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At least 1,657 records · Page 92

A new approach to model geomaterials with heterogeneous properties in thermo-hydro-mechanical coupled problems

The main objective of this article is to present a new approach to model coupled thermo-hydro-mechanical problems considering geomaterials with heterogeneous properties. This approach has been implemented in the software CODE_BRIGHT and it provides the possibility of considering geomaterials with a spatially correlated heterogeneous field of porosity, following a normal distribution. This spatial correlation can be isotropic or anisotropic. An important feature of this approach is that material properties such as intrinsic permeability, thermal conductivity, diffusivity, retention curve, elastic modulus or cohesion are defined as a function of porosity and, thus, they become heterogeneous with spatial correlation and, eventually, anisotropic. A validation exercise and other basic numerical examples have been carried out to illustrate the possibilities of the proposed approach. The results, which have been compared with a homogeneous case, show that considering heterogeneous fields can be relevant in different modelling problems, especially coupled thermo-hydro-mechanical problems.

42 ENGINEERING↗

2019 Computing Sciences Strategic Plan

Computing has transformed nearly every aspect of scientific inquiry — across disciplines and across scales — from the behavior of subatomic particles to the formation of structures in the early universe, from the assembly of the human genome to the evolution of earth systems. Over the past two decades, computing has become an integral part of how Berkeley Lab is “Bringing Science Solutions to the World.” Advances in computing and mathematics have been key, with new mathematical models of complex physical phenomena, new methods for analyzing complex data, new algorithms for accuracy and scaling and sophisticated software systems that encapsulate these techniques into open, reusable tools. The performance of NERSC computers and the ESnet network have grown by several orders of magnitude, along with our understanding of how to map scientific computations and workflows onto these systems. From research to facility operations, the passion, talent and dedication of the Computing Sciences Area staff has been the cornerstone of our success. The plan outlined in this document describes the next step in a journey to expand the influence and impact of our efforts, building an increasingly connected global enterprise for science that places more powerful instruments in the hands of scientists, along with more powerful methods and tools for modeling, analysis and prediction.

97 MATHEMATICS AND COMPUTING↗

Full event interpretation with machine-learning-based particle-flow reconstruction in the CMS detector

The particle-flow (PF) algorithm constructs a global description of each particle collision by producing a comprehensive list of final-state particles, and is central to event reconstruction in the CMS experiment at the CERN LHC. The existing PF implementation relies on physics-motivated heuristics and assumptions that can be replaced by machine-learning (ML) models trained directly on simulated data and naturally suited to modern graphics processing units (GPUs). A state-of-the-art ML-based PF (MLPF) reconstruction algorithm, implemented within the CMS software framework, is presented. The MLPF algorithm performs a learnable full-event reconstruction on GPUs, generalizes across detector conditions and collision energies, and replaces multiple modular reconstruction steps with a single unified model. Physics performance comparable to standard PF reconstruction is achieved in both simulation and data, with improved jet energy resolution and inference time. In simulated top quark-antiquark events under LHC Run-3 (2023-2024) conditions, the jet energy resolution improves by 10-20% for jets with transverse momentum between 30-100 GeV. Inference time is evaluated using simulated multijet events, with a median of $20\,\hbox {ms}$ per event on an Nvidia L4 GPU, compared to approximately $110\,\hbox {ms}$ for the standard CMS PF reconstruction.

Hayrapetyan, Aram [Yerevan Phys. Inst.]↗

A simple method for modelling fatigue spectra of small wind turbine blades

Small-scale wind turbines have market opportunities in distributed energy generation applications but face future challenges in remaining cost competitive compared with solar photovoltaic systems. High unit costs can be attributed to design conservatism when calculating fatigue loads of key structural components such as the blades. In this study, we use the aeroelastic software FAST to highlight limitations of the International Electrotechnical Commission 61400-2:2013 small wind turbine design standard for calculating fatigue life using the simplified load model. We present a modified method for calculating the fatigue spectra of small wind turbine blades. An advantage of this method is that it does not require complex aeroelastic simulations or field measurements. This modified method is intended to be implemented early in the blade design stage, such as during rotor optimization simulations, allowing for multiple rotor configurations to be rapidly compared.

