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At least 1,261 records · Page 70

Elucidating the Role of Hydrogen Bonding in the Optical Spectroscopy of the Solvated Green Fluorescent Protein Chromophore: Using Machine Learning to Establish the Importance of High-Level Electronic Structure

Hydrogen bonding interactions with chromophores in chemical and biological environments play a key role in determining their electronic absorption and relaxation processes, which are manifested in their linear and multidimensional optical spectra. For chromophores in the condensed phase, the large number of atoms needed to simulate the environment has traditionally prohibited the use of high-level excited-state electronic structure methods. By leveraging transfer learning, we show how to construct machine-learned models to accurately predict the high-level excitation energies of a chromophore in solution from only 400 high-level calculations. Here, we show that when the electronic excitations of the green fluorescent protein chromophore in water are treated using EOM-CCSD embedded in a DFT description of the solvent the optical spectrum is correctly captured and that this improvement arises from correctly treating the coupling of the electronic transition to electric fields, which leads to a larger response upon hydrogen bonding between the chromophore and water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

District EnErgy Planner (DEEP) v2

The District EnErgy Planner - DEEP is an Mixed Integer Linear Programming (MILP) optimization software tool to solve district energy system, technology configuration, operation strategies, and energy retail business schemes. DEEP takes user input energy demand on heating, cooling and electricity demand. Energy loss through pipeline is calculated for heating and cooling from central plants. The optimal system configuration to minimize the district energy system life cycle cost or minimize CO2 emission is calculated based on energy balance equations and various constraints. The recent update on DEEP include a feature of waste heat utilization energy balance based optimization to take into accounts of different temperature bands of heat into account to maximize system efficiency. Another feature is to optimize district energy retail by provide optimal pricing scheme for heating, cooling and electricity to end users to incorporate district to grid demand response.

Feng, Wei↗

First M87 Event Horizon Telescope Results. VII. Polarization of the Ring

In 2017 April, the Event Horizon Telescope (EHT) observed the near-horizon region around the supermassive black hole at the core of the M87 galaxy. These 1.3 mm wavelength observations revealed a compact asymmetric ring-like source morphology. This structure originates from synchrotron emission produced by relativistic plasma located in the immediate vicinity of the black hole. Here we present the corresponding linear-polarimetric EHT images of the center of M87. We find that only a part of the ring is significantly polarized. The resolved fractional linear polarization has a maximum located in the southwest part of the ring, where it rises to the level of ~15%. The polarization position angles are arranged in a nearly azimuthal pattern. We perform quantitative measurements of relevant polarimetric properties of the compact emission and find evidence for the temporal evolution of the polarized source structure over one week of EHT observations. The details of the polarimetric data reduction and calibration methodology are provided. We carry out the data analysis using multiple independent imaging and modeling techniques, each of which is validated against a suite of synthetic data sets. The gross polarimetric structure and its apparent evolution with time are insensitive to the method used to reconstruct the image. These polarimetric images carry information about the structure of the magnetic fields responsible for the synchrotron emission. Their physical interpretation is discussed in an accompanying publication.

79 ASTRONOMY AND ASTROPHYSICS↗

Effect of artificial viscosity on shocked particle-laden flows for staggered grid Lagrangian methods

Abstract Shocked particle-laden flows are important to many natural and industrial processes. When simulating these systems, artificial viscosity is often required to prevent numerical artifacts, such as ringing, from arising in the pressure and density fields. The linear and quadratic coefficients of the artificial viscosity determine the amount of smoothing that occurs in these fields. For particle-laden flows, however, many of the fluid–particle interaction forces, for example, the pressure gradient force and unsteady forces, depend on gradients in the fluid fields. Furthermore, while the shock passes over a particle, these forces can be more dominant than drag. This means that the artificial viscosity coefficients affect how a particle and fluid interact when simulating shocked particle systems. Here this effect is investigated for isolated particles and for a particle curtain using a staggered grid Lagrangian approach. The artificial viscosity coefficients have a significant impact on the maximum force that a fluid imparts to a particle, which is important for determining whether a particle will break up in response to the shock. Furthermore, it is found that the density ratio between the particle and the fluid is important in determining whether the artificial viscosity coefficients have a significant impact on the particle’s motion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Machine Learning (ML) Classifier to Assist Metadata Creation

