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At least 343 records · Page 19

Explaining word embeddings with perfect fidelity: a case study in predicting research impact

The best-performing approaches for scholarly document quality prediction are based on embedding models. In addition to their performance when used in classifiers, embedding models can also provide predictions even for words that were not contained in the labelled training data for the classification model, which is important in the context of the ever-evolving research terminology. Although model-agnostic explanation methods, such as Local interpretable model-agnostic explanations, can be applied to explain machine learning classifiers trained on embedding models, these produce results with questionable correspondence to the model. We introduce a new feature importance method, Self-Model Entities Rated (SMER), for logistic regression-based classification models trained on word embeddings. We show that SMER has theoretically perfect fidelity with the explained model, as the average of logits of SMER scores for individual words (SMER explanation) exactly corresponds to the logit of the prediction of the explained model. Quantitative and qualitative evaluation is performed through five diverse experiments conducted on 50,000 research articles (papers) from the CORD-19 corpus. In conclusion, through an AOPC curve analysis, we experimentally demonstrate that SMER produces better explanations than LIME, SHAP and global tree surrogates.

Coarse-grained models↗

High fidelity model of directed energy deposition: Laser-powder-melt pool interaction and effect of laser beam profile on solidification microstructure

Metal additive manufacturing technologies keep receiving a great deal of interest as well as strong requests to develop methods to link the process science to printed parts performance and understand how to overcome inherent limitations. Here, a high-fidelity model based on the multiphysics ALE3D code was developed to reproduce the directed energy deposition process down to the powder scale. This includes resolving the laser-powder-melt pool interactions (powder impingement and incorporation into melt pool, hydrodynamics flow condition and laser absorption inefficiencies) as well as the resulting solidification microstructure. This micrometer scale digital twin captured the effect of powder incorporation process and powder flow rate on porosity. Furthermore, it was used to explore how a ring laser beam profile instead of the standard Gaussian laser profile could decrease the thermal gradient along the solidification front in the melt pool, which in turn can increase propensity for more desirable equiaxed grains.

36 MATERIALS SCIENCE↗

Hydrogen Production System Scaling Using a High-Fidelity Simulation-Optimization Framework

Proton exchange membrane (PEM) electrolyzers are widely used for hydrogen production, yet few validated, high-fidelity tools can reliably guide scale-up. Using measured performance from a 50-hour hardware-in-the-loop pilot test, a physics-based, plant-level model of a 1.25 MW PEM electrolyzer and its balance-of-plant (BoP) subsystems is developed and validated. The model couples electrochemistry and thermal/flow submodels and is calibrated against pilot test data via a genetic algorithm (GA) workflow. Validation yields a mean absolute percentage error (APE) of 0.43% for cell voltage and stack power. Two scale-out strategies are then benchmarked under a common 7-day wind-and-photovoltaic (PV) profile: (i) linear duplication of 1.25 MW blocks and (ii) shared-BoP architectures. Sharing BoP between stacks reduces BoP energy by 27% at 10 MW and 34% at 100 MW (vs. linear duplication) and improves system specific energy consumption (SEC) to 52.9 and 52.6 kWh/kg, respectively (from 54.0 kWh/kg with linear duplication). Partial-load studies (25-100% set-point) show that cumulative hydrogen production remains nearly constant down to 50% load because all cases use the same weekly renewable-energy input. Below 50%, the power cap limits how much energy can be used within 168 h, which reduces hydrogen output. The model further indicates that the practical operating optimum lies between 50% and 85% load, where efficiency gains begin to appear without significant loss in hydrogen output. Moreover, the efficiency gains at lower loads are offset by reduced production. The validated framework supports scenario-based engineering trade-off studies for large configurations (10-100 MW) and for operating policies under variable renewables.

