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At least 739 records · Page 41

Supplementary Material for ORNL_AISD-Ex

This dataset provides supplementary material for the previously published dataset ORNL_AISD-Ex (1), which is available at the following website: https://www.osti.gov/biblio/1907919 The dates comprises one compressed folder called ornl_aisd_ex.zip. The compressed folder ornl_aisd_ex.zip contains 1,000 CSV files, each of them titled ornl_aisd_ex_ID.csv, where ID is a number that ranges between 1 and 1,000. The information contained in ornl_aisd_ex_ID.csv corresponds to the information of the molecules compresses inside the ornl_aisd_ex_ID.tar.gz of the dataset ORNL_AISD-Ex. Each row in each .CSV file is associated with a molecule, and the columns contain the following information: 1) molecules ID 2) SMILES string representation 3) DFTB-PE (eV): formation energy 4) first 50 electronic excitation modes 5) oscillators strengths of the first 50 electronic excitation modes The compression of this information into CSV files will allow a more agile extraction and management of information to the users that do not have access to large scale HPC platforms. REFERENCES (1) Lupo Pasini, Massimiliano, Mehta, Kshitij, Yoo, Pilsun, and Irle, Stephan. ORNL_AISD-Ex: Quantum chemical prediction of UV/Vis absorption spectra for over 10 million organic molecules. United States: N. p., 2023. Web. doi:10.13139/OLCF/1907919.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design

Group contribution (GC) methods are conventionally used in thermodynamics analysis of metabolic pathways to estimate the standard Gibbs energy change ( Δ r G ′ o ) of enzymatic reactions from limited experimental measurements. However, these methods are limited by their dependence on manually curated groups and inability to capture stereochemical information, leading to low reaction coverage. Herein, we introduce an automated molecular fingerprint-based thermodynamic analysis tool called dGPredictor that enables the consideration of stereochemistry within metabolite structures and thus increases reaction coverage. dGPredictor has comparable prediction accuracy compared to existing GC methods and can capture Gibbs energy changes for isomerase and transferase reactions, which exhibit no overall group changes. We also demonstrate dGPredictor’s ability to predict the Gibbs energy change for novel reactions and seamless integration within de novo metabolic pathway design tools such as novoStoic for safeguarding against the inclusion of reaction steps with infeasible directionalities. To facilitate easy access to dGPredictor, we developed a graphical user interface to predict the standard Gibbs energy change for reactions at various pH and ionic strengths. The tool allows customized user input of known metabolites as KEGG IDs and novel metabolites as InChI strings ( https://github.com/maranasgroup/dGPredictor ).

59 BASIC BIOLOGICAL SCIENCES↗

SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences

Background Synthetic biology involves combining different DNA fragments, each containing functional biological parts, to address specific problems. Fundamental gene-function research often requires cloning and propagating DNA fragments, such as those from the iGEM Parts Registry or Addgene, typically distributed as circular plasmids. Addgene’s repository alone offers around 150,000 plasmids. To ensure data integrity, cryptographic checksums can be calculated for the sequences. Each sequence has a unique checksum, making checksums useful for validation and quick lookups of associated annotations. For example, the SEGUID checksum uniquely identifies protein sequences with a 27-character string. Objectives The original SEGUID, while effective for protein sequences and single-stranded DNA (ssDNA), is not suitable for circular DNA since there is no natural starting position nor for double-stranded DNA (dsDNA) since two separate sequences are present. Challenges include how to uniquely represent linear dsDNA, circular ssDNA, and circular dsDNA. To meet these needs, we propose SEGUID v2, which extends the original SEGUID to handle additional types of sequences. Conclusions SEGUID v2 produces orientation and rotation invariant checksums for single-stranded, double-stranded, possibly staggered, linear, and circular DNA and RNA sequences. Customizable alphabets allow for other types of sequences. In contrast to the original SEGUID, which uses Base64, SEGUID v2 uses Base64url to encode the SHA-1 hash. This ensures SEGUID v2 checksums can be used as-is in filenames, regardless of platform, and in URLs, with minimal friction. Availability SEGUID v2 is readily available for major programming languages, distributed under the MIT license. JavaScript package seguid is available on npm, Python package seguid on PyPi, R package seguid on CRAN, and a Tcl script on GitHub. These tools, along with documentation, examples, and an online SEGUID Calculator , can be found at https://www.seguid.org .