The Atmospheric Radiation Measurement (ARM) Data Center is responsible for the timely collection, archival, and curation of science data products. These products are freely available through an online data repository. Metadata creation is paramount for scientific users to find and access over seven petabytes of atmospheric science data. The hierarchical metadata structure allows users to search for information at both broad and narrow levels. This project aims to leverage 30 years’ worth of manually created metadata to enable machine predictions of broad-term classifications from narrow-term descriptions. These classification predictions would assist metadata coordinators with their term selections. This paper discusses the cleaning and preprocessing of the training data, the pipeline developed to determine the best model for this task, and the creation of an API metadata classifier for ARM measurement metadata. Our results show that the Linear Support Vector Classification (LinearSVC) algorithm, along with the Term Frequency – Inverse Document Frequency (TF-IDF) vectorizer, is well-suited for our multi-class classification task. Lengthier input training data led to better results, and artificial balancing was unnecessary for this particular use case. This predictive classifier enhances efficiency in metadata creation, as well as supports greater consistency and accuracy in metadata tagging.

Collier, Hannah [ORNL] (ORCID:0000000341284292)↗

Pressure-Induced Spectroscopic Changes in a Californium 1D Material Are Twice as Large as Found in the Holmium Analog

Here, in this study, the synthesis, characterization, and pressure response of a 1D californium mellitate (mellitate = 1,2,3,4,5,6-benzenehexacarboxylate) coordination polymer, Cf 2 (mell)(H 2 O) 10 ·4H 2 O (Cf-1), are reported. The Cf–O lengths within the crystal structure are compared to its gadolinium (Gd-1) and holmium (Ho-1) analogs as well. These data show that the average Cf–O bond distance is slightly longer than the average Gd–O bond, consistent with trends in effective ionic radii. UV–vis-NIR absorption spectra as a function of pressure were collected using diamond-anvil techniques for both Cf-1 and Ho-1. These experiments show that the Cf(III) f → f transitions have a stronger dependence on pressure than that of the holmium analog. In the former case, the shift is nearly linear with applied pressure and averages 6.6 cm –1 /GPa, whereas in the latter, it is <3 cm –1 /GPa.

absorption spectroscopy↗

Protecting and Defending against Autonomous Control Systems and Digital Twin Cyber Attacks: Response Strategy for Hyperparameter attacks of Digital Twin Machine Learning Models in Nuclear Power Plants (Final)

Navigating through the complex tapestry of technological advancements, "Response Strategy for Hyperparameter attacks of Digital Twin Machine Learning Model in Nuclear Power Plants" stands at the intersection of cybersecurity and nuclear power plant operations, embarking on a journey through the intricacies of securing digital twins against malicious cyber activities. As nuclear power plants progressively integrate digital twin technology and machine learning models to optimize operations and ensure system reliability, they inadvertently expose themselves to a new spectrum of vulnerabilities, notably in the realm of hyperparameter attacks. Hyperparameters, integral in machine learning model tuning and optimal performance of digital twins, have emerged as a target for adversaries aiming to destabilize the predictive capabilities and therefore, the operational accuracy of these digital entities within critical infrastructures like nuclear plants. This paper, therefore, meticulously threads the needle through the development of a robust response strategy, poised to shield these digital reflections against calculated hyperparameter manipulations, ensuring that the digital twin can effectively and securely function as a reliable proxy for its physical counterpart. The ensuing sections delve into the orchestrated maelstrom of multi-rate time-changing intelligent coordinated hyperparameter attacks and the implementation of event-triggered predictive control, laying down a structured, predictive, and responsive framework that safeguards the nexus where the digital and physical realms of nuclear power plants coalesce. The operational integrity of digital twins in nuclear power plants depends critically on the security of machine learning hyperparameters. This study makes two different contributions. First, a decision-based idea known as a multi-rate time changing intelligent coordinated hyperparameter attack is put forth. In this attack, many hyperparameters are repeatedly changed using both random and intelligent optimal techniques by the attacker. These assaults introduce varied rates at different attack steps, compromise various amounts of hyperparameters, and improve stealth and flexibility. Second, a technique is developed for event triggered predictive control to rapidly respond to potential hyperparameter attacks. This control integrates a sliding window framework, retaining a history of previous data points and employing linear regression to predict the next data point from the current dataset. The control gain K is determined using the Lyapunov-Krasovskii method, and subsequently, an action is developed. Finally, the outcome of the simulation demonstrates the viability of the proposed method for defending nuclear power plant digital twins from hyperparameter attacks.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Simulation of the PBX 9501 Self-Ignited Heavily Confined Cookoff Test

