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At least 703 records · Page 39

Agilent AgileBioFoundry CRADA (Final Report)

The mission of this CRADA with Agilent was to couple powerful MS platforms (QQQ, IM-QTOF-MS) with Agilent’s novel Ultra-High-Performance Liquid Chromatography (UHPLC) fast metabolomic workflows and perform ABF Machine Learning (ML) to generated datasets. Agilent transferred UHPLC methods to PNNL and LBNL and methods were implemented and demonstrated in both labs, achieving total acquisition times of < 10 min. Metabolites analyzed using Agilent’s shared methods included metabolites from central carbon metabolism, common across hosts, and metabolites unique to engineered strains. Standards were acquired in an UHPLC-Drift Tube Ion Mobility Mass Spectrometer (DTIMS) system for the first time within the context of ABF and methods were optimized based on Agilent’s protocols. Samples from ABF hosts Pseudomonas putida, Aspergillus pseudoterreus, Aspergillus niger and Rhodosporidium toruloides were analyzed using the UHPLC-DTIMS platform for a total of 276 runs. A data analysis workflow compatible with the Experimental Data Depot (EDD) and completely shareable was developed for the acquired UHPLC-DTIMS data. Samples were analyzed using a Data Independent Acquisition Approach (DIA), which for most of the standards provided more transitions therefore increasing detection confidence. Using the data acquired by PNNL, LBNL, and Agilent’s specifications from previous ML projects, SNL applied an ensemble ML strategy to pick the best performing model for automated LC-method selection. Finally, with the contribution of the participant labs and Agilent, SNL developed an Automated Method Selection (AMS) software tool to predict the best liquid chromatography method for analysis of any new molecules of interest. Samples with novel pathways and new metabolite targets of interest are generated at a high pace in the ABF. Therefore, our accomplishment in this CRADA improved the efficiency and accuracy of strain testing by developing and implementing fast analytical methods, robust processing tools, and software for predicting the best methods for UHPLC analysis.

97 MATHEMATICS AND COMPUTING↗

Audible Noise Modeling of Hydrogen Release Sonic Hazards in Rail Maintenance Facilities

This study implemented validated literature models to predict audible noise due to pressurized gaseous hydrogen releases through a thermally-activated pressure relief device (TPRD) and attached vent stack. A literature survey discovered limited hydrogen-specific noise prediction models validated by experiments. However, empirical noise prediction models for air flowing through pipes and valves were identified. These empirical models were used to predict noise levels and compared against hydrogen noise data reported in two studies: one experimental study of noise from hydrogen leaking through a pipe and another which modeled hydrogen flowing through a solenoid valve during a fuel cell vehicle refueling. The valve flow model was then applied to predict noise for hydrogen releases through a TPRD. Results show that hydrogen releases through a TPRD can produce harmful noise levels varying from 134 to 150 dB. However, further model validation and additional experimental data are needed to improve prediction confidence and accuracy.

08 HYDROGEN↗

Development and implementation of high-throughput proteomic and metabolomics assays by using advanced chromatographic and mass spectrometric systems (CRADA Final Report)

The mission of this CRADA with Agilent was to couple powerful MS platforms (QQQ, IM-QTOFMS) with Agilent’s novel Ultra-High-Performance Liquid Chromatography (UHPLC) fast metabolomic workflows and perform ABF Machine Learning (ML) to generated datasets. Agilent transferred UHPLC methods to PNNL and LBNL and methods were implemented and demonstrated in both labs, achieving total acquisition times of < 10 min. Metabolites analyzed using Agilent’s shared methods included metabolites from central carbon metabolism, common across hosts, and metabolites unique to engineered strains. Standards were acquired in an UHPLC-Drift Tube Ion Mobility Mass Spectrometer (DTIMS) system for the first time within the context of ABF and methods were optimized based on Agilent’s protocols. Samples from ABF hosts Pseudomonas putida, Aspergillus pseudoterreus, Aspergillus niger and Rhodosporidium toruloides were analyzed using the UHPLC-DTIMS platform for a total of 276 runs. A data analysis workflow compatible with the Experimental Data Depot (EDD) and completely shareable was developed for the acquired UHPLC-DTIMS data. Samples were analyzed using a Data Independent Acquisition Approach (DIA), which for most of the standards provided more transitions therefore increasing detection confidence. Using the data acquired by PNNL, LBNL, and Agilent’s specifications from previous ML projects, SNL applied an ensemble ML strategy to pick the best performing model for automated LC-method selection. Finally, with the contribution of the participant labs and Agilent, SNL developed an Automated Method Selection (AMS) software tool to predict the best liquid chromatography method for analysis of any new molecules of interest. Samples with novel pathways and new metabolite targets of interest are generated at a high pace in the ABF. Overall, the project advanced rapid metabolomics by combining liquid chromatography, ion mobility spectrometry, and data-independent mass spectrometry with machine learning. This multidimensional approach uses retention time, collision cross-section, precursor mass, and fragment-ion information to distinguish chemically similar metabolites that can be difficult to resolve using conventional liquid- or gas-chromatography methods. The resulting workflow also provided automated metabolite-identification error estimates, addressing a recognized need for statistical confidence measures in metabolomics.

