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DOE OSTI2020

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments

Although biodiversity and ecosystem functions are strongly shaped by contemporary environments, such as climate and local biotic and abiotic attributes, relatively little is known about how they depend on long-term geological processes. Here, along a 3000-m elevational gradient with tectonic faults on the Tibetan Plateau (that is, Galongla Mountain in Medog County, China), we study the joint effects of geological and contemporary environments on biological communities, such as the diversity and community composition of plants and soil bacteria, and ecosystem functions. We find that these biological communities and ecosystem functions generally show consistent elevational breakpoints at 2000–2800 m, which coincide with Indus-Yalu suture zone fault and are similar to the elevational breakpoints of soil bacteria on another mountain range 1000 km away. Mean annual temperature, soil pH and moisture are the primary contemporary determinants of biodiversity and ecosystem functions, which support previous findings. However, compared with the models excluding geological processes, inclusion of geological effects, such as parent rock and weathering, increases 67.9 and 35.9% of the explained variations in plant and bacterial communities, respectively. Such inclusion increases 27.6% of the explained variations in ecosystem functions. The geological processes thus provide additional links to ecosystem properties, which are prominent but show divergent effects on biodiversity and ecosystem functions: parent rock and weathering exert considerable direct effects on biodiversity, whereas indirectly influence ecosystem functions via interactions with biodiversity and contemporary environments. Thus, the integration of geological processes with environmental gradients could enhance our understanding of biodiversity and, ultimately, ecosystem functioning across different climatic zones.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Floquet Cavity Electromagnonics

Hybrid magnonics has recently attracted intensive attention as a promising platform for coherent information processing. In spite of its rapid development, on-demand control over the interaction of magnons with other information carriers, in particular, microwave photons in electromagnonic systems, has been long missing, significantly limiting the potential broad applications of hybrid magnonics. Here, we show that, by introducing Floquet engineering into cavity electromagnonics, coherent control on the magnon-microwave photon coupling can be realized. Leveraging the periodic temporal modulation from a Floquet drive, our first-of-its-kind Floquet cavity electromagnonic system enables the manipulation of the interaction between hybridized cavity electromagnonic modes. Moreover, we have achieved a new coupling regime in such systems: the Floquet ultrastrong coupling, where the Floquet splitting is comparable with or even larger than the level spacing of the two interacting modes, beyond the conventional rotating-wave picture. As a result, our findings open up new directions for magnon-based coherent signal processing.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

IDAES-PSE 2.6.0 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 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 2.6.0 Release Highlights Upcoming Changes IDAES will be switching to the new Pyomo solver interface in the next release. Whilst this will hopefully be a smooth transition for most users, there are a few important changes to be aware of. The new solver interface uses a different version of the IPOPT writer (“ipopt_v2”) and thus any custom configuration options you might have set for IPOPT will not carry over and will need to be reset. By default, the new Pyomo linear presolver will be activated with ipopt_v2. Whilst are working to identify any bugs in the presolver, it is possible that some edge cases will remain. IDAES will begin deploying a new set of scaling tools and APIs over the next few releases that make use of the new solver writers. The old scaling tools and APIs will remain for backward compatibility but will begin to be deprecated. New Models, Tools and Features New Intersphinx extension automatically linking Jupyter notebook examples to project documentation New end-to-end diagnostics example demonstrated on a real problem New complementarity formulation for VLE with cubic equations of state, backward compatibility for old formulation New solver interface with presolve (ipopt_v2) in support of upcoming changes to the initialization and APIs methods, with default set to ipopt to maintain backwards compatibility; this will deprecate once all examples have been updated New forecaster and parameterized bidder methods within grid integration library Updated surrogates API and examples to support Keras 3, with backwards compatibility for older formats such as TensorFlow SavedModel (TFSM) Updated costing base dictionary to include the 2023 cost year index value Updated ProcessBlock to include information on the constructing block class Updated Flowsheet Visualizer to allow visualize() method to return value and functions Bug Fixes Fixed bug in the Modular Property Framework that would cause errors when trying to use phase-based material balances with phase equilibria. Fixed bug in Modular Properties Framework that caused errors when initializing models with non-vapor-liquid phase equilibria. Fixed typos flagged by June update to crate-ci/typos and removed DMF-related exceptions Minor corrections of units of measurement handling in power plant waste/transport costing expressions, control volume material holdup expressions, and BTX property package parameters Fixed throwing >7500 numpy deprecation warnings by replacing scalar value assignment with element extraction and item iteration calls Testing and Robustness Migrated slow tests (>10s) to integration, impacting test coverage but also yielding a nearly 30% decrease in local test runtime Pinned pint to avoid issues with older supported Python versions Pinned codecov versions to avoid tokenless upload behavior with latest version Bumped extensions to version 3.4.2 to allow pointing to non-standard install location Deprecations and Removals Python 3.8 is no longer supported. The supported Python versions are 3.9 through 3.12 The Data Management Framework (DMF) is no longer supported. Importing idaes.core.dmf will cause a deprecation warning to be displayed until the next release The SOFC Keras surrogates have been removed. The current version of the SOFC surrogate model in the examples repository is a PySMO Kriging model.