The PBX 9501 self-ignited thermally damaged explosive (SITX) test was carried out by Holmes et al. A 6-inch diameter sphere made of the PBX 9501 was heated inside a steel confinement vessel until it underwent a thermal explosion. This test provided measured temperature data that was used to define a boundary condition to carry out post-experiment finite element (FE) thermal simulations and comparisons of the FE thermal response with the experimental time to thermal ignition and internal temperature measurements at the center of the PBX 9501 sphere. Finite element models of this experiment were constructed using the heat transfer code Aria. A cookoff model for PBX 9501 was used to simulate the thermal decomposition of PBX 9501 and to predict the time to thermal ignition. An inverse heat conduction scheme was designed and applied to estimate a 1D temperature boundary condition.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

An mRNA vaccine encoding the Ebola virus glycoprotein induces high neutralizing antibody titers and provides strong protection against lethal infections in mouse models

Ebola virus (EBOV) is the causative agent of Ebola disease (EBOD), a viral hemorrhagic fever with a notably high case fatality rate. Current treatments for EBOD are limited to monoclonal antibodies or two licensed viral vector vaccines, a recombinant vesicular stomatitis virus (rVSV)-vectored vaccine or an adenovirus and modified vaccinia Ankara regimen. However, comparisons of protection, efficacy, and durability with alternative nucleotide platforms remain understudied. Here, we evaluated the immunogenicity of an mRNA vaccine expressing the EBOV glycoprotein (GP) in parallel with rVSV- and DNA-based vaccine platforms. The mRNA EBOV-GP vaccine, formulated in lipid nanoparticles, elicited significantly higher levels of total IgG and neutralizing antibody titers compared to the rVSV-EBOV-GP vaccine. Linear antibody epitope analysis indicated a preference for targeting the mucin-like domain in EBOV-GP1 following rVSV-based vaccination, while the mRNA platform distinctly targeted the internal fusion loop of EBOV-GP2. After characterizing the immunogenicity of the mRNA vaccine, two models of EBOD were used to demonstrate its protective efficacy: a surrogate rVSV-based challenge model of EBOD using type-I interferon deficient C57BL/6 mice and infection of BALB/c mice with authentic mouse-adapted EBOV. In both studies, the EBOV mRNA vaccine fully protected the mouse cohorts against morbidity and mortality. Additionally, the EBOV mRNA vaccine produced greater neutralizing antibody titers compared to the DNA EBOV-GP vaccine. These results suggest that an mRNA vaccine expressing EBOV-GP can induce robust, functional humoral responses that are protective against EBOD, warranting further development as an alternative to, or as part of a vaccine strategy including, viral vectored vaccines.