Pereira, Humberto↗

Utah FORGE: Well 16B(78)-32 Drilling Data

This drilling data for Utah FORGE well 16B(78)-32 include a well survey, core summary, mud and mud temperature logs, daily reports of the drilling process, and additional data from the Pason oil and gas company. Well 16B(78)-32 serves as the production well for reservoir creation, fluid circulation, and demonstration of heat extraction for the FORGE project. It has been drilled as a doublet approximately 300 feet parallel to and above the injection well 16A(78)-32. The proposed total depth was 10,658 feet, which was exceeded. Spudding began on April 26th, 2023. As of June 20th, 2023, the total depth measured 10,947 feet and the vertical depth measured 8,357 feet. Drilling included the trial use of insulated drill pipe (IDP) from Eavor Technologies, which was considered a success. IDP restricts counter-current heat transfer between drilling fluid inside the drill string and hotter returning fluid in the annulus, thereby ensuring the bottomhole assembly (BHA) remains submerged in cool fluid. Eavor rented 350 joints of IDP to FORGE which were run in two consecutive BHAs at the well. The results of this trial are included here.

15 GEOTHERMAL ENERGY↗

Utah FORGE: Neubrex Well 16B(78)-32 DAS Data - April, 2024

This dataset comprises Distributed Acoustic Sensing (DAS) data collected from the Utah FORGE monitoring well 16B(78)-32 (the producer well) during hydraulic fracture stimulation operations conducted in April 2024. The data were acquired continuously over the stimulation period at a temporal sampling rate of 10,000 Hz (10 kS/s) and a spatial resolution of approximately 3.35 feet (1.02109 meters). The measurements were captured using a Neubrex NBX-S4100 Time Gated Digital DAS interrogator unit connected to a single-mode fiber optic cable, which was permanently installed within the casing string. All recorded channels correspond to downhole segments of the fiber optic cable, from a measured depth (MD) of 5,369.35 feet to 10,352.11 feet. The DAS data reflect raw acoustic energy generated by physical processes within and surrounding the well during stimulation activities at wells 16A(78)-32 and 16B(78)-32. These data have potential applications in analyzing cross-well strain, far-field strain rates (including microseismic activity), induced seismicity, and seismic imaging. Metadata embedded in the attributes of the HDF5 files include detailed information on the measured depths of the channels, interrogation parameters, and other acquisition details. The dataset also includes a recording of a seminar held on September 19, 2024, where Neubrex's Chief Operating Officer presented insights into the data collection, analysis, and preliminary findings. The raw data files, stored in HDF5 format, are organized chronologically according to the recording intervals from April 9 to April 24, 2024, with each file corresponding to a 12-second recording interval.

15 GEOTHERMAL ENERGY↗

Atomic-level mechanisms of short-circuit diffusion in materials

This paper reviews the recent progress in understanding the atomic mechanisms of short-circuit diffusion along materials interfaces, such as grain and interphase boundaries, as well as lattice and interfacial dislocations/disconnections. Recent atomistic computer simulations have shown that short-circuit diffusion is dominated by collective atomic rearrangements in the form of strings and rings of mobile atoms. The process is dynamically heterogeneous in space and time and has many features in common with atomic dynamics in supercooled glass-forming liquids. We discuss examples of grain boundary, interphase boundary, and dislocation diffusion in metals and alloys, including the solute effect on the diffusion rates and mechanisms. Interphase boundaries are exemplified by Al–Si interfaces with diverse orientation relationships and atomic structures. The hierarchy of short-circuit diffusion paths in materials is reviewed by comparing the rates of grain boundary, interphase boundary, and dislocation diffusion. Future directions in the field of short-circuit diffusion in defect core regions are discussed.