08 HYDROGEN↗

Toward a high-fidelity tritium transport modeling for retention and permeation experiments

We report Tritium Migration Analysis Program version 8 (TMAP8), the latest version of TMAP, was developed within the framework of the Multiphysics Object-Oriented Simulation Environment (MOOSE). Created at Idaho National Laboratory (INL), MOOSE is an open-source, dimension-agnostic, fully coupled, and fully implicit multiphysics platform featuring massively parallel computation capabilities. Using TMAP8, tritium transport in a divertor monoblock was analyzed to elucidate the effects of pulsed operation (up to fifty 1,600 s plasma discharge and cool-down cycles) on the tritium in-vessel inventory source term and ex-vessel release term (i.e., tritium retention and permeation) for safety analysis. With its built-in Message Passing Interface capability, TMAP8 can, in under 2 h, simulate tritium transport in three different layered materials (i.e., tungsten, copper, and copper-chromium-zirconium alloy) in 2D geometry, using a single device/computer with 10 cores. The MOOSE-based TMAP8 code can leverage other MOOSE tools developed under the Nuclear Energy Advanced Modeling and Simulation program to perform tritium and thermal transport in complex geometries and multiphysics environments. And via its massively parallel computation, MOOSE will enable the fusion pilot plant designers to conduct high-fidelity multiphysics modeling for the design of the divertor and blanket systems as well as for the safety analysis.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Scalable Generation of High-fidelity Synthetic Population Ensembles

Used within social simulations, synthetic population ensembles enable uncertainty quantification (UQ) methods for obtaining more robust model inference and prediction. A synthetic population ensemble is a series of plausible virtual reconstructions of an area’s population at the granularity of people and residences, generated stochastically to preserve privacy of the source population survey’s respondents. In this paper, we demonstrate the production of large synthetic population ensembles for the U.S. via Oak Ridge National Laboratory’s UrbanPop framework to support modeling of high spatial resolution energy affordability metrics from nationwide social surveys in collaboration with the fusionACS project. The study involves two scenarios: creating ensembles for (1) 17 U.S. metropolitan areas in 2019 and (2) full U.S. Census Divisions in 2023, with each scenario consisting of 41 population instances (a base realization and 40 replicates). To accomplish this task at scale, we configured an integrated system within a research cloud, comprised of virtual containerizations, GPU-enhanced functionality, and orchestrated deployments of UrbanPop’s maturing Likeness Python ecosystem. Results demonstrate we maintained high-fidelity approximations of residential totals by areas of interest and the demographic characteristics of neighborhoods while reducing manual workflow burdens. Finally, we discuss plans to fine-tune and further develop our automated workflows for truly distributed job orchestration to increase computational efficiency, as well as provide an outlook for broadening applications of the ensembles.

Cluster computing↗

Assessing the fidelity of shallow-water carbonates as records of the Ni isotope composition of surface seawater

Nickel is a bioessential metal that is used in enzymes important to the C, N, and O cycles, and changes in its marine abundance and bioavailability may have affected the evolutionary trajectory of early life. Changes over time in the Ni isotope composition (δ 60 Ni) of surface seawater, which reflects biological demand for Ni, could allow for the reconstruction of the dynamics of Ni demand over Earth’s history, but this approach would require geologic records of surface seawater. Here, we investigate the fidelity of shallow-water carbonates as a record of the Ni isotope composition of surface seawater by determining how Ni is first partitioned into natural carbonates and then how post-depositional processes influence the Ni signal. Our samples come from the Great Bahama Bank, which is a well-studied, modern carbonate platform often used to study ancient platforms. We found that Ni is fractionated from seawater upon incorporation into carbonates capturing shallow (<18 cm), recent deposition (0.1 ‰–0.4 ‰ lighter than seawater). Variation among these [Ni] and δ 60 Ni values may be controlled by variation in mineral proportions. Meteoric diagenesis shifts δ 60 Ni to lower values, which we attribute to isotopically light meteoric fluids. In contrast, carbonates that experienced sediment-buffered marine diagenesis with respect to Ca isotopes and Sr/Ca ratios do not appear to differ in δ 60 Ni values from sediments generally representative of their initial deposition. The sensitivity of δ 60 Ni to diagenetic reset in these samples appears comparable to the sensitivities of Ca isotopes and Sr/Ca ratios, to first order. Thus, in general, carbonates that experienced sediment-buffered marine diagenesis with respect to these elements may hold the most promise as a record of the δ 60 Ni of coeval surface seawater. Additionally, we use our results to infer that the fraction of Ni removed from seawater into carbonates is less than 10 % of the total Ni output from the global oceans and incorporation of this Ni sink into global biogeochemical models will only have a minor impact on the modeled modern Ni budget.