DNA vaccines↗

Dry Season Transpiration and Soil Water Dynamics in the Central Amazon

With current observations and future projections of more intense and frequent droughts in the tropics, understanding the impact that extensive dry periods may have on tree and ecosystem-level transpiration and concurrent carbon uptake has become increasingly important. Here, we investigate paired soil and tree water extraction dynamics in an old-growth upland forest in central Amazonia during the 2018 dry season. Tree water use was assessed via radial patterns of sap flow in eight dominant canopy trees, each a different species with a range in diameter, height, and wood density. Paired multi-sensor soil moisture probes used to quantify volumetric water content dynamics and soil water extraction within the upper 100 cm were installed adjacent to six of those trees. To link depth-specific water extraction patterns to root distribution, fine root biomass was assessed through the soil profile to 235 cm. To scale tree water use to the plot level (stand transpiration), basal area was measured for all trees within a 5 m radius around each soil moisture probe. The sensitivity of tree transpiration to reduced precipitation varied by tree, with some increasing and some decreasing in water use during the dry period. Tree-level water use scaled with sapwood area, from 11 to 190 L per day. Stand level water use, based on multiple plots encompassing sap flow and adjacent trees, varied from ∼1.7 to 3.3 mm per day, increasing linearly with plot basal area. Soil water extraction was dependent on root biomass, which was dense at the surface (i.e., 45% in the upper 5 cm) and declined dramatically with depth. As the dry season progressed and the upper soil dried, soil water extraction shifted to deeper levels and model projections suggest that much of the water used during the month-long dry-down could be extracted from the upper 2–3 m. Results indicate variation in rates of soil water extraction across the research area and, temporally, through the soil profile. These results provide key information on whole-tree contributions to transpiration by canopy trees as water availability changes. In addition, information on simultaneous stand level dynamics of soil water extraction that can inform mechanistic models that project tropical forest response to drought.

54 ENVIRONMENTAL SCIENCES↗

High-resolution measurements of microphysics and entrainment in marine stratocumulus clouds

High-resolution measurements from the Airborne Cloud-Turbulence Observation System (ACTOS) during the Azores Stratocumulus Measurements of Radiation, Turbulence and Aerosols (ACORES) campaign are analysed for an investigation of the vertical profiles of microphysical properties and entrainment velocity ( W e ) in marine stratocumulus clouds. Here, the vertical profiles show the transition from the cloudy layer to free troposphere with nearly linear profiles of total water mixing ratio, liquid water potential temperature and virtual potential temperature, but the thickness of entrainment interfacial layer varies significantly. Sharp transitions of cloud microphysical and optical properties within a single horizontal flight leg are found in one stratocumulus cloud system. They seem to be related to the local environmental conditions, such as the wind shear and turbulent dissipation rate. W e values estimated by three methods show consistent tendencies in general and are clearly related to the local environmental conditions, such as vertical shear of the horizontal wind and turbulence intensity. However, the magnitudes of W e values differ by up to two orders of magnitude depending on the methods, which suggests that the estimation of W e from in situ measurements is still a challenge. Analysis of the microphysical response to entrainment suggests that inhomogeneous mixing occurs dominantly. On the other hand, the analysis results for the clouds under more humid conditions indicate a higher likelihood of homogeneous mixing.

54 ENVIRONMENTAL SCIENCES↗

Correlation between Spin and Orbital Dynamics during Laser-Induced Femtosecond Demagnetization

Spin and orbital angular momenta are two intrinsic properties of an electron and are responsible for the physics of a solid. How the spin and orbital evolve with respect to each other on several hundred femtoseconds is largely unknown, but it is at the center of laser-induced ultrafast demagnetization. In this paper, we introduce a concept of the spin–orbital correlation diagram, where spin angular momentum is plotted against orbital angular momentum, much like the position-velocity phase diagram in classical mechanics. We use four sets of highly accurate time-resolved X-ray magnetic circular dichroism data to construct four correlation diagrams for iron and cobalt. To our surprise, a pattern emerges. The trace on the correlation diagram for iron is an arc, and at the end of demagnetization, it has a pronounced cusp. The correlation diagram for cobalt is different and appears more linear but with kinks. We carry out first-principles calculations with two different methods: time-dependent density functional theory (TDDFT) and time-dependent Liouville density functional theory. These two methods agree that the experimental findings for both Fe and Co are not due to experimental errors. It is the spin–orbit coupling that correlates the spin dynamics to the orbital dynamics. Microscopically, Fe and Co have different orbital occupations, which leads to distinctive correlation diagrams. We believe that this correlation diagram presents a useful tool to better understand spin and orbital dynamics on an ultrafast time scale. A brief discussion on the magnetic anisotropy energy is also provided.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Veridical data science

