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At least 685 records · Page 38

SBbadger: biochemical reaction networks with definable degree distributions

Abstract Motivation An essential step in developing computational tools for the inference, optimization and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the assembly of benchmark models include collection from the literature, creation via subnetwork extraction and de novo generation. However, with respect to biochemical reaction networks, these approaches and their associated tools are either poorly suited to generate models that reflect the wide range of properties found in natural biochemical networks or to do so in numbers that enable rigorous statistical analysis. Results In this work, we present SBbadger, a python-based software tool for the generation of synthetic biochemical reaction or metabolic networks with user-defined degree distributions, multiple available kinetic formalisms and a host of other definable properties. SBbadger thus enables the creation of benchmark model sets that reflect properties of biological systems and generate the kinetics and model structures typically targeted by computational analysis and inference software. Here, we detail the computational and algorithmic workflow of SBbadger, demonstrate its performance under various settings, provide sample outputs and compare it to currently available biochemical reaction network generation software. Availability and implementation SBbadger is implemented in Python and is freely available at https://github.com/sys-bio/SBbadger and via PyPI at https://pypi.org/project/SBbadger/. Documentation can be found at https://SBbadger.readthedocs.io. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Security Catch and Release Automation Manager (SCRAM) v1.0

This is a security automation tool heavily influenced by the tool written at NCSA https://github.com/ncsa/bhr-site. The tool is a web interface that aims to centralize information on blocking malicious traffic. There is a list of currently blocked traffic, a place for other tools to automatically add traffic they deem malicious, as well as for human users to input blocks. * Logging and auditing, to determine who made what change and when * Automated expiration of changes (e.g. an exception is added for 2 weeks, after which time it will be removed) * Validation of changes and verification that the change has been applied * Fine-grained role-based access

Oehlert, Samuel↗

KENO V.a Primer: Performing Calculations using SCALE’s Criticality Safety Analysis Sequence (CSAS5) with Fulcrum

The SCALE code system developed at Oak Ridge National Laboratory is widely used and accepted around the world for criticality safety analyses. The well-known KENO V.a three-dimensional Monte Carlo criticality computer code is one of the primary criticality safety analysis tools in SCALE. The KENO V.a primer is designed to help a new user understand and use the SCALE/KENO V.a Monte Carlo code for nuclear criticality safety analyses. It assumes that the user has a college education in a technical field. There is no assumption of familiarity with Monte Carlo codes in general or with SCALE/KENO V.a in particular. The primer is designed to teach by example, with each example illustrating two or three features of SCALE/KENO V.a that are useful in criticality analyses. The primer is based on SCALE 6.2 and 6.3, which includes the Fulcrum graphical user interface (GUI). Each example uses Fulcrum to provide the framework for preparing input data and viewing output results. Starting with a Quickstart section, the primer gives an overview of the basic requirements for SCALE/KENO V.a input and allows the user to quickly run a simple criticality problem with SCALE/KENO V.a. The sections that follow Quickstart include a list of basic objectives at the beginning that identifies the goal of the section and the individual SCALE/KENO V.a features that are covered in detail in the sample problems in that section. Upon completion of the primer, a new user should be comfortable using Fulcrum to set up criticality problems in SCALE/KENO V.a. The primer provides a starting point for the criticality safety analyst who uses SCALE/KENO V.a. Complete descriptions are provided in the SCALE/KENO V.a manual. Although the primer is self-contained, it is intended as a companion volume to the SCALE/KENO V.a training and documentation. The SCALE manual and training schedule are available at https://scale.ornl.gov. The primer provides specific examples of using SCALE/KENO V.a for criticality analyses; the SCALE/KENO V.a manual provides information on the use of SCALE/KENO V.a and all its modules. The primer also contains an appendix with sample input files. In addition, this primer, its errata and sample inputs are also available at https://code.ornl.gov/scale/primers/kenova.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Emulating the Android Boot Process

Critical vulnerabilities continue to be discovered in the boot process of Android smartphones used around the world. The entire device's security is compromised if boot security is compromised, so any weakness presents undue risk to users. Vulnerabilities persist, in part, because independent security analysts lack access and appropriate tools. In response to this gap, we implemented a procedure for emulating the early phase of the Android boot process. This work demonstrated feasibility and utility of emulation in this space. By using HALucinator, we derived execution context and data flow, as well as incorporated peripheral hardware behavior. While smartphones with shared processors have substantial code overlap regardless of vendor, generational changes can have a significant impact. By applying our approach to older and modern devices, we learned interesting characteristics about the system. Such capabilities introduce new levels of introspection and operation understanding not previously available to mobile researchers.