Great Bahama Bank carbonates↗

Boundary-consistent B-spline filtering schemes and application to high-fidelity simulations of turbulence

A filtering operation, based on B-spline discretizations, is introduced to target weakly growing mesh-scale oscillations that can arise in high-fidelity turbulence simulations. This is a spectral regularization that can be described using the singular values of a banded matrix operator, with the filtering strength set by a scalar- or vector-valued penalty parameter. The penalty parameter can be specified though it can also be advantageously selected to minimize the generalized cross validation (GCV) measure of distance between the pre- and post-filtered solutions. Efficient algorithms are developed to compute both the scalar and vector penalty parameters. The B-spline filter has a sharper localization to high-wavenumber than compact or explicit filters of the same stencil width and is demonstrated for solutions of the Burgers' equation, decaying Burgers' turbulence, and compressible Navier–Stokes turbulent channel flow. Furthermore, these simulations confirm the scheme's numerical stability and ability to narrowly target the high wavenumber components of numerical solutions. An advantage over finite-difference filters is that these B-spline filters are stable on bounded domains and even preserve formal order of accuracy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

High fidelity multiphysics tightly coupled model for a lead cooled fast reactor concept and application to statistical calculation of hot channel factors

A tightly coupled multiphysics code system is established using the MOOSE framework for hot channel factor (HCF) evaluation on a Lead Fast Reactor (LFR) concept. The coupled system is driven by the Griffin multiphysics coupling capability under which the MOOSE Heat Transfer module and NekRS computational fluid dynamics solver are coupled for conjugate heat transfer using the Cardinal application. The coupled capability is demonstrated on an LFR assembly model based on materials and geometry of a prototypical lead-cooled fast reactor design by Westinghouse Electric Company, LLC. Moreover, the work integrates the Multiphysics Object Oriented Simulation Environment (MOOSE) Stochastic Tools Module (STM) to perform calculations for statistical analysis of HCF. Furthermore, the coupling strategy and workflow demonstrated in this paper is not only useful for predicting accurate hot channel factors for different kinds of advanced reactors but also for other engineering applications such as control rod worth assessment, generation of high-fidelity database for Artificial intelligence (AI)/machine learning (ML) training, design optimization and multi-resolution modeling.

Cardinal↗

Exploiting Colorimetry for Fidelity in Data Visualization

Advances in multimodal characterization methods fuel the generation of increasing immense hyper-dimensional data sets. Color mapping is employed for conveying higher dimensional data in two-dimensional (2D) representations for human consumption without relying on multiple projections. How one constructs these color maps, however, critically affects how accurately one perceives data. For simple scalar fields, perceptually uniform color maps and color selection have been shown to improve data readability and interpretation across research fields. In this work, we review core concepts underlying the design of perceptually uniform color maps and extend the concepts from scalar fields to two-dimensional vector fields and three-component composition fields frequently found in materials-chemistry research to enable high-fidelity visualization. Additionally, we develop the software tools PAPUC and CMPUC to enable researchers to utilize these colorimetry principles and employ perceptually uniform color spaces for rigorously meaningful color mapping of higher dimensional data representations. Last, we demonstrate how these approaches deliver immediate improvements in data readability and interpretation in microscopies and spectroscopies routinely used in discerning materials structure, chemistry, and properties.

36 MATERIALS SCIENCE↗

Diversifying Composition Leads to Hierarchical Composites with Design Flexibility and Structural Fidelity

Although significant progress has been made in the self-assembly of nanostructures, present successes heavily rely on precision in building block design, composition, and pair interactions. These requirements fundamentally limit our ability to synthesize macroscopic materials where the likelihood of impurity inclusion escalates and, more importantly, to access molecular-to-nanoscopic-to-microscopic-to-macroscopic hierarchies, since the types and compositions of building blocks vary at each stage. Inspired by biological blends and high-entropy alloys, we hypothesize that diversifying the blend’s composition can overcome these limitations. Increasing the number of components increases mixing entropy, leading to the dispersion of different components and, as a result, enhances interphase miscibility, weakens the dependence on specific pair interactions, and enables long-range cooperativity. This hypothesis is validated in complex blends containing small molecules, block copolymer-based supramolecules, and nanoparticles/colloidal particles. Hierarchically structured composites can be obtained with formulation flexibility in the filler selection and blend composition. It is worth noting that, by adding small molecules, we can solve the size constraint that plagues traditional block copolymer/nanoparticle blends. Detailed characterization and simulation further confirm that each component is distributed to locally mediate unfavorable interactions, cooperatively mitigate composition fluctuations, and retain structural fidelity. Furthermore, the blends have sufficient mobility to access tunable microstructures without compromising the order of the nanostructure. Besides establishing a kinetically viable pathway to release current constraints in the composite design and to navigate uncertainties during structure formation over multiple length scales, the present study demonstrates that entropy-driven behaviors can be realized in systems beyond high-entropy alloys despite inherent differences between metal alloys and organic/inorganic hybrids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PNA-Assisted DNAzymes to Cleave Double-Stranded DNA for Genetic Engineering with High Sequence Fidelity