36 MATERIALS SCIENCE↗

Hawaii Wave Surge Energy Converter (HAWSEC) OSU O.H. Hinsdale Basin

The following information and metadata applies to both the Phase I (Hydrodynamics) and Phase II (Full System Power Take-Off) zip folders which contain testing data from the OSU (Oregon State University) O.H. Hinsdale Wave Research Laboratory, from both OSU and the University of Hawaii at Manoa (UH). See zip folders provided further below in the downloads section. For experimental data of the full system, including PTO, see Phase II dataset. There are two main directories in each Phases's zip folder: "OSU_data" and "UH_data". The "OSU_data" directory contains data collected from their DAQ (data acquisition system), which includes all wave gauge observations, as well as body motions derived from their Qualisys motion tracking system. The organization of the directory follows OSU's convention. Detailed information on the instrument setup can be found under "OSU_data/docs/setup/instm_locations". The experiments conducted are documented in the "OSU_data/docs/daq_logs", which provides the trial number to the corresponding data located under "OSU_data/data" in several formats (e.g., ".mat" and ".txt"). Inside the trial directory, data is provided for each of the instruments defined in "OSU_data/docs/setup/instm_locations". The "UH_data" directory contains data collected from their DAQ. The data is stored in a ".tdms" file format. There are free plug-ins for Microsoft Excel and MathWorks MATLAB to read the ".tdms" format. Below are a few links providing methods to read in the data, but a Google search should identify alternatives sources if these no longer exist (valid as of January 2024): Excel: http://www.ni.com/example/27944/en/ MATLAB: https://www.mathworks.com/matlabcentral/fileexchange/30023-tdms-reader The Excel plugin is recommend to get a quick overview of the data. The UH data is organized by directory name, in which the sub-directories for each experiment contains a directory whose name defines the wave height and period for the experimental data within. For example, a directory name "H02_T0275" corresponds to an experiment with wave height 0.1m and a period of 2.75s. For random wave data, the gamma value is also included in the directory name. For example, a directory name "H02_T0225_G18" corresponds to an experiment with a significant wave height of 0.2m, a peak period of 2.25s, and a gamma value of 1.8, with each spectra being a TMA spectrum. For the free decay experiments, the directory name is defined by the initial angular displacement. For example, a directory name "ang05_run01" corresponds to an experiment with an initial angular displacement of 5 degrees. There is a dataset in the UH data for each corresponding experiment defined in the OSU DAQ logs. The ".tdms" data is output from the DAQ at fixed intervals. Therefore, if multiple files are contained within the folder, the data will need to be stitched together. Within the UH dataset, there are two input channels from the OSU DAQ providing a random square wave signal for time synchronization ("ENV-WHT-0010") and a high/low signal ("ENV-WHT-0012") to identify when the wave maker is active (+5V). The UH data is logged as a collection of channel outputs. Channels not in use for the OSU testing (either Phase I or Phase II) are marked "nan" below. If the sensor is disconnected, it will record noise throughout the experiment. Below are the channel definitions in terms of what they measure: GPS Time = time CYL-POS-0001 = position between flap and fixed reference CYL-LCA-0001 = force between flap and hydraulic cylinder REC-LPT-0001 = nan REC-HPT-0001 = nan REC-HPT-0002 = nan REC-HPT-0003 = nan HHT-HPT-0001 = pressure at exhaust ("head" only) REC-FQC-0001 = nan REC-FQC-0002 = nan HHT-FQC-0001 = flow at exhaust ("head" only) ENV-WHT-0001 = nan ENV-WHT-0002 = nan ENV-WHT-0003 = nan ENV-WHT-0010 = random signal from OSU DAQ ENV-WHT-0012 = high/low signal from OSU DAQ Also included is a calibration curve to convert the string pot data to flap pi...

16 TIDAL AND WAVE POWER↗

On the optimized 3D printing and post-processing of PETG materials

Glycol-modified polyethylene terephthalate (PETG) is a reliable middle ground between polylactic acid and acrylonitrile butadiene styrene due to its light weight, impact resistance, toughness, flexibility, and cost-effectiveness. However, during 3D printing, the filament form is prone to oozing and stringing. In this study, we optimized the PETG printability via g-code setting and printing parameter modification, and consideration of filament quality, build plate temperature and leveling, and printing design complexity. Printed PETGs were thermally and chemically annealed, and post-processing conditions including annealing time, temperature, and solvent use were investigated. Mechanical properties were evaluated in terms of print parameter changes and post-processing techniques.