97 MATHEMATICS AND COMPUTING↗

Dual Purpose – Heating & Cooling – Thermal Battery for Flexible and Energy-Efficient Heat Pump Systems

The integration of heat pumps with thermal energy storage (HP-TES) systems is gaining attention as a viable solution for managing peak building demand driven by immense cooling and heating loads. With growing reliance on renewable energy sources, thermal energy storage offers an excellent opportunity to mitigate mismatches in thermal load between energy supply and demand. The use of phase-change material (PCM) TES is especially promising, as PCMs offer significant latent energy storage capacity with smaller temperature glides in smaller volumes compared to other TES technologies. However, challenges arise because current HP-TES architectures can load-shift only cooling or heating, not both, requiring two systems and thus doubling cost, weight, and footprint. Furthermore, current research efforts lack specific tools and techniques to advance integrated systems from concept design to end-user application, focusing on only discharge performance. To address these challenges, this research proposes a dual-mode (heating and cooling) integrated HP-TES system that uses room-temperature PCM-TES as a high-temperature heat source in heating mode and a low-temperature heat sink in cooling mode, thereby reducing temperature lifts and compressor power. Design criteria for PCM-TES heat exchangers were developed, balancing thermal-hydraulic performance with practical constraints such as available building space and weight requirements along with PCM selection considerations such as shipping conditions, moisture exposure, and number of available cycles. A detailed transient model for HP-TES systems was developed to enable rapid annual performance assessments in any US climate zone.

42 ENGINEERING↗

Numerical Investigation of Fluid Flow and Space Charge in Liquid Argon Time Projection Chamber (LArTPC) Detectors

Overview This project focused on developing a high-fidelity numerical framework to simulate the multiphysics environment within Liquid Argon Time Projection Chamber (LArTPC) detectors. The primary objective was to characterize the complex interplay between ion transport, background fluid dynamics, and electric field distortions—a critical factor for the calibration and sensitivity of next-generation High Energy Physics experiments, such as DUNE. Technical Achievements The research successfully yielded a hybrid numerical space-charge solver utilizing a Cell-Centered Finite Volume Method (FVM) for ion transport coupled with a Finite Element Method (FEM) for electric potential. Key accomplishments include: • Verification & Validation: The 3-D solver was rigorously verified against 1-D analytical solutions, demonstrating high numerical accuracy in predicting space-charge-induced field deviations. • Field Distortion Analysis: 3D simulations revealed that space charge effects introduce significant non-uniformities in the electric field. Critically, the research identified that background LAr flow velocities, when comparable to ion drift velocities, markedly exacerbate these distortions. • Technology Transfer: The resulting source code and comprehensive user manuals were successfully transferred to collaborators at Fermilab, providing a portable computational tool for the broader scientific community. Challenges and Future Directions While the space-charge solver achieved all performance metrics, the integrated fluid dynamics modeling encountered convergence challenges stemming from the extreme 200-fold disparity in length scales between the detector's 37 mm inlet pipes and the 8-meter global domain. To address this, the project has identified a clear technical pivot toward Hierarchical Geometric Adaptive Mesh Refinement (HG-AMR). By implementing an h-type refinement strategy with hanging nodes, future iterations of this solver will be capable of resolving localized high-gradient inlet flows without the prohibitive computational costs of regular grids. This advancement, combined with data-driven uncertainty quantification based on MicroBooNE-style calibration, will enable the precise modeling of detector responses in large-scale cryogenic environments where direct measurement remains difficult. Impact The computational tools developed under this award provide a foundation for enhancing the energy resolution and spatial reconstruction of noble liquid detectors. By bridging the gap between theoretical fluid dynamics and experimental field calibration, this work supports the DOE’s mission to advance the frontiers of neutrino physics and dark matter detection.