17 WIND ENERGY↗

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.↗

Influence of physical and chemical hydrology on bioremediation of a U-contaminated aquifer informed by reactive transport modeling incorporating 238 U/ 235 U ratios

Microbially-catalyzed reductive immobilization of aqueous uranium (U) as a solid phase has been proposed as a U remediation technique. Both laboratory and field experiments have demonstrated that this reduction reaction alters the 238 U/ 235 U ratio, producing a 238 U-enriched U(IV) solid. In contrast, other major U reactive transport processes fractionate these isotopes much less. This suggests the potential to quantify the extent of bioreduction occurring in groundwater containing U using the 238 U/ 235 U ratio, which would substantially improve upon current practices largely relying on U concentration measurements alone. Current reactive transport models for uranium dynamics include only concentration measurements, which are strongly influenced by highly coupled reactive transformation and aqueous transport processes. The complex physical and chemical behavior of U potentially compromises such quantitative analysis of U storage and release. Here we report the first numerical reactive transport model which explicitly incorporates variations in the 238 U/ 235 U ratio of U and demonstrates improved interpretation of the principal chemical reactions and groundwater transport processes affecting the subsurface mobility and distribution of this widespread contaminant. Recent U bioreduction studies performed in a contaminated aquifer in Rifle, Colorado, USA applied Rayleigh distillation models to interpret U stable isotope fractionation observed as a result of acetate amendment. These simplified models were unable to resolve the spatiotemporal pattern of U isotope fractionation recorded in the aqueous solutes. Here, we employ the multi-component, isotope-enabled CrunchTope reactive transport software to interpret these measured U isotope ratios, and demonstrate accurate reproduction of observed trends in both geochemistry and 238 U/ 235 U ratios for two consecutive years of field experiments. Overall, our results indicate that accurately modeling both the U concentration and isotope ratio distributions greatly constrains the parameter space of the model. We find that the transport properties of U in the Rifle aquifer are governed by the presence of low-permeability regions, which the isotopes are uniquely sensitive to. When U reduction is spatially constrained by these low-permeability regions, the shift in the 238 U/ 235 U ratio becomes more muted. Accurate modeling of observed U isotope ratios thus provides a powerful means to better understand bioremediation, and the current study serves to advance the application of this novel method.

238U/235U↗

CODE-TO-CODE BENCHMARK STUDY FOR THERMAL STRESS MODELING AND PRELIMINARY ANALYSIS OF THE HIGH-TEMPERATURE SINGLE HEAT PIPE EXPERIMENT

Microreactors are very small nuclear reactors with typical thermal-energy output of up to 20 MWth. The microreactor concept is gaining more and more attention for safe, robust, and reliable supply of electricity for remote locations and to meet industrial process heat needs. Heat-pipe-cooled microreactor is one of the microreactors being investigated at Idaho National Laboratory. In the heat-pipe-cooled microreactor, heat pipes remove heat from the reactor core as a passive heat-transfer device, so the fluid circulation is not required for cooling, which can substantially simplify the overall reactor design. However, given the extremely high temperatures in the core region and potentially large temperature gradients across the structure materials, thermal stresses need to be well-analyzed to ensure structural integrity during normal operations and accident scenarios for the heat-pipe-cooled microreactor designs. This paper discusses finite element method-based thermal-stress analysis for the high-temperature single heat-pipe test article in the Single Primary Heat Extraction and Removal Emulator (SPHERE) facility at Idaho National Laboratory, using two commercial software packages, Abaqus and STAR-CCM+. A code-to-code benchmark study was performed to crosscheck the model setup and capability of each code and to gain insights into the potential thermal stress concerns from the current experimental setup. It is observed the significant thermal stresses happen at the locations where the largest temperature gradients appeared between heat pipe and electric heater. The temperature fields have good agreements between Abaqus and STAR-CCM+, while the induced thermal stresses show modest deviations probably due to differences of meshing engines used in these two codes.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Model-based data center cooling controls comparative co-design

This article presents a comparative simulation-based control logic design process. It uses the Control Description Language (CDL) and the ASHRAE Guideline 36 high-performing building control sequences with the Modelica Buildings Library (MBL) to demonstrate a comparative analysis of two control designs for a data center chilled water plant. Details include a description of the closed-loop plant and control design methodology, including sizing and parameterization, base and alternative (Guideline 36) control logic with software implementation structure, and outline of the simulation experimentation process. The selected control designs are paired with comparable chilled water plant configurations. The models include a chiller, a water-side economizer, and an evaporative cooling tower. The plant provides cooling at 27ºC zone supply air temperature to a data center in Sacramento, CA. The comparative simulation results examined the impacts of a selected control logic detail, and present an example model-based design application. Overall, the simulation results showed a 25% annual and a 18% summer energy use reduction for alternative controls. This shows that simulation-based control logic design performance evaluation can improve energy efficiency and resilience aspects of system controls at large.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

ArQTiC: A Full-stack Software Package for Simulating Materials on Quantum Computers

ArQTiC is an open-source, full-stack software package built for the simulations of materials on quantum computers. It currently can simulate materials that can be modeled by any Hamiltonian derived from a generic, one-dimensional, time-dependent Heisenberg Hamiltonian. ArQTiC includes modules for generating quantum programs for real- and imaginary-time evolution, quantum circuit optimization, connection to various quantum backends via the cloud, and post-processing of quantum results. By enabling users to seamlessly design, execute, and analyze materials simulations on quantum computers, ArQTiC opens this field to a broader community of scientists from a wider range of scientific domains.