36 MATERIALS SCIENCE↗

IDAES-PSE 2.1.0 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 2.1.0 Release Highlights New IDAES Examples Repository Starting with this release, the IDAES examples are developed in the new IDAES/examples repository. Along with many content and usability improvements, the most significant changes are: To install the examples, after installing IDAES, run pip install idaes-examples The idaes get-examples command, previously used for this, has been removed The HTML version is now available at https://idaes-examples.readthedocs.io The previous URL, https://idaes.github.io/examples-pse, will not be updated and may be removed at some point in the future For more details, refer to the resources available at IDAES/examples. Removal of Non-Functional Apps A review of the code in the idaes/apps and idaes/models_extra folders was undertaken, and a number of tools were identified as being outdated or non-functional and no longer supported by their development teams. Due to this, the following tools have been removed: idaes/apps/alamopy_depr (note that the new ALAMOpy interface remains avaialble in idaes/core/surrogates) idaes/apps/helmet idaes/apps/ripe idaes/apps/roundingRegression idaes/models_extra/carbon_capture Pyomo 6.6 This version of IDAES is the first requiring Pyomo 6.6. This version of Pyomo contains multiple internal improvements and refactorings. While for the majority of cases this should have positive or no impact on solvability of IDAES models, we are aware of a small number of models that have been affected as a result of these changes. For more information, refer to the Pyomo 6.6.1 release notes. Other highlights Model Initialization A prototype API for a new approach to initializing IDAES models is now available which makes available some new techniques for initializing models. This is documented in the Initializing Models Reference Guide Modular Properties Framework Support for some transport properties Helmholtz Equation of State properties Better error checking for case where unit models are set to include phase equilibrium but the property package is set to support only a single phase Multi-Stream Contactor model: a new base model for systems involving contacting of two or more streams with mass transfer. This model is intended to be used as the foundation for models such as membrane separators, solvent extraction and other similar processes. This is documented in the Multi-Stream Contactor Reference Guide idaes/models_extra/power_generation report() methods for unit models using Helmholtz equation of state General Code Maintenance Streamlining of dependencies and creation of new optional dependency groupings to support non-core tools General linting of codebase to ensure compliance with most pylint checks Spell checking of all code and doc strings Removal of backward compatibility code for Python 2

IDAES↗

Validating pyORBIT for Modeling Beam Dynamics in the IOTA Ring

The Integrable Optics Test Accelerator (IOTA) ring is a new Fermilab facility dedicated to beam physics experiments, currently operating with 150 MeV electrons. Space charge effects are expected to be significant when it operates with 2.5 MeV protons. In this contribution, we present results of a suite of validation tests of PyORBIT, a PICstyle space charge code. Single particle dynamics of quasiintegrable optics using an octupole string in IOTA is compared with MADX, and shown to be in good agreement. Requirements for the convergence of space charge computations are systematically established and when possible, tests involving space charge are compared with theoretical predictions.

Li, Runze↗

Computer Vision Techniques Used to Monitor the Alignment of Cavities and Solenoids in the PIP-II Prototype SSR1 Cryomodule

The alignment of the SRF PIP-II string components is studied as the acceptable beam deflection, offset and defocusing, which may otherwise cause beam loss. Simulations and measurements established that the maximum deviation of the beam pipe from the reference orbit should not exceed a small fraction of the beam aperture. To observe the translations and rotations of each single component within the cryomodule, optical instruments (H-BCAM) surveying highly reflective targets, installed in the internal assembly of the module were used. The alignment monitoring concept for the PIP II SSR1 prototype cryomodule, along with relevant measurements of the components’ position monitoring during coldmass cooldown is presented in this contribution. This development paves the way to new computer vision applications in the field of cryomodule assemblies in cleanroom environment, in which robotically-assisted operations have the potential to dramatically reduce the risk of chemical and particulate contamination.

43 PARTICLE ACCELERATORS↗

Study of Conduction-Cooled Superconducting Quadrupole Magnets Combined with Dipole Correctors for the ILC Main Linac

A superconducting rf (SRF) cryomodule for International Linear Collider(ILC) Main Linac equips focus/steering magnets. The magnets are "superferric" magnets with four superconducting (SC) race track coils conductively cooled from the cryomodule LHe supply pipe. The quadrupole field gradient and dipole field are 40 T/m and 0.1 T, respectively. The magnet length and iron-pole radius are 1 m and 0.045 m, respectively. It is known that dark current is generated at SRF cavities and accelerated through the following linac string. The dark current reaches and heats the SC magnets. It is estimated that the power deposition in the magnet may reach more than a few watts and temperature of the SC coils may locally reach to critical temperature of NbTi. It is important to make the magnet not reach quench with sufficient conduction cooling. We aim to realize the SC magnet which can stably operate under such condition. We plan to develop test coils made of three types of SC materials, NbTi, Nb₃Sn, and MgB₂ and study thermal characteristics and stability . We will develop a short model magnet, based on the test coil results. Here, we will present the magnet design study and the R&D plan.