Building and expanding on principles of statistics, machine learning, and scientific inquiry, we propose the predictability, computability, and stability (PCS) framework for veridical data science. Our framework, composed of both a workflow and documentation, aims to provide responsible, reliable, reproducible, and transparent results across the data science life cycle. The PCS workflow uses predictability as a reality check and considers the importance of computation in data collection/storage and algorithm design. It augments predictability and computability with an overarching stability principle. Stability expands on statistical uncertainty considerations to assess how human judgment calls impact data results through data and model/algorithm perturbations. As part of the PCS workflow, we develop PCS inference procedures, namely PCS perturbation intervals and PCS hypothesis testing, to investigate the stability of data results relative to problem formulation, data cleaning, modeling decisions, and interpretations. We illustrate PCS inference through neuroscience and genomics projects of our own and others. Moreover, we demonstrate its favorable performance over existing methods in terms of receiver operating characteristic (ROC) curves in high-dimensional, sparse linear model simulations, including a wide range of misspecified models. Finally, we propose PCS documentation based on R Markdown or Jupyter Notebook, with publicly available, reproducible codes and narratives to back up human choices made throughout an analysis. The PCS workflow and documentation are demonstrated in a genomics case study available on Zenodo.

97 MATHEMATICS AND COMPUTING↗

Enhancement of terahertz fields in LiTaO 3 waveguides using a conical pulse front

The development of methods for the generation of strong ultrafast electromagnetic pulses in the terahertz (THz) spectral range has led to a surge of progress in nonlinear THz spectroscopy and THz control of molecular and collective responses. For spectroscopy in the 1-THz range, the submillimeter wavelengths and associated large spot sizes, large optical elements, and short distances between final focusing elements and samples can lead to cumbersome experimental setups that are incompatible with some sample environments. Here, we introduce a novel terahertz ring excitation (TREx) optical pumping geometry to generate superposing, focusing fields in planar THz waveguides made out of the electro-optic material lithium tantalate. High THz fields, >175 kV/cm, are generated and measured optically with no free-space THz propagation. The field level achieved by pumping with a sequence of concentric rings of excitation light exceeds by about 20× the result of a single cylindrically focused line of pump light that has been used routinely in previous work. The technique opens new prospects for compact waveguide-based linear and nonlinear THz spectroscopy and signal processing.

47 OTHER INSTRUMENTATION↗

Unsupervised Learning for Improved Gamma-Ray Spectrometry in Pixelated Cadmium Zinc Telluride (CZT) Detectors

Machine learning has been found to be ubiquitously useful across many industries, presenting an opportunity to improve radiation detection performance using data-driven algorithms. Improved detector resolution can aid in the detection, identification, and quantification of radionuclides. Here, in this work, a novel, data-driven, unsupervised learning approach is developed to improve detector spectral characteristics by learning, and subsequently rejecting, poorly performing regions of the pixelated detector. Feature engineering is used to fit individual characteristic photo peaks to a Doniach lineshape with a linear background model. Then, principal component analysis is used to learn a lower-dimension latent space representation of each photo peak where the pixels are clustered, and subsequently ranked, based on the cluster mean distance to an optimal point. Pixels within the worst cluster(s) are rejected to improve the full-width at half-maximum (FWHM) by 10% to 15% (relative to the bulk detector) at 50% net efficiency when applied to training data obtained from measurements of a 100 μCi 154 Eu source using a H3D M400i pixelated cadmium zinc telluride detector. These results compare well with, but do not outperform, a greedy algorithm that accumulates pixels in order of FWHM from lowest to highest used as a benchmark. In the future, this approach can be extended to include the detector energy and angular response. Finally, the model is applied to newly seen natural and enriched uranium spectra relevant for nuclear safeguards applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Meta-uncertainty for particle image velocimetry