AS↗

DOE OSTI2024

IDAES-PSE 2.7.0 Release

AS↗

DOE OSTI2025

IDAES-PSE 2.8.0 Release

AS↗

DOE OSTI2025

PFSA-Ionomer Dispersions to Thin-Films: Interplay Between Sidechain Chemistry and Dispersion Solvent

In fuel-cell catalyst layers (CLs), ionomers exists as nanoscale thin-films binding catalyst particles, wherein ionic and gaseous species transport to catalyst sites. To improve film function, ionomers have been designed based on the prototypical perfluorosulfonic acid (PFSA). Since CLs are fabricated through solution-based processing of inks, understanding how ink/dispersion solvent impacts ionomer interactions and function is important to guide future ionomer design. Herein, PFSA and its chemical derivatives are characterized from dispersion (in solvent) to thin film (cast on support) to investigate the impact of solvent water content on ionomer dispersion (structure, acidity) and resulting film properties. Dispersion characterization reveals that secondary aggregate structure depends on the sidechain chemistry, but all PFSA-based ionomers evolve similarly as dispersion becomes water-rich. The differences in aggregation alter ionomer adsorption and thin film morphology. Further, hydrophilic domain spacing and orientation are affected primarily by sidechain chemistry, and modulated by solvent composition. Thin-film conductivity correlates with hydration and nanodomain alignment, signifying the role of morphology in properties. Overall, this work provides insights into how chemistry can be used to coarse-tune structure–property relationships, while processing solvent is for fine-tuning of dispersion-film interplay for controlling CL-ionomer function, which can be translated to other chemistries and ink formulations.

25 ENERGY STORAGE↗

DOE OSTI2024

Stairway to discovery: A report on the CMS programme of cross section measurements from millibarns to femtobarns

The Large Hadron Collider at CERN, delivering proton-proton collisions at much higher energies and far higher luminosities than previous machines, has enabled a comprehensive programme of measurements of the standard model (SM) processes by the CMS experiment. These unprecedented capabilities facilitate precise measurements of the properties of a wide array of processes, the most fundamental being cross sections. The discovery of the Higgs boson and the measurement of its mass became the keystone of the SM. Knowledge of the mass of the Higgs boson allows precision comparisons of the predictions of the SM with the corresponding measurements. These measurements span the range from one of the most copious SM processes, the total inelastic cross section for proton-proton interactions, to the rarest ones, such as Higgs boson pair production. They cover the production of Higgs bosons, top quarks, single and multibosons, and hadronic jets. Associated parameters, such as coupling constants, are also measured. These cross section measurements can be pictured as a descending stairway, on which the lowest steps represent the rarest processes allowed by the SM, some never seen before.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Initial Stage of Nanoscale Imaging in Positive Tone Extreme UV Photoresists: The Influence of the Polymer Sequence

Photolithographic patterning using extreme ultraviolet (EUV, 92.5 eV) light is a radiolytic process that initially forms electrons, radical cations, anions, and neutral radicals in the polymeric photoresist matrix. These species may participate in the chemical reactions that define the ultimate resolution of the printed image, and their concentrations and nanometer-scale stochastic variations in their formation influence printed image quality. Proposals have been made that polymer chain uniformity may be advantageous in reducing stochastics due to spatial inhomogeneities, and this aspect of radiolysis is examined in this work. We have simulated the initial subpicosecond stages of the imaging process for a series of photoresist films that are identical in composition but vary in their polymer chain structures. We use detailed, physically accurate stochastic reaction-diffusion calculations to evaluate the influence of defined sequence and random copolymer structures on radiolytic spur formation, i.e., a cluster of species formed by electron-polymer interactions that defines the initial spatial characteristic of the imaging process. Predictions of electron thermalization in the present work are shown to be consistent with the literature, indicating that our overall computational approach for ultrafast nanoscale processes is sound. The computational results show that the polymer sequence has no significant effect on the spur composition. This suggests that any potential imaging improvements to be gained by sequence control must originate from postimaging lithographic process steps.