43 PARTICLE ACCELERATORS↗

Modeling for the phased injector upgrade for 12 GeV CEBAF

As a follow on to the 12 GeV upgrade to the Continuous Electron Beam Accelerator Facility, the front end of the DC photo-gun-based injector has gone through a phased upgrade. The first phase focused on the beamline between the gun and the RF chopper system, and the second phase addresses the beamline after the RF chopper system including replacing the capture section and quarter cryomodule with a new booster module containing a 2-cell and 7-cell cavity string. Throughout the design process, we maintained and developed three models, one for the existing injector and one for each of the upgrade phases. With these models, we evaluated proposed hardware upgrades, evaluated and determined optimized beamline element positions, developed buncher voltage requirements, and settings for optimal injector running. In this paper, we will describe the models and results from these various studies and provide a brief summary of Phase 1 commissioning.

Kazimi, R.↗

Results from extended range SRF cavity tuner tests for LCLS-II-HE

The LCLS-II HE superconducting linac can produce multi-energy beams by supporting multiple undulator lines simultaneously. This could be achieved by using the cavity SRF tuner in the off-frequency detune mode. This off-frequency operation method was tested in 8 cryomodules at Fermilab at 2 K. In all the tests the tuners successfully achieved a frequency shift of -565±80 kHz from the 1.3 GHz value. This study discusses the cavity frequency during each stage of assembly from the cryomodule string to when they are finally tested at 2 K. Monitoring the cavity frequency from this initial stage contributed in reaching this large frequency shift. The specific procedures of tuner setting during assembly will be presented.

43 PARTICLE ACCELERATORS↗

INFN LASA in-kind contribution to PIP-II

This paper reports the status and recent progress of INFN LASA’s in-kind contribution to the PIP-II project at Fermilab, with updates on key activities and major procurements. Production efforts for the 38 INFN LASA-designed, 5-cell cavities (β=0.61) for the LB650 section of the linac are underway and two pre-series prototypes are being realized as a first step to validate the manufacturing and treatment sequence. Concurrently, preliminary testing on existing prototypes is progressing to gain a deeper understanding of the surface preparation and qualification procedures, including cross-validation at different infrastructures. Series LB650 cavities will be industrially produced and surface-treated to achieve the stringent performance targets, qualified via vertical cold tests at DESY AMTF, and delivered installation-ready for string assembly.

Paparella, Rocco [INFN, Pisa; LASA, Segrate]↗

Integration of computer vision system to track the alignment SRF cavities into the test cryostat for PIP-II at Fermilab

PIP-II cryomodules use a computer vision system (H-BCAMs system) to monitor the alignment of SRF cavities and focusing lenses during assembly, testing, and operation. This contribution details the integration of the H-BCAMs into the Spoke Test Cryostat (STC) at Fermilab, which is utilized for cold testing SRF cavities prior to their integration into the string assembly. Thermal and structural finite element analyses were employed to estimate the cavities’ deformations, to be validated during cold testing in the STC using H-BCAMs. Notably, this marks the first instance of H-BCAMs integration into a cryostat and operation within a cryogenic environment.

43 PARTICLE ACCELERATORS↗

Status of the INFN LASA in-kind contribution to PIP-II project

The status of INFN LASA in-kind contribution to the PIP-II project at Fermilab is reported in this paper. The effort for the series production of the 38 INFN LASA designed, 5-cell cavities with beta 0.61 for the LB650 section of the linac commenced and the status of ongoing activities and major procurements is here conveyed. At the same time, preliminary tests on INFN LB650 cavity prototypes are progressing in order to optimize the complete preparation and qualification cycle. All cavities will be produced, and surface treated in industry to reach the unprecedented performances required, qualified through vertical cold test at state-of-the art infrastructures and delivered as installation ready at the string assembly site.

43 PARTICLE ACCELERATORS↗

FAIRLinked: Data FAIRification Tools for Materials Data Science

FAIRLinked is a software package created to support the FAIRification of materials science data, ensuring proper alignment with FAIR principles: Findable, Accessible, Interoperable, and Reusable. It is built to be compatible with MDS-Onto, an ontology designed to capture the semantics of various types of materials data, enabling integration and sharing across different research workflows. The package is subdivided into three subpackages: InterfaceMDS, RDFTableConversion, and QBWorkflow. The first subpackage, InterfaceMDS allows users to search for terms using either string search or various filters, explore different domains and subdomains, and add terms to MDS-Onto. RDFTableConversion is used for serialization and deserialization of data from CSV into JSONLDs and vice versa in a way that captures the semantics of the data using MDS-Onto. Lastly, QBWorkflow is a serialization and deserialization workflow that incorporates RDF Data Cube vocabulary, useful for working with multidimensional datasets. By offering these packages, FAIRLinked lowers the barrier of creating FAIR, machine-actionable data for researchers in the materials science community.

FAIR↗