42 ENGINEERING↗

Experimental Steps toward a Density Law for Chlorine-Crediting Criticality Models of Aqueous Plutonium solutions

Criticality accident prevention is an essential safety consideration for all operations involving fissionable and fissile materials. Predictive criticality calculations using advanced neutron transport codes, such as Monte Carlo N-Particle Transport (MCNP), are invaluable tools for designing and implementing operational limits. While indispensable, these tools are limited by the quality and accuracy of the inputs that the user provides to define the modeled system. Parameters such as atomic composition, shape, and material density must be accurately defined to obtain a meaningful result. In the case of material property details for a plutonium model, accurate material characterization data is sometimes sparse. Thus limitations in calculation accuracy can be reduced by improving our knowledge of material properties in the targeted fissile systems. One of the biggest remaining challenges to accurately defining fissile systems is the description of aqueous fissile solutions. Even simple properties, such as density, are not well-known for fissile solutions relevant to nuclear energy and security. Described here are initial efforts undertaken to improve criticality calculation inputs for fissile plutonium chloride solutions in water. This effort is focused on experimentally determining accurate solution characteristics for ternary plutonium chloride/hydrochloric acid/water systems, by measurement of water activity and solution density. The effect of inputting experimental densities for these solutions into MCNP criticality calculations is compared to the traditional approach of modeling an idealized (and fictitious) plutonium-water mixture. Expansion of these efforts to a working density law for aqueous plutonium chloride solutions is also discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A tool for assessing demand side management and operating strategies for isolated microgrids

Globally, power system operators are exploring ways to leverage the capabilities of smart meters to implement fine-grained demand side management (DSM). Here this paper presents a new simulation tool to evaluate operating strategies for smart-meter-enabled (SME) islanded microgrids being advanced for sustainable rural electrification in emerging economies. Based on MATLAB/Simulink, the tool's component-level models of small microgrids can be easily configured. Alternative rule-based operating strategies are implemented with controllable supply and storage components as well as other components driven by external factors (e.g., weather and time of day). To account for the wide range of possible operating conditions in real-world applications, statistical metrics can be evaluated using Monte Carlo (MC) methods based on user-defined, time-dependent probability distributions for demands, supplies, and environmental variables. Features of the tool are demonstrated with case studies for a representative microgrid in rural Rwanda.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Distributed Ledger Technology Preliminary Performance Assessment for Applications in Utilities Operational Technology

This paper provides descriptions of the key components of different distributed ledger technology platforms. Distributed ledger technology (DLT) allows for distribution of databases among different organizations and devices. The platforms use cryptographically linked “blocks” to store and verify transactional information between these organizations. DLT increases data security, data integrity, trust among its participants. Different organizations are looking to deploy this distributed and decentralized approach to avoid the single-point-of-failure vulnerabilities associated with centralized data repositories. In this study we examine twelve different DLT platforms. There is agreement within the community that of all the platforms considered here, Hyperledger and Ethereum are the most mature when it comes to privacy and permissions. These DLT platforms are being used for applications such as transactive energy, health care, and the food and goods supply chain. However, further development is required to realize the full promise of DLT. Our assessment includes a general description of each DLT and its key characteristics. Such characteristics include consensus protocol and cryptography used, public vs. private, and permissioned or permissionless. The selection and implementation of a DLT architecture depends heavily on the use case and performance requirements. During this research we found key parameters to measure performance and existing tools for assessment. Four different parameters were identified 1) consensus, 2) throughput, 3) latency, and 4) scalability. The architectures of Hyperledger Caliper and Blockbench are described as different performance assessment frameworks. From this preliminary study it is evident that there are dissimilarities on the performance assessments methods developers and users are characterizing DLT architectures. The purpose of this paper is to identify key parameters to test performance, tools that are being used and provide information on results from previous studies.