DNAzymes have been widely used in many sensing and imaging applications but have rarely been used for genetic 5 engineering since their discovery in 1994, because their substrate scope is mostly limited to single-stranded DNA or RNA, whereas 6 genetic information is stored mostly in double-stranded DNA (dsDNA). To overcome this major limitation, in this paper we report 7 peptide nucleic acid (PNA)-assisted double-stranded DNA nicking by DNAzymes (PANDA) as the first example to expand 8 DNAzyme activity toward dsDNA. We show that PANDA is programmable in efficiently nicking or causing double strand breaks on 9 target dsDNA, which mimics protein nucleases and can act as restriction enzymes in molecular cloning. In addition to being much 10 smaller than protein enzymes, PANDA has a higher sequence fidelity compared with CRISPR/Cas under the condition we tested, 11 demonstrating its potential as a novel alternative tool for genetic engineering and other biochemical applications.

59 BASIC BIOLOGICAL SCIENCES↗

High-Fidelity Analysis of ULF Wave Mode Structure Following Interplanetary Shock Compression of the Dayside Magnetopause Using MMS Multi-Point Observations

During the 9 March 2018 event with two consecutive interplanetary shocks compressing the dayside magnetosphere, the azimuthal mode structure and frequency spectrum of ultra low frequency magnetic pulsations are resolved using a cross-spectral analysis based on high-fidelity multi-probe Magnetospheric Multiscale Mission (MMS) magnetometer data. The results based on the MMS 4 and MMS 3 pair of measurements show that shock arrival leads to low mode (|m| ≤ 3) magnetic fluctuations in the Pc4-5 regimes, and smaller spatial scale fluctuations implied by the dominant high mode numbers are observed after both shock signatures hit and passed the magnetosphere. Detailed evolution of the mode structure is also shown for the first shock to reveal the development of high mode structure from a bump-on-tail distribution at m≈20 to a dominant peak at m≈50 in about 10 min. In addition, an interesting change of sign in m from negative to positive is observed as MMS crosses ~11 MLT pre-noon, which is consistent with the picture of wave generation by dayside magnetopause compression and then anti-sunward propagation. Finally, for both shocks, the contribution of higher frequency waves (Pc-4 range compared with Pc-5) to the total wave power is found to be negligible before and after the shock impact, but it becomes more significant during the shock impact.

79 ASTRONOMY AND ASTROPHYSICS↗

Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path

Proofreading by replicative DNA polymerases is a fundamental mechanism ensuring DNA replication fidelity. In proofreading, mis-incorporated nucleotides are excised through the 3'-5' exonuclease activity of the DNA polymerase holoenzyme. The exonuclease site is distal from the polymerization site, imposing stringent structural and kinetic requirements for efficient primer strand transfer. Yet, the molecular mechanism of this transfer is not known. Here we employ molecular simulations using recent cryo-EM structures and biochemical analyses to delineate an optimal free energy path connecting the polymerization and exonuclease states of E. coli replicative DNA polymerase Pol III. We identify structures for all intermediates, in which the transitioning primer strand is stabilized by conserved Pol III residues along the fingers, thumb and exonuclease domains. We demonstrate switching kinetics on a tens of milliseconds timescale and unveil a complete pol-to-exo switching mechanism, validated by targeted mutational experiments.