97 MATHEMATICS AND COMPUTING↗

Towards Next-Generation Urban Decision Support Systems through AI-Powered Construction of Scientific Ontology Using Large Language Models—A Case in Optimizing Intermodal Freight Transportation

The incorporation of Artificial Intelligence (AI) models into various optimization systems is on the rise. However, addressing complex urban and environmental management challenges often demands deep expertise in domain science and informatics. This expertise is essential for deriving data and simulation-driven insights that support informed decision-making. In this context, we investigate the potential of leveraging the pre-trained Large Language Models (LLMs) to create knowledge representations for supporting operations research. By adopting ChatGPT-4 API as the reasoning core, we outline an applied workflow that encompasses natural language processing, Methontology-based prompt tuning, and Generative Pre-trained Transformer (GPT), to automate the construction of scenario-based ontologies using existing research articles and technical manuals of urban datasets and simulations. From these ontologies, knowledge graphs can be derived using widely adopted formats and protocols, guiding various tasks towards data-informed decision support. The performance of our methodology is evaluated through a comparative analysis that contrasts our AI-generated ontology with the widely recognized pizza ontology, commonly used in tutorials for popular ontology software. We conclude with a real-world case study on optimizing the complex system of multi-modal freight transportation. Our approach advances urban decision support systems by enhancing data and metadata modeling, improving data integration and simulation coupling, and guiding the development of decision support strategies and essential software components.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Special Nuclear Geometric Modeling

This report is a summary of our summer interns project that focused on investigating the usefulness of the Gamma Detector Response and Analysis Software (GADRAS) into the Material Control & Accountability (MC&A) Measurements Team. The project's findings highlight the advantages of using GADRAS and demonstrate its value in improving the MC&A Measurements Team's analytical capabilities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

ARQUIN: Architectures for Multinode Superconducting Quantum Computers

Many proposals to scale quantum technology rely on modular or distributed designs wherein individual quantum processors, called nodes, are linked together to form one large multinode quantum computer (MNQC). One scalable method to construct an MNQC is using superconducting quantum systems with optical interconnects. However, internode gates in these systems may be two to three orders of magnitude noisier and slower than local operations. Surmounting the limitations of internode gates will require improvements in entanglement generation, use of entanglement distillation, and optimized software and compilers. Still, it remains unclear what performance is possible with current hardware and what performance algorithms require. In this article, we employ a systems analysis approach to quantify overall MNQC performance in terms of hardware models of internode links, entanglement distillation, and local architecture. We show how to navigate tradeoffs in entanglement generation and distillation in the context of algorithm performance, lay out how compilers and software should balance between local and internode gates, and discuss when noisy quantum internode links have an advantage over purely classical links. Here, we find that a factor of 10–100× better link performance is required and introduce a research roadmap for the co-design of hardware and software towards the realization of early MNQCs. While we focus on superconducting devices with optical interconnects, our approach is general across MNQC implementations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Experimental and Numerical Investigation of a Miniature Additively Manufactured Vortex Tube

Ranque–Hilsch vortex tubes are simple devices that can produce a cooling effect using compressed air. A key advantage of vortex tubes is the lack of moving solid parts; however, their efficiencies are relatively low. The present study focuses on the development of a miniature variable-diameter tube using additive manufacturing. A metal-based 3D printing technique was utilized to fabricate this vortex tube monolithically. Computational fluid dynamics simulations employing software STAR-CCM + with a compressible Reynolds-Averaged Navier–Stokes (RANS) approach and the elliptic-blending lag k-epsilon turbulence model have been applied to model thermofluid processes inside the vortex tube, to good agreement with the experiment. In conclusion, a temperature decrease of 13.3 °C and a cooling power of approximately 4 W were experimentally achieved with a pressure ratio of 4 in the air at normal conditions. This result shows promise for the goal of utilizing additive manufacturing to design and build complex-geometry vortex tubes intended for use with cryogenic fluids.