97 MATHEMATICS AND COMPUTING↗

WorkJournalMaker (WJMaker) v0.5

The software generates and maintains daily work journal entries in text format, via a web browser. The journal entries are saved in a structured directory file tree on the system running the software. The software also incorporates a database so that it can track the location of files in the file system and various other metadata. The software allows the users to access their journal entries either through the browser or as discrete text files, facilitating sharing and open science. Additionally, to assist with the yearly PMP process, this tool connects to LLM APIs to provide summarization of the journal entries on a month-by-month or weekly basis. The advantage over similar technologies such as Apple Notes (extremely popular for notetaking) is that the instant software does not force the user to stay inside the Apple ecosystem, since it allows for export of the user's text files. This facilitates open science, so that researchers who use the tool can easily transfer their research notes to any other system. The WebJournalMaker repository is here: https://github.com/lbnl-science-it/WorkJournalMaker The WebJournalMaker repository is forked from the JournalSummarizer: https://github.com/tyfong-lbl/JournalSummarizer and builds on its code. I wrote the code for both of these software repos, using generative AI.

Fong, Timothy [Lawrence Berkeley National Laborato↗

IDAES-PSE 2.0 Release

The Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform is a versatile computational environment offering extensive process systems engineering (PSE) capabilities for optimizing the design and operation of complex, interacting technologies and systems. IDAES enables users to efficiently search vast, complex design spaces to discover the lowest cost, most environmentally sustainable solutions while supporting the full process modeling lifecycle, from conceptual design to dynamic optimization and control. The extensible, open platform empowers users to create models of novel processes and rapidly develop custom analyses, workflows, and end-user applications. IDAES-PSE 2.0.0 Release Highlights Removal of deprecated features from IDAES v1 Update to Pyomo v6.5 – this required a number of updates to support the new NL solver writer and to address some changes in Pyomo Creation of new testing suite for backward compatibility, model robustness and verification More general implementation of the Helmholtz EoS. This brings some new features like standard property diagrams, choice of mass or mole basis, and new state variable options Standardizing names in Heat Exchanger models (breaking change from v2.0.0a2): Control Volumes named hot_side and cold_side Ports names hot_side_inlet, hot_side_outlet, cold_side_inlet and cold_side_outlet Config Blocks names hot_side_config and cold_side_config Config arguments for user provided names for each side: hot_side_name and cold_side_name. Updating Keras surrogate tool to use v1.1 of OMLT New prototype API for model initialization (idaes.core.initialization) The new API uses "Model Initializer" objects instead of class methods, allowing for the definition of multiple initialization routines for a single model A number of common, model agnostic initialization routines have also been defined, including initialization from data, block-decomposition and a general hierarchical approach equivalent to the existing method for common unit models New metadata for thermophysical properties – valid_range This can be used to record the range of values over which a property value can be trusted, such as the range of experimental data used to regress parameters A number of new utility functions have been added to check for properties with values outside the valid range and to set bounds based on this metadata Updated construction of balance expressions in Control Volumes to remove unneeded terms In the past, unneeded terms were added as a constant 0 term, however they will now be dropped entirely from the expression This was necessary due to more strict unit checking in the new Pyomo solver writer which no longer ignores 0 terms Updates to metadata for thermophysical properties to better define known properties and units of measurement This results in more strict enforcement of standard naming for thermophysical and reaction properties Users can still define custom properties, but these must be done explicitly using the define_custom_properties() method instead of being implicitly created by add_property() Updated convergence tester utility tool to support definition of benchmark files (JSON format) and comparison of performance to benchmarks Set default iteration limit for IPOPT in IDAES config to 200 iterations Update scaling of example models to work with new Pyomo NL solver writer Improve testing of extensions and examples infrastructure to avoid need for downloading files Updated distillation column to centralize common functionality and remove a number of Pyomo warnings

IDAES↗

The ARM Data-oriented Metrics and Diagnostics Package for Climate Models - A New Tool for Evaluating Climate Models with Field Data