Uncertainty quantification for Particle Image Velocimetry (PIV) is critical for comparing experimentally measured flow fields with Computational Fluid Dynamics (CFD) results, and model design and validation. However, PIV features a complex measurement chain with coupled, non-linear error sources, and quantifying the uncertainty is challenging. Multiple assessments show that none of the current methods can reliably measure the actual uncertainty across a wide range of experiments, and estimates can vary. Because the current methods differ in assumptions regarding the measurement process and calculation procedures, it is not clear which method is best to use for an experiment where the error distribution is unknown. To address this issue, we propose a method to estimate an uncertainty method's sensitivity and reliability, termed the Meta-Uncertainty. The novel approach is automated, local, and instantaneous, and based on perturbation of the recorded particle images. We developed an image perturbation scheme based on adding random unmatched particles to the interrogation window pair considering the signal-to-noise (SNR) of the correlation plane. Each uncertainty scheme's response to several trials of random particle addition is used to estimate a reliability metric, defined as the rate of change of the inter-quartile range (IQR) of the uncertainties with increasing levels of particle addition. We also propose applying the meta-uncertainty as a weighting metric to combine uncertainty estimates from individual schemes, based on ideas from the consensus forecasting literature. We use planar and stereo PIV measurements across a range of canonical flows to assess the performance of the uncertainty schemes. Further, a novel method is introduced to assess an uncertainty scheme's performance based on a quantile comparison of the error and uncertainty distributions, generalizing the current method of comparing the RMS of the two distributions. Here, the results show that the combined uncertainty method outperforms the individual methods, and this work establishes the meta-uncertainty as a useful reliability assessment tool for PIV uncertainty quantification.

47 OTHER INSTRUMENTATION↗

Protonic nickelate device networks for spatiotemporal neuromorphic computing

Computation in biological neural circuits arises from the interplay of nonlinear temporal responses and spatially distributed dynamic network interactions. Replicating this richness in hardware has remained challenging, as most neuromorphic devices emulate only isolated neuron- or synapse-like functions. Here we introduce an integrated neuromorphic computing platform in which both nonlinear spatiotemporal processing and programmable memory are realized within a single perovskite nickelate material system. By engineering symmetric and asymmetric hydrogenated NdNiO 3 junction devices on the same wafer, we combine ultrafast, proton-mediated transient dynamics with stable multilevel resistance states. Networks of symmetric NdNiO 3 junctions exhibit emergent spatial interactions mediated by proton redistribution, while each node simultaneously provides short-term temporal memory, enabling nanosecond-scale operation with an energy cost of ~0.2 nJ per input. When interfaced with asymmetric output units serving as reconfigurable long-term weights, these networks allow both feature transformation and linear classification in the same material system. Leveraging these emergent interactions, the platform enables real-time pattern recognition and achieves high accuracy in spoken digit classification and early seizure detection, outperforming temporal-only or uncoupled architectures. These results position protonic nickelates as a compact, energy-efficient, CMOS-compatible platform that integrates processing and memory for scalable intelligent hardware.

Electrical and electronic engineering↗

Natural diversity provides a broad spectrum of cyanobacteriochrome-based diguanylate cyclases

Cyanobacteriochromes (CBCRs) are spectrally diverse photosensors from cyanobacteria distantly related to phytochromes that exploit photoisomerization of linear tetrapyrrole (bilin) chromophores to regulate associated signaling output domains. Unlike phytochromes, a single CBCR domain is sufficient for photoperception. CBCR domains that regulate the production or degradation of cyclic nucleotide second messengers are becoming increasingly well characterized. Furthermore, cyclic di-guanosine monophosphate (c-di-GMP) is a widespread small-molecule regulator of bacterial motility, developmental transitions, and biofilm formation whose biosynthesis is regulated by CBCRs coupled to GGDEF (diguanylate cyclase) output domains. In this study, we compare the properties of diverse CBCR-GGDEF proteins with those of synthetic CBCR-GGDEF chimeras. Our investigation shows that natural diversity generates promising candidates for robust, broad spectrum optogenetic applications in live cells. Since light quality is constantly changing during plant development as upper leaves begin to shade lower leaves—affecting elongation growth, initiation of flowering, and responses to pathogens, these studies presage application of CBCR-GGDEF sensors to regulate orthogonal, c-di-GMP-regulated circuits in agronomically important plants for robust mitigation of such deleterious responses under natural growing conditions in the field.

59 BASIC BIOLOGICAL SCIENCES↗