Petzold, Christopher [Lawrence Berkeley National L↗

Preliminary Modeling of Triply Periodic Minimal Surface (TPMS) Structures with RELAP5-3D

This poster goes over preliminary work performed on modeling triply periodic minimal surfaces (TPMS) with RELAP5-3D. The poster starts off with the need for advanced nuclear fuel designs for future reactors, and how TPMS are being researched for this purpose. There is then a focus on what a TPMS is and then moves onto the motivation for why this geometry is being modeled and looked into. The methodology is then shown for how data from different experiments will be used for pre-test predictions and eventual creation of empirical coefficients and multipliers to be used in models. Then there is a show of how data would be compared between the experimental tests, CFD, and RELAP5-3D values. The results from the simulations and comparisons are then presented to show how the CFD and RELAP5-3D compare to each other currently, with no experimental data to compare to for one test model. Results from the second test model are also presented to show that there is stability in the solving of that model.

42 - ENGINEERING↗

Development of an Amine Oxide Polyzwitterion Brush Martini Model with Polarizable Water and Ions

Abstract In order to accurately simulate the fouling process of proteins onto polyzwitterion brushes, models that accurately capture the hydration properties and chain conformations of such brushes must first be established. We developed a Martini coarse-grained (CG) model for amine oxide polyzwitterion (PNOMA) brushes, a promising class of antifouling materials, in polarizable water and ions by fitting to all-atom bond and angle distributions, monomer hydration free energy, monomer–monomer distance potential of mean force (PMF), and monomer–salt radial distribution functions (RDFs). Martini 2.2P was selected for compatibility with the established polarizable water and ion models. For comparison with PNOMA, we also constructed models for conventional sulfobetaine (PSBMA) and phosphorylcholine (PMPC) polyzwitterions and the polycation PMETAC using established nonbonded bead types from the literature and refitting bond and angle potentials. We simulated each polymer brush chemistry for varying grafting density and chain length, validating brush height scaling relations against experimental data. The CG models captured the relative hydration strengths among different polyzwitterion chemistries, and brush heights extrapolated to higher molecular weights are in agreement with experimental ellipsometry data. We find that chain swelling of the superhydrophilic PNOMA brushes lies between that of the traditional polyzwitterions PSBMA/PMPC and the polycation PMETAC. For PNOMA brushes in NaCl solution, simulated brush height decreases with salt concentration due to the selectively strong interactions between amine oxide and sodium ions.

Walker, Christopher C. [Oak Ridge National Laborat↗

Probing the limits of statistical neutron capture for the r process: Experimental constraints on 141 Cs nuclear level densities

The r-process abundance peaks, particularly near mass number A ∼ 130, reflect underlying nuclear structure effects such as closed neutron shells, yet modeling the nucleosynthesis in this region remains hindered by uncertain neutron-capture rates. These rates are especially sensitive to nuclear level densities (NLDs) and γ-ray strength functions of neutron-rich nuclei, where experimental data are scarce. We present the first experimental constraint on the NLD of 141 Cs using the β-Oslo method, extending sensitivity to the neutron-rich regime near the N = 82 closed shell. Our data allow for critical calibration of microscopic NLD models and reveal that 141 Cs lies near the limit of statistical model applicability. Using this experimental input, we evaluate radiative neutron-capture rates across neighboring isotones using both Hauser–Feshbach (HF) and High Fidelity Resonance (HFR) models. Our results show order-of-magnitude rate increases for nuclei along the N = 86 line, signaling a transition to resonance-dominated capture in this region. These findings underscore the importance of constraining NLDs to improve r-process reaction network predictions, particularly in environments where the validity of statistical models breaks down.