The U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) program User Facility produces ground-based long-term continuous unique measurements for atmospheric state, precipitation, turbulent fluxes, radiation, aerosol, cloud and the land surface, which are collected at multiple sites. These comprehensive datasets have been widely used to calibrate climate models and are proven to be invaluable for climate model development and improvement. This article introduces an evaluation package to facilitate the use of ground-based ARM measurements in climate model evaluation. The ARM data-oriented metrics and diagnostics package (ARM-DIAGS) includes both ARM observational datasets and a Python-based analysis toolkit for computation and visualization. The observational datasets are compiled from multiple ARM data products and specifically tailored for use in climate model evaluation. In addition, ARM-DIAGS also includes simulation data from models participating the Coupled Model Inter-comparison Project (CMIP), which will allow climate-modeling groups to compare a new, candidate version of their model to existing CMIP models. The analysis toolkit is designed to make the metrics and diagnostics quickly available to the model developers.

54 ENVIRONMENTAL SCIENCES↗

The Building Science Advisor: A Web-Based Tool to Assess the Durability of Building Envelope Components

The Department of Energy (DOE) and Oak Ridge National Laboratory (ORNL) have developed an innovative new design tool that will put building science expert advice in the hands of every building designer who cares to manage moisture risk in high-R envelope components. As modern buildings become increasingly more airtight, constructed with modern labor-saving materials, and equipped with air-conditioning, they have become less forgiving to moisture intrusion. The Building Science Advisor (BSA) provides building science knowledge and advice based on expert experience, field measurements, laboratory tests, and computer simulations.BSA users are prompted to enter relevant information about the building location, design, and material selection options like cladding, structural system, and insulation. Influential factors such as climate, building air tightness, material properties, and internal moisture loads are also considered to estimate and compare the moisture durability performance of several design options. If the BSA deems the assembly’s performance unsatisfactory, it will provide the reasons why, and suggest necessary changes to wall design to ensure more robust performance.Using the BSA tool enables building designers to confidently select assembly design characteristics that achieve their design goals with the least moisture durability risk. Links to design-specific guidance are also be provided to help users manage any remaining risk. This tool will further enable DOE’s Building Technologies Office (BTO) to meet its long-term energy goal of a 50% reduction in building energy consumption by reducing builder concern about using highly energy efficient wall systems.

Desjarlais, Andre Omer↗

NETL Electrical Conductivity Relaxation(ECR) Analysis Tool

This application was developed within the solid oxide fuel cell (SOFC) work plan. It calculates the oxygen surface exchange coefficient (k) and oxygen diffusion coefficient (D) for an oxide sample using electrical conductivity relaxation (ECR) data. The tool also produces a heat map showing the associated uncertainty in fitting the ECR data for given pairs of k and D values, so the user can determine the most likely range of k and D values for the tested values. Multiple datasets for the same material can be plotted to decrease uncertainty. The tool can also simulate ECR curves for inputted k and D values and overlay the simulated curves with experimental data for comparison.

electrical conductivity relaxation↗

Practical Probabilistic Programming

Recent advances in probabilistic programming languages (PPLs) have provided the capability for exact inference: computing a closed-form probability distribution for a given probabilistic program. In particular, the new language Roulette uses a language oriented programming (LOP) approach, wherein analysts build new programming languages on top of a set of primitives provided by Roulette, which then translates these structures into a weighted model counting problem which can be solved by automated reasoning tools. However, because Roulette provides few convenience features, developing these new languages is challenging even for expert users. We developed a standard library of common probability functions for Roulette with the goal of improved usability. This included approximation of continuous probability density functions using discrete probability mass functions. We demonstrated this approach by modeling a cosmic ray striking a RAM controller. We found that Roulette provides a powerful interface for highly expressive probabilistic programs to be generated. In collaboration with the NNSA Advanced Simulation and Computing program, which resulted in development of a tool called Circulette, we were able to model complex circuits expressed in Verilog using probabilistic programs with an expressivity not previously possible. Our research question that motivated the development of a Roulette standard library was to determine whether non-experts could use a PPL to model relevant problems regarding radiation effects on microelectronics. This standard library improved the expressivity of Roulette by implementing common probability density functions, mathematical operators on distributions, and support for empirical distributions. While Roulette is a powerful modeling language, the untyped, LOP approach makes error messages difficult to understand and requires expert aid. We recommend further research on Roulette, especially with its error messages, to enable improved usability. At the same time, this project demonstrated that for users familiar with Roulette and the LOP approach, Roulette provides powerful new capabilities that can be integrated with other Sandia modeling capabilities.