08 HYDROGEN↗

The Synchronic Web

The Synchronic Web is a distributed network for securing data provenance on the World Wide Web. By enabling clients around the world to freely commit digital information into a single shared view of history, it provides a foundational basis of truth on which to build decentralized and scalable trust across the Internet. Its core cryptographical capability allows mutually distrusting parties to create and verify statements of the following form: “I commit to this information—and only this information—at this moment in time.” The backbone of the Synchronic Web infrastructure is a simple, small, and semantic-free blockchain that is accessible to any Internet-enabled entity. The infrastructure is maintained by a permissioned network of well-known servers, called notaries, and accessed by a permissionless group of clients, called journals. Through an evolving stack of flexible and composable semantic specifications, the parties cooperate to generate synchronic commitments over arbitrary data. When integrated with existing infrastructures, adapted to diverse domains, and scaled across the breadth of cyberspace, the Synchronic Web provides a ubiquitous mechanism to lock the world’s data into unique points in discrete time and digital space. This document provides a technical description of the core Synchronic Web system. The distinguishing innovation in our design—and the enabling mechanism behind the model—is the novel use of verifiable maps to place authenticated content into canonically defined locations off-chain. While concrete specifications and software implementations of the Synchronic Web continue to evolve, the information covered in the body of this document should remain stable. We aim to present this information clearly and concisely for technical non-experts to understand the essential functionality and value proposition of the network. In the interest of promoting discourse, we take some liberty in projecting the potential implications of the new model.

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↗

Ab Initio Direct Dynamics

The reactivity and dynamics of molecular systems can be explored computationally by classical trajectory calculations. The traditional approach involves fitting a functional form of a potential energy surface (PES) to the energies from a large number of electronic structure calculations and then integrating numerous trajectories on this fitted PES to model the molecular dynamics. The ever-decreasing cost of computing and continuing advances in computational chemistry software have made it possible to use electronic structure calculations directly in molecular dynamics simulations without first having to construct a fitted PES. In this “on-the-fly” approach, every time the energy and its derivatives are needed for the integration of the equations of motion, they are obtained directly from quantum chemical calculations. This approach started to become practical in the mid-1990s as a result of increased availability of inexpensive computer resources and improved computational chemistry software. The application of direct dynamics calculations has grown rapidly over the last 25 years and would require a lengthy review article. The present Account is limited to some of our contributions to methods development and various applications. To improve the efficiency of direct dynamics calculations, we developed a Hessian-based predictor-corrector algorithm for integrating classical trajectories. Hessian updating made this even more efficient. Furthermore, this approach was also used to improve algorithms for following the steepest descent reaction paths. For larger molecular systems, we developed an extended Lagrangian approach in which the electronic structure is propagated along with the molecular structure. Strong field chemistry is a rapidly growing area, and to improve the accuracy of molecular dynamics in intense laser fields, we included the time-varying electric field in a novel predictor-corrector trajectory integration algorithm. Since intense laser fields can excite and ionize molecules, we extended our studies to include electron dynamics. Specifically, we developed code for time-dependent configuration interaction electron dynamics to simulate strong field ionization by intense laser pulses. Our initial application of ab initio direct dynamics in 1994 was to CH 2 O → H 2 + CO; the calculated vibrational distributions in the products were in very good agreement with experiment. In the intervening years, we have used direct dynamics to explore energy partitioning in various dissociation reactions, unimolecular dissociations yielding three fragments, reactions with branching after the transition state, nonstatistical dynamics of chemically activated molecules, dynamics of molecular fragmentation by intense infrared laser pulses, selective activation of specific dissociation channels by aligned intense infrared laser fields, angular dependence of strong field ionization, and simulation of sequential double ionization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding

Abstract Motivation The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster and more sensitive methods to assess evolutionary and functional relationships between proteins. Representing proteins as sets of short peptide sequences (kmers) has been used for rapid, accurate classification of proteins into functional categories; however, this approach employs an exact-match methodology and thus may be limited in terms of sensitivity and coverage. We have previously used similarity groupings, based on the chemical properties of amino acids, to form reduced character sets and recode proteins. This amino acid recoding (AAR) approach simplifies the construction of protein representations in the form of kmer vectors, which can link sequences with distant sequence similarity and provide accurate classification of problematic protein families. Results Here, we describe Snekmer, a software tool for recoding proteins into AAR kmer vectors and performing either (i) construction of supervised classification models trained on input protein families or (ii) clustering for de novo determination of protein families. We provide examples of the operation of the tool against a set of nitrogen cycling families originally collected using both standard hidden Markov models and a larger set of proteins from Uniprot and demonstrate that our method accurately differentiates these sequences in both operation modes. Availability and implementation Snekmer is written in Python using Snakemake. Code and data used in this article, along with tutorial notebooks, are available at http://github.com/PNNL-CompBio/Snekmer under an open-source BSD-3 license. Supplementary information Supplementary data are available at Bioinformatics Advances online.

59 BASIC BIOLOGICAL SCIENCES↗