Absorption↗

DOE OSTI2023

The Role of Cloud–Cloud Interactions in the Life Cycle of Shallow Cumulus Clouds

Some of the climate research puzzles relate to a limited understanding of the critical factors governing the life cycle of cumulus clouds. These factors force the initiation and the various mixing processes during cloud life cycles. To shed some light into these processes, we tracked the life cycle of thousands of individual shallow cumulus clouds in a large-eddy simulation during the Holistic Interactions of Shallow Clouds, Aerosols, and Land-Ecosystems field campaign in the U.S. southern Great Plains. Concurrent evolution of clouds is tracked and their respective neighboring clouds are examined. Results show that the clouds initially smaller than neighboring clouds can grow larger than the neighboring clouds by a factor of 2 within 20% of their lifetime. Two groups of the tracked clouds with growing and decaying neighboring clouds, respectively, show distinct characteristics in their life cycles. Clouds with growing neighboring clouds form above regions with larger surface heterogeneity, whereas clouds with decaying neighboring clouds are associated with less heterogeneous surfaces. Also, those with decaying neighboring clouds experience larger instability and a more humid boundary layer, indicating evaporation below the cloud base is likely occurring before those clouds are formed. Larger instability leads to higher vertical velocity and convergence within the cloud, which causes stronger surrounding downdrafts and water vapor removal in the surrounding area. The latter appears to be the reason for the decaying neighboring clouds. Finally, understanding those processes provide insights into how cloud–cloud interactions modulate the evolution of cloud population and into how this evolution can be represented in future cumulus parameterizations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Ink-substrate interactions during 3D printing revealed by time-resolved coherent X-ray scattering

Additive printing techniques are regarded as revolutionary and versatile methods of advanced device manufacturing, stemming from the possibility to pattern materials on a custom-based approach and the potential to create novel microstructures and achieve new functionalities. Despite these advantages, the inherent anisotropy of the printing process is a source of property gradients within the printed materials, often associated with variable and/or poor performance. Up to date, the evolutionary pathways associated with printing have largely remained unaddressed, mainly owing to the difficulty to study the transformations induced in the material during processing. Time-resolved coherent X-ray scattering techniques, such as X-ray photon correlation spectroscopy, enable the in situ study of transient nanoscale and mesoscale states in a large variety of materials, including amorphous ones, by directly accessing the most relevant timescales and length scales of their nanoscale and mesoscale dynamics, self-assembly, and mesostructure evolution. In this work, we conduct in operando studies of continuous-flow direct writing with colloidal inks, focusing on how the ink formulation and ink-substrate interactions affect the processes that determine the macroscopic properties of the printed materials. We find fundamental differences in the ink structural relaxations emerging from the primary colloid properties (monodisperse versus aggregated colloids) and the substrates surface energy and mechanical properties. Our work helps to reveal and quantify the basic science governing the evolution of 3D-printed materials during processing, ultimately improving engineering criteria for the design of printable materials.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Background cancellation for frequency-selective quantum sensing

A key challenge in quantum sensing is the detection of weak time dependent signals, particularly those that arise as specific frequency perturbations over a background field. Conventional methods usually demand complex dynamical control of the quantum sensor and heavy classical post-processing. We propose a quantum sensor that leverages time independent interactions and entanglement to function as a passive, tunable, thresholded frequency filter. By encoding the frequency selectivity and thresholding behavior directly into the dynamics, the sensor is responsive only to a target frequency of choice whose amplitude is above a threshold. This approach circumvents the need for complex control schemes and reduces the post-processing overhead.

Puig, Ricard [Los Alamos; Ecole Polytechnique, Lau↗

DOE OSTI2023

Denitrification and the challenge of scaling microsite knowledge to the globe

Here, our knowledge of microbial processes—who is responsible for what, the rates at which they occur, and the substrates consumed and products produced—is imperfect for many if not most taxa, but even less is known about how microsite processes scale to the ecosystem and thence the globe. In both natural and managed environments, scaling links fundamental knowledge to application and also allows for global assessments of the importance of microbial processes. But rarely is scaling straightforward: More often than not, process rates in situ are distributed in a highly skewed fashion, under the influence of multiple interacting controls, and thus often difficult to sample, quantify, and predict. To date, quantitative models of many important processes fail to capture daily, seasonal, and annual fluxes with the precision needed to effect meaningful management outcomes. Nitrogen cycle processes are a case in point, and denitrification is a prime example. Statistical models based on machine learning can improve predictability and identify the best environmental predictors but are—by themselves—insufficient for revealing process-level knowledge gaps or predicting outcomes under novel environmental conditions. Hybrid models that incorporate well-calibrated process models as predictors for machine learning algorithms can provide both improved understanding and more reliable forecasts under environmental conditions not yet experienced. Incorporating trait-based models into such efforts promises to improve predictions and understanding still further, but much more development is needed.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Two DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids

