the guidance of 18F- FMISO PET/CT. Based on the same dataset, experimental single arc non-uniform VAMT plans were generated with the same dose prescription using customized software tools. Dosimetric parameters, quality assurance and the efficiency of the treatment delivery were compared between the uniform and non-uniform VMAT plans. Results: To develop the non-uniform VMAT technique, a specific optimization model was successfully established. Both techniques generate high-quality plans with pass rate (>98%) with the 3mm, 3% criterion. HTV received dose of 84.1±0.75Gy and 84.1±1.2Gy from uniform and non-uniform VMAT plans, respectively. In terms of target coverage and dose homogeneity, there was no significant statistical difference between actual and experimental plans for each case. However, for critical organs at risk (OAR), including the parotids, oral cavity and larynx, dosimetric difference was significant with better dose sparing form experimental plans. Regarding plan implementation efficiency, the average machine time was 3.5 minutes for the actual VMAT plans and 3.7 minutes for the experimental nonuniform VMAT plans (p>0.050). Conclusion: Compared to conventional VMAT technique, the proposed non-uniform VMAT technique has the potential to produce efficient and safe treatment plans, especially in cases with complicated anatomical structures and demanding dose boost to subvolumes.

60 APPLIED LIFE SCIENCES↗