Nuclear level density↗

Differential cross sections of the 16 O (𝑛,𝛼) reaction at neutron energies from 3.8 to 15 MeV

The importance of studying the 16 O (𝑛,𝛼) reaction is motivated by multiple nuclear applications which rely on an accurate nuclear reaction data library for oxygen. Discrepancies between past experimental data on the 16 O (𝑛,𝛼) 13 C reaction and its time-reverse 13 C ⁡(𝛼,𝑛) 16 O reaction have led to various different nuclear data evaluations. Here, we have measured 16 O (𝑛,𝛼) reaction cross sections using the LENZ instrument with the unmoderated white neutron source at LANSCE. Results from 2016/2017 data are discussed and used to benchmark the mcnp and geant simulations of the LENZ experimental setup. We report partial differential cross sections of 16 O (𝑛,𝛼 0 ) at 𝐸 𝑛 = 3.8–15 MeV and 16 O ⁡(𝑛,𝛼 1 +𝛼 2 +𝛼 3 ) at 𝐸 𝑛 =9–15 MeV, based on the new measurement in 2021. The resonances that we observed are in good agreement with the levels in 17 O that were previously measured. The LENZ cross sections are in better agreement with the ENDF/B-VIII.0 evaluation than the with reduced cross section found in ENDF/B-VII.1 up to 6 MeV. However, the current results for 16 O ⁡(𝑛,𝛼 0 ) 13 C g.s. appear to be in the best agreement over the entire energy range with that of JENDL/AN-2005 (ENDF/B-VI.0).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Nonstatistical fluctuations in the 35 Cl(n,p) 35 S reaction cross section at fast-neutron energies from 0.6 to 6 MeV

The lack of experimental data on the 35 Cl(n,p) 35 S reaction above 100 keV has led to nuclear data evaluations that are relatively unconstrained at fast neutron energies. As a result, efforts to explore, develop, and potentially certify next generation reactor designs that incorporate chloride salts as a coolant material have been hindered. Here, we report partial cross section data for the 35 Cl(n,p) 35 S and 35 Cl(n,α) 32 P reactions at incident neutron energies between 0.6 MeV and 6 MeV. The measurement was performed using the pulsed beam of neutrons at the unmoderated WNR spallation neutron source at the Los Alamos Neutron Science Center, with the outgoing charged particles detected by the LENZ experimental setup, consisting of annular silicon detectors. Nonstatistical fluctuations in the 35 Cl(n,p 0 ) cross section were observed up to around 3 MeV, and the magnitude of the cross section was systematically lower than all available data evaluations at energies above 1 MeV. Modifications to the ENDF/B-VIII.0 data evaluation are suggested to better reproduce the energy averaged experimental data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Accuracy of kinetic equilibrium reconstruction of NSTX and NSTX-U plasmas and its impact on the transport and stability analysis

An accurate magnetohydrodynamic (MHD) equilibrium reconstruction is an essential starting point for stability and transport plasma analysis. Herein this work describes an approach for obtaining kinetic equilibrium reconstructions using the OMFIT framework, which has been applied for the first time to spherical tokamak data from NSTX and NSTX-U. The EFIT equilibrium solver is integrated with experimental data analysis procedures and subsequent TRANSP transport simulations to enhance the accuracy of the reconstruction, in particular, at the edge region, by adding constraints on the total pressure and current density profiles, based on the transport code solution. The accuracy of the equilibrium reconstruction depends on the uncertainty and number of constraints, as well as the choice of basis functions to represent the pressure and current density profiles. Improved fidelity of the equilibrium reconstruction is demonstrated by reducing the variability of the magnetic axis and boundary locations from several centimeters, for reconstructions based on magnetic and experimental pressure constraints, to only several millimeters, for kinetic reconstructions based on transport code constraints, when different representations of basis functions were tested. The variability of the safety factor on axis was reduced ten times in the same sensitivity study. The accuracy of the equilibrium reconstruction and subsequent mapping of the experimental kinetic profile data have a significant impact on the trapped gyro Landau fluid and linear CGYRO turbulence simulations, which predict different spectra of unstable modes and turbulent fluxes for cases with different numbers of constraints in the equilibrium reconstruction. Conversely, the stability analysis performed using the GATO code shows plasmas that are stable to n = 1 MHD modes in both equilibria using magnetic and experimental pressure constraints as well as the transport code constrained equilibrium. However, a scan of parameters away from these conditions shows considerable deviation in the threshold of unstable modes between these reconstructions. Therefore, for reliable plasma analysis and use in turbulence and stability calculations, a high-fidelity equilibrium reconstruction with accurate kinetic constraints based on transport code solutions is necessary.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Maximized Information Gain of Next Generation Pulsed Power Using Optimized Design of Z-Machine Experiments

This project develops a Bayesian optimization approach to extracting insights from Z Machine experimental data to determine if and how these insights can be used to extrapolate to a larger facility. The primary goal is to address the scientific challenge of informing how confidently experimental conditions can be predicted on a next generation facility, the design of which requires the reliable extrapolation of current high energy density technologies to regimes yet unobserved, except by costly high-fidelity computational models. Maximizing the use of presently available data and understanding how it informs future endeavors is critically important to enable transformative pulsed power and the science of extreme conditions. We explore a Bayesian optimization approach to experimental design which combines information theory, experimental data, and computational modeling to explore how information gain can be maximized.