In higher eukaryotes, a single DOT1 histone H3 lysine 79 (H3K79) methyltransferase processively produces H3K79me2/me3 through histone H2B mono-ubiquitin interaction, while the kinetoplastid Trypanosoma brucei di-methyltransferase DOT1A and tri-methyltransferase DOT1B efficiently methylate the homologous H3K76 without H2B mono-ubiquitination. Based on structural and biochemical analyses of DOT1A, we identify key residues in the methyltransferase motifs VI and X for efficient ubiquitin-independent H3K76 methylation in kinetoplastids. Substitution of a basic to an acidic residue within motif VI (Gx 6 K ) is essential to stabilize the DOT1A enzyme-substrate complex, while substitution of the motif X sequence VYGE by CAKS renders a rigid active-site loop flexible, implying a distinct mechanism of substrate recognition. We further reveal distinct methylation kinetics and substrate preferences of DOT1A (H3K76me0) and DOT1B (DOT1A products H3K76me1/me2) in vitro, determined by a Ser and Ala residue within motif IV, respectively, enabling DOT1A and DOT1B to mediate efficient H3K76 tri-methylation non-processively but cooperatively, and suggesting why kinetoplastids have evolved two DOT1 enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Probing radical–molecule interactions with a second generation energy decomposition analysis of DFT calculations using absolutely localized molecular orbitals

Intermolecular interactions between radicals and closed-shell molecules are ubiquitous in chemical processes, ranging from the benchtop to the atmosphere and extraterrestrial space. While energy decomposition analysis (EDA) schemes for closed-shell molecules can be generalized for studying radical–molecule interactions, they face challenges arising from the unique characteristics of the electronic structure of open-shell species. In this work, we introduce additional steps that are necessary for the proper treatment of radical–molecule interactions to our previously developed unrestricted Absolutely Localized Molecular Orbital (uALMO)-EDA based on density functional theory calculations. A “polarize-then-depolarize” (PtD) scheme is used to remove arbitrariness in the definition of the frozen wavefunction, rendering the ALMO-EDA results independent of the orientation of the unpaired electron obtained from isolated fragment calculations. The contribution of radical rehybridization to polarization energies is evaluated. It is also valuable to monitor the wavefunction stability of each intermediate state, as well as their associated spin density profiles, to ensure the EDA results correspond to a desired electronic state. The examples suggest that this second generation uALMO-EDA is a useful tool for furthering one's understanding of both energetic and property changes associated with radical–molecule interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

iPNHOT: a knowledge-based approach for identifying protein-nucleic acid interaction hot spots

The interaction between proteins and nucleic acids plays pivotal roles in various biological processes such as transcription, translation, and gene regulation. Hot spots are a small set of residues that contribute most to the binding affinity of a protein-nucleic acid interaction. Compared to the extensive studies of the hot spots on protein-protein interfaces, the hot spot residues within protein-nucleic acids interfaces remain less well-studied, in part because mutagenesis data for protein-nucleic acids interaction are not as abundant as that for protein-protein interactions. In this study, we built a new computational model, iPNHOT, to effectively predict hot spot residues on protein-nucleic acids interfaces. One training data set and an independent test set were collected from dbAMEPNI and some recent literature, respectively. To build our model, we generated 97 different sequential and structural features and used a two-step strategy to select the relevant features. The final model was built based only on 7 features using a support vector machine (SVM). The features include two unique features such as ΔSASsa 1/2 and esp3, which are newly proposed in this study. Based on the cross validation results, our model gave F1 score and AUROC as 0.725 and 0.807 on the subset collected from ProNIT, respectively, compared to 0.407 and 0.670 of mCSM-NA, a state-of-the art model to predict the thermodynamic effects of protein-nucleic acid interaction. The iPNHOT model was further tested on the independent test set, which showed that our model outperformed other methods. Here, by collecting data from a recently published database dbAMEPNI, we proposed a new model, iPNHOT, to predict hotspots on both protein-DNA and protein-RNA interfaces. The results show that our model outperforms the existing state-of-art models. Our model is available for users through a webserver: http://zhulab.ahu.edu.cn/iPNHOT/.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Cloud-atmosphere impacts on the central Arctic surface energy budget (Final Report)