97 MATHEMATICS AND COMPUTING↗

PathTrace and MPVEASI: A Path Analysis Comparative Validation Study

Developed in 2018, PathTrace is a software package built with the intention of making path analysis simple and intuitive. PathTrace is a top-down pathway analysis software where a user is able to explore vulnerable pathways into a facility. The intention of utilizing a software tool like PathTrace is to characterize an existing physical protection system (PPS) and to upgrade the system to achieve a high level of response interruption, or probability of interruption (P I ) of the adversary. There are four steps for conducting path analysis using PathTrace. The first step is to identify an image to use to build the model and scale the model within PathTrace using a section of known distance (wall or fence perimeter, for example). The scaling process will produce a grid of cells through which the user is able to build a model. The second step is to fill out the grid of cells with four categories of materials: Barriers, Detection Areas, Jumps, and Targets. These materials apply associated delay and detection values to the cells in which they are applied. The third step is to represent the adversary and response forces. The adversaries are represented by their capabilities in interacting with the materials identified in step two, and the response is represented by how quickly they will be able to respond to an adversary attack. Finally, the user is able to take all of the information from the previous three steps and perform a Most Vulnerable Path (MVP) analysis. In this stage, the user is able to visualize vulnerable adversary pathways and reason about how to upgrade these pathways to provide a high level of P I .

97 MATHEMATICS AND COMPUTING↗

User-oriented Improvements in the MOOSE Framework in Support of Multiphysics Simulation

The Multiphysics Object-Oriented Simulation Environment (MOOSE) framework is a foundational capability used by the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program to create over 15 different simulation tools for advanced nuclear reactors. Due to this ubiquity, improvements to the framework in support of modeling and simulation goals are critical to the program. These improvements can take many forms, including optimization, improved user experience, streamlined application programming interfaces (APIs), parallelism, and new capabilities. The work transcribed in this report was conducted in direct support of the simulation tools and has already been deployed or will be deployed in the coming months. The capabilities were implemented in the same order as they are covered in this report: chainable execution objects or executors, support for transfers between same-level applications in a coupling scheme, support for boundary/subdomain restricted transfers, support for transfers between applications with different coordinate or unit systems, support for MOOSE applications in the NEAMS Workbench, deployment of the MOOSE application of the Idaho National Laboratory (INL) high-performance computing (HPC) OnDemand platform, the addition of a triangular meshing library in libMesh, and increased support of face variables.

97 MATHEMATICS AND COMPUTING↗

Geospatial and Information Substitution and Anonymization Tool (GISA)

The Geospatial and Information Substitution and Anonymization Tool (GISA) incorporates techniques for obfuscating identifiable information from point data or documents, while simultaneously maintaining chosen variables to enable future use and meaningful analysis. This approach promotes collaboration and data sharing while also reducing the risk of exposure to sensitive information. GISA can be used in a number of different ways, including the anonymization of point spatial data, batch replacement/removal of user-specified terms from file names and from within file content, and aid with the selection and redaction of images and terms based on recommendations using natural language processing. Version 1 of the tool, published here, has updated functionality and enhanced capabilities to the beta version published in 2023. Please see User Documentation for further information on capabilities, as well as a guide for how to download and use the tool. If there are any feedback you would like to provide for the tool, please reach out with your feedback to edxsupport@netl.doe.gov. Disclaimer: This project was funded by the United States Department of Energy, National Energy Technology Laboratory, in part, through a site support contract. Neither the United States Government nor any agency thereof, nor any of their employees, nor the support contractor, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. The Geospatial and Information Substitution and Anonymization Tool (GISA) was developed jointly through the U.S. DOE Office of Fossil Energy and Carbon Management’s EDX4CCS Project, in part, from the Bipartisan Infrastructure Law.

Bipartisan Infrastructure Law↗