97 MATHEMATICS AND COMPUTING↗

CT_Data_of_Gas_Migration_in_Setting_Cement

Computed tomography experimental data associated with the submitted manuscript "Migration of air bubbles in a column of cement slurry" by N’dri Arthur Konan, Eilis Rosenbaum, Dustin Crandall, Mehrdad Massoudi. Full description with citation to be updated when manuscript is accepted.

Computed Tomography↗

181 Ta - fast neutron evaluation [Slides]

Reliable fast-neutron evaluation can be entirely encapsulated in the reaction model and related input. Ta181 is a particularly relevant case due to extraordinary coverage of various observables by differential experiments that offer much help and relatively little headache. Differences from the similar ENDF/B-VIII evaluation include: more advanced modeling (CC OMP, MSD, MSC, decay schemes), more careful selection of models and parameters, new experimental data, and isomers. Overall, improved agreement with differential data and hints of better performance in integral testing.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A Physics-Based Data-Driven Approach for Modeling of Environmental Degradation in Elastomers

Abstract Elastomers are now commonly used in a number of industries, including aerospace, structure, transportation, shipbuilding, and automotive, due to their excellent workability, formability, and flexibility. During their activity, elastomers are subjected to harsh environmental conditions, which decreases their resilience. False predictions made early in their lives can have major financial and environmental implications. Elastomers’ performance and properties, such as strength, durability, and density, are influenced by chemical changes in these materials, known as degradation, which occurs over time. This process can alter the morphology of a polymer matrix as well as cause chain scission and cross-linking, resulting in different behaviors than that of the unaged material. To demonstrate the effect of thermaloxidative aging on the mechanical behavior of elastomers, several experimental and theoretical models have been proposed. In view of the large volume of experimental data available on micro-structural evolution in the course of aging, we propose a physics-based data-driven approach to overcome the shortcomings of both phenomenological and micro-mechanical models. This work presents a novel thermodynamically consistent, multiagent machine-learned model for predicting the constitutive behavior of cross-linked elastomers during environmental aging, such as thermo-oxidative and hydrolytic aging for various states of deformation. Single mechanism degradation changes the polymer matrix over time where it is causing chain scission, reduction of cross-links, and morphology change. To capture the idealized Mullins effect and permanent set due to the effect of single aging mechanisms on nonlinear mechanical responses of elastomers, we propose a data-driven model for simulating inelastic elements in a polymer matrix. By using a sequential order reduction, we were able to reduce the 3D stress-strain tensor mapping problem to a small number of super-constrained 1D mapping problems. To systematically classify such mapping problems into a few categories, an assembly of multiple replicated conditional neural network learning agents (L-agents) is used based on our recent work. Each category is represented by a different type of agent. The effect of deformation history, aging time, and aging temperature is captured by this model. The model is validated using a broad collection of data, ranging from our experimental results to data from the literature. In addition, thermodynamic consistency and frame independence are investigated. The most significant achievements of this model are its precision, simplicity, and prediction of inelasticity under various states of deformation. The model’s accuracy and simplicity make it a good option for commercial and industrial applications. Conveniently, due to the model modular nature, it can be expanded in the future to include viscoelasticity and non-isotropic formation for better precision.

Ghaderi, Aref↗

Neutron elastic and inelastic scattering differential cross sections on carbon

Elastic and inelastic neutron scattering angular distributions were measured on natural carbon samples to confirm existing experimental data and evaluations in the fast neutron region and to guide improvements in resonance parameters, where needed. Sixty-four (n,n') differential cross section measurements were performed at 45 incident neutron energies between 0.5 and 8.0 MeV. Experimental angle-integrated elastic scattering cross sections are consistent with ENDF/B-VIII.0 values with the exception of the region from 3.2 to 4.0 MeV where our results are ~3% higher. In the 3.4 to 3.6 MeV region our differential cross sections are slightly lower at forward angles and somewhat higher at backward angles than the ENDF/B-VIII.0 calculations; however, our results are consistent with measured data from other research groups. The first- through fourth-order elastic scattering Legendre coefficients from fits to these experimental data are consistent with ENDF/B-VIII.0 values across this range of incident neutron energies. Inelastic scattering cross sections were measured at 12 incident neutron energies between 5.6 and 7.8 MeV. Angle-integrated cross sections agree well with the 1978 Perey and ENDF/B-VIII.0 values; however, the angular-distribution shapes deviate somewhat from the ENDF/B-VIII.0 calculations. These data will allow refinement of the resonance parameter description in this difficult energy region.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