This project investigated how clouds and atmosphere-sea ice interactions shape the central Arctic surface energy budget using observations from the MOSAiC expedition and coordinated model experiments. Analyses focused on three themes. First, a new method applied to thermistor string data revealed that snow thermal conductivity is systematically higher than assumed in most models, strongly influencing conductive heat flux and sea ice growth, especially under clear skies. Second, a full annual cycle of surface energy budget observations, combined with detailed cloud microphysical retrievals, demonstrated how cloud regimes regulate radiative, turbulent, and conductive fluxes, driving seasonal contrasts in sea ice energy balance: in winter, radiative forcing elicits strong turbulent and conductive responses, while in summer excess energy is primarily partitioned into surface melt. Third, these observations were used to evaluate and improve regional and global forecast models. While some models captured key Arctic cloud-radiation states, most exhibited persistent deficiencies in representing liquid-containing clouds, snow-on-sea-ice processes, and flux responses to radiative forcing. Together, these results provide unprecedented benchmarks for understanding coupled Arctic processes, improve parameterizations of snow, sea ice, and cloud interactions, and highlight critical pathways by which atmospheric variability drives sea ice change in a rapidly evolving Arctic system. Lastly, the project was a resounding success, resulting in 38 peer-reviewed publications and dozens of presentations, while also supporting an early career scientist.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Deep-Learning Interatomic Potential Connects Molecular Structural Ordering to the Macroscale Properties of Polyacrylonitrile

Polyacrylonitrile (PAN) is an important commercial polymer, bearing atactic stereochemistry resulting from nonselective radical polymerization. As such, an accurate, fundamental understanding of governing interactions among PAN molecular units is indispensable for advancing the design principles of final products at reduced processability costs. While ab initio molecular dynamics (AIMD) simulations can provide the necessary accuracy for treating key interactions in polar polymers, such as dipole–dipole interactions and hydrogen bonding, and analyzing their influence on the molecular orientation, their implementation is limited to small molecules only. Herein, we show that the neural network interatomic potentials (NNIPs) that are trained on the small-scale AIMD data (acquired for oligomers) can be efficiently employed to examine the structures and properties at large scales (polymers). NNIP provides critical insight into intra- and interchain hydrogen-bonding and dipolar correlations and accurately predicts the amorphous bulk PAN structure validated by modeling the experimental X-ray structure factor. Furthermore, the NNIP-predicted PAN properties, such as density and elastic modulus, are in good agreement with their experimental values. Overall, the trend in the elastic modulus is found to correlate strongly with the PAN structural orientations encoded in the Hermans orientation factor. In conclusion, this study enables the ability to predict the structure–property relations for PAN and analogues with sustainable ab initio accuracy across scales.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Two-neutrino double-𝛽 decay in pionless effective field theory from a Euclidean finite-volume correlation function

Two-neutrino double-β decay of certain nuclear isotopes is one of the rarest Standard Model processes observed in nature. Its neutrinoless counterpart is an exotic lepton-number nonconserving process that is widely searched to determine if the neutrinos are Majorana fermions. In order to connect the rate of these processes to the Standard Model and beyond the Standard Model interactions, it is essential that the corresponding nuclear matrix elements are constrained reliably from theory. Lattice quantum chromodynamics (LQCD) and low-energy effective field theories (EFTs) are expected to play an essential role in constraining the matrix element of the two-nucleon subprocess, which could in turn provide the input into ab initio nuclear-structure calculations in larger isotopes. Focusing on the two-neutrino process $nn\rightarrow pp(ee\bar{v}_{e}\bar{v}_e)$, the amplitude is constructed in this work in pionless EFT at next-to-leading order, demonstrating the emergence of a renormalization-scale independent amplitude and the absence of any new low-energy constant at this order beyond those present in the single-weak process. Most importantly, it is shown how a LQCD four-point correlation function in Euclidean and finite-volume spacetime can be used to constrain the Minkowski infinite-volume amplitude in the EFT. The same formalism is provided for the related single-weak process, which is an input to the double-β decay formalism. The LQCD-EFT matching procedure outlined for the double-weak amplitude paves the road toward constraining the two-nucleon matrix element entering the neutrinoless double-β decay amplitude with a light Majorana neutrino.

79 ASTRONOMY AND ASTROPHYSICS↗