59 BASIC BIOLOGICAL SCIENCES↗

Nickase fidelity drives EvolvR-mediated diversification in mammalian cells

Abstract In vivo genetic diversifiers have previously enabled efficient searches of genetic variant fitness landscapes for continuous directed evolution. However, existing genomic diversification modalities for mammalian genomic loci exclusively rely on deaminases to generate transition mutations within target loci, forfeiting access to most missense mutations. Here, we engineer CRISPR-guided error-prone DNA polymerases (EvolvR) to diversify all four nucleotides within genomic loci in mammalian cells. We demonstrate that EvolvR generates both transition and transversion mutations throughout a mutation window of at least 40 bp and implement EvolvR to evolve previously unreported drug-resistantMAP2K1variants via substitutions not achievable with deaminases. Moreover, we discover that the nickase’s mismatch tolerance limits EvolvR’s mutation window and substitution biases in a gRNA-specific fashion. To compensate for gRNA-to-gRNA variability in mutagenesis, we maximize the number of gRNA target sequences by incorporating a PAM-flexible nickase into EvolvR. Finally, we find a strong correlation between predicted free energy changes underlying R-loop formation and EvolvR’s performance using a given gRNA. The EvolvR system diversifies all four nucleotides to enable the evolution of mammalian cells, while nuclease and gRNA-specific properties underlying nickase fidelity can be engineered to further enhance EvolvR’s mutation rates.

Science & Technology - Other Topics↗

High-fidelity topochemical polymerization in single crystals, polycrystals, and solution aggregates

Topochemical polymerization (TCP) emerges as a leading approach for synthesizing single crystalline polymers, but is traditionally restricted to transformations in solid-medium. The complexity in achieving single-crystal-to-single-crystal (SCSC) transformations due to lattice disparities and the untapped potential of performing TCP in a liquid medium with solid-state structural fidelity present unsolved challenges. Herein, by using X-rays as the primary means to overcome crystal disintegration, we reveal the details of SCSC transformation during the TCP of chiral azaquinodimethane (AQM) monomers through in situ crystallographic analysis while spotlighting a rare metastable crystalline phase. Complementary in situ investigations of powders and thin films provide critical insights into the side-chain dependent polymerization kinetics of solid-state reactions. Furthermore, we enable TCP of AQM monomers in a liquid medium via an antisolvent-reinforced aggregated state, yielding polymer nanofibers with high crystallinity akin to that of solid-state. This study testifies high structural precision of TCP performed in different states and media, offering critical insights into the synthesis of processable nanostructured polymers with desired structural integrity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coherent control and high-fidelity readout of chromium ions in commercial silicon carbide

Abstract Transition metal ions provide a rich set of optically active defect spins in wide bandgap semiconductors. Chromium (Cr 4+ ) in silicon-carbide (SiC) produces a spin-1 ground state with a narrow, spectrally isolated, spin-selective, near-telecom optical interface. However, previous studies were hindered by material quality resulting in limited coherent control. In this work, we implant Cr into commercial 4H-SiC and show optimal defect activation after annealing above 1600 °C. We measure an ensemble optical hole linewidth of 31 MHz, an order of magnitude improvement compared to as-grown samples. An in-depth exploration of optical and spin dynamics reveals efficient spin polarization, coherent control, and readout with high fidelity (79%). We report T 1 times greater than 1 s at cryogenic temperatures (15 K) with a T 2 * = 317 ns and a T 2 = 81 μs, where spin dephasing times are currently limited by spin–spin interactions within the defect ensemble. Our results demonstrate the potential of Cr 4+ in SiC as an extrinsic, optically active spin qubit.

74 ATOMIC AND MOLECULAR PHYSICS↗

High-fidelity and high-resolution phase mapping of granites via confocal Raman imaging

Abstract In physical sciences such as chemistry and earth sciences, specifically for characterization of minerals in a rock, automated, objective mapping methods based on elemental analysis have replaced traditional optical petrography. However, mineral phase maps obtained from these newer approaches rely on conversion of elemental compositions to mineralogical compositions and thus cannot distinguish mineral polymorphs. Secondly, these techniques often require laborious sample preparations such as sectioning, polishing, and coating which are time-consuming. Here, we develop a new Raman imaging protocol that is capable of mapping unpolished samples with an auto-focusing Z-mapping feature that allows direct fingerprinting of different polymorphs. Specifically, we report a new methodology for generating high fidelity phase maps by exploiting characteristic peak intensity ratios which can be extended to any multi-phase, heterogenous system. Collectively, these enhancements allow us to rapidly map an unpolished granite specimen (~ 2 × 2 mm) with an exceptionally high accuracy (> 97%) and an extremely fine spatial resolution (< 0.3–2 µm).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