A Python Instrument Control and Data Acquisition Suite for Reproducible Research

Tools that standardize and automate experimental data collection are needed for greater confidence in research results. The National Synchrotron Light Source-II (NSLS-II) has generated an open-source Python data acquisition, management, and analysis software suite that automates X-ray experiments and collects an experimental record that facilitates complete reproducibility. Here, we show that the NSLS-II tools are not only useful for X-ray science at large-scale facilities by presenting an add-on package that adapts these tools for use in a small laboratory with common physics and electrical engineering instruments. The composite software suite eases and automates the execution of experiments, records extensive metadata, stores data in portable containers, and speeds up the analysis through tools for comprehensive searches. In total, this software suite increases the reproducibility of laboratory experiments. We demonstrate the software via the evaluation of two lock-in amplifiers-the miniature ADA2200 and the ubiquitous Stanford Research Systems (SRS) SR810. The frequency resolution, signal-to-noise ratio, and dynamic reserve of the lock-in amplifiers are measured and presented. The usage of the software suite is described throughout these measurements so that the reader can implement the tools in their lab.

97 MATHEMATICS AND COMPUTING↗

The Gene Ontology resource: enriching a GOld mine

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20,000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.

59 BASIC BIOLOGICAL SCIENCES↗

Nuclear excitation functions for medical isotope production: Targeted radionuclide therapy via nat IR$(d, x)$ 193m Pt

193m Pt is an Auger emitting radionuclide which may have therapeutic potential, particularly when labeled to the chemotherapeutic drug cisplatin. One challenge to broader explorations of its clinical potential is the need for production routes with high specific activity. As part of a larger campaign to address gaps in reaction data for emerging medical radionuclides, this work seeks to characterize the nat Ir(d,x) reactions as a potential production pathway for 193m Pt. A stacked target irradiation, consisting of natural iridium, iron, nickel, and copper foils, was performed using a 33 MeV deuteron beam at the Lawrence Berkeley National Laboratory 88-Inch Cyclotron. This measurement, along with previous experimental data, suggests an energy window between 11 to 18 MeV to maximize the production and radiopurity of 193m Pt. This experiment has yielded cross sections for 43 channels of deuteron-induced reactions from threshold to 30 MeV, including the first experimental results of nat Ir(d,x) 188m1+g,190m1+g Ir (cumulative), nat Ni(d,x) 56,57,58 m,58g Co (independent), nat Cu(d,x) 61 Co (cumulative) and nat Fe(d,x) 53 Fe, 48 V (cumulative). The results were compared with literature data, the TENDL-2023 database, and default theoretical calculations from the TALYS-2.04, CoH-3.6.0, EMPIRE 3.2.3, and ALICE-2020 reaction modeling codes. Here, this work presents another example of the lack of predictive capabilities for this set of modern nuclear-reaction modeling codes, and highlights the unsatisfactory modeling of experimental cross sections. Experimental data are important to improve the codes in general, and new experimental results can be used to improve the models. Finally, this measurement has revealed the need for an updated evaluation of the nat Cu(d,x) 63 Zn deuteron monitor reaction.

193mPt↗

Experimental shock Hugoniot and melt boundary temperatures of aluminum

Aluminum is a ubiquitous component in dynamic compression, pulsed power, and other high energy density physics studies. Its high-pressure behavior and phase diagram are extensively studied standards in shockwave physics. While theoretical calculations and multiphase equations of state have been benchmarked to velocity measurements of loading and unloading waves, pressure and density under shock, and other mechanical data, experimental temperature data under these conditions have not been reported. We conducted a series of experiments shocking and releasing aluminum 6061 and 1100 samples into lithium fluoride windows. We measured temperature at the sample–window interface under steady compression and subsequent isentropic release. These results allow us to constrain the temperature of the solid Hugoniot and the boundary between the liquid and face-centered cubic solid phases.

Hartsfield, Thomas Murray [Sandia National Laborat↗