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At least 271 records · Page 15

Development of high throughput and in vitro assays for analyzing RNA modifications

Modifications on RNAs play major roles in their stability, translation, and enzymatic activity. Despite its importance, the current techniques are insufficient to study the structure and function of RNA modifications. Indeed, the National Academies of Science, Engineering and Medicine indicate that developing new tools and further study the function of RNA modifications is strategically a high priority for advancing science in the coming years (https://www.nationalacademies.org/our-work/toward-sequencing-and-mapping-of-rna-modifications). RNA modifications occur in all domains of life controlling processes such as RNA turnover, translation regulation, cellular defenses and bioproduction. Our preliminary data indicated that the insulin mRNA might get ADP-ribosylated by the ADP-ribosyltransferase PARP12. RNA ADP-ribosylation has been described in Escherichia coli. Combined to the fact that ADP-ribosyltransferase (PARP) genes are conserved throughout evolution we hypothesize that this modification might play essential roles in cells. Therefore, we proposed to develop sequencing techniques and in vitro enzymatic assays to identify and validate ADP-ribosylation motifs and sites. Here we report the development of RNA-seq and qPCR assays to identify ADP-ribosylated RNAs, in addition to a nicotinamide adenosine dinucleotide (NAD – ADP-ribosylation donor) consumption assay and an enzyme-linked immunosorbent assay (ELISA) to measure ADP-ribosyltransferase activity. Testing these assays with the insulin mRNA confirmed that this transcript is ADP-ribosylated. These assays will not only enable studying the function of ADP-ribosylation but can be easily adapted for studying other RNA modifications. This will open opportunities to study RNA modifications in different model systems from bacteria to viruses to plants, bringing insights into their cellular functions and the possibility of targeting them for biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗

Single crystal structure, vibrational spectroscopy, gas sorption and antimicrobial properties of a new inorganic acidic diphosphates material (NH 4 ) 2 Mg(H 2 P 2 O 7 ) 2 • 2 H 2 O

We report on the successful synthesis of diammonium magnesium dihydrogendiphosphate (V) dihydrate compound (NH 4 ) 2 Mg(H 2 P 2 O 7 ) 2 •2H 2 O using a wet chemical route. Single crystal X-ray diffraction analysis and micro Raman spectroscopy are employed to characterize the compound. We demonstrate, using a multidisciplinary approach, that this compound is ideal for carbon dioxide (CO 2 ) capture in addition to other anthropogenic gasses. We show here -from both an experimental as well as from a density functional theory (DFT) calculations routes- the potential for adopting this compound into domestic air-conditioning units (ACUs). From these experiments, the resistance to bacterial growth is also investigated, which is critical for the adoption of this compound in ACUs. Our compound exhibits a higher methane (CH 4 ) sorptivity as compared to CO 2 at 25 °C and 45 °C under pressures up to 50 bars. Furthermore, DFT electronic structure calculations are used to compute the main structural and electronic properties of the compound, taking into consideration the characteristics of the identified pores as a function of the progressive CO 2 vs. CH 4 loadings. Finally, the antibacterial assay reveals a strong antibacterial activity against the tested Gram-positive and Gram-negative bacteria, with a large zone of inhibition against the tested E. Coli, S. Aureus and K. Pneumonia

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Abstract for CRADA between NETL and Praxair Surface Technologies, Inc. (AGMT-1288)

The National Energy Technology Laboratory (NETL) and Praxair Surface Technologies (Participant) will collaborate in the design and manufacturing of new high-performance thermal barrier coatings (TBCs) for hydrogen gas turbine applications. High-throughput first-principles density functional theory (DFT) calculations will be performed to accelerate novel TBCs discovery with expanded phase field, increased temperature and erosion capabilities, low thermal conductivity, and significant toughness imparted by ferroelastic toughening for the non-transformable tetragonal oxide phase. Down-selected materials will be manufactured using solid state powder processing techniques. Testing will include isothermal aging followed by Raman and x-ray diffraction (XRD) phase analysis, indentation fracture toughness measurements, erosion testing, and thermal conductivity measurements. The collaboration will facilitate the deployment of hydrogen gas turbine technologies that are a key to the decarburization of power generation in the United States.

08 HYDROGEN↗

A Lizard-inspired Tube Inspector (LTI) Robot

This final report summarizes the research findings of the current project. This project is a collaboration between New Mexico State University (NMSU) as a lead (Recipient) and Arizona State University (ASU) as a Co-Recipient. Tubular structures are common components of boilers and heat exchangers in power plants. Over time, these components may suffer corrosion, cracks, and stress-corrosion cracks in either the body or the welded connections. A single tube leakage can cause an outage of several weeks. Regular inspection is a key safety factor when ensuring that power plants are maintained in reliable, operational condition. This inspection, however, is challenging, time-consuming, and in many cases impossible due to accessibility issues and safety concerns. Recent developments in robotic-based inspection can offer a great solution. Hard-to-reach places can be inspected without overhauling the unit, saving time and cost. Although several robots have been designed and implemented successfully for inspecting power plant components, in particular tubular structures, their mobility and flexibility are limited. Most of these robots use wheels for mobility which reduces their maneuverability of these robots. Moreover, they usually use magnets to attach to tubes which will not work on tubes with non-ferromagnetic materials. These robots usually carry measurement tools for a particular non-destructive testing (NDT) method such as ultrasound testing (UT) that requires a couplant to perform a point-by-point (scanning) inspection of the tubular structure. In this project, we developed a versatile lizard-inspired tube inspector (LTI) robot with embedded inspection sensing components for tube inspection which removes the need for point-by-point scanning of tube surface for crack and corrosion detection. Inspired by a “lizard”, the novelty of the current project is the integration of couplant-free ultrasound sensing and transmission, advanced data-driven defect detection and imaging, and friction-based mechanical mobility components in a single robot to eliminate a need for smooth surfaces and simple geometry for mobility and scanning. The LTI robot could replace the wheel-based approach with friction-based mobility to significantly increase the flexibility and maneuverability of the robot. The LTI robot can get into a power plant unit, such as a boiler, from a small area allowing it to access a component of interest for inspection (e.g., move on OD, curved and flat surfaces, non-ferromagnetic or ferromagnetic materials, and tubes with rough surfaces and complex geometries). Additionally, an advanced data-driven method using ultrasound data was pioneered to allow the robot to detect defects in the entire area between the robot’s multi-functional mobility system (grippers). Integrating a couplant-free ultrasound sensing in the robot’s grippers as well as using advanced data-driven methods allowed the LTI to detect defects in the entire cross-section of a tube using its grippers when stationary and when mobile.

20 FOSSIL-FUELED POWER PLANTS↗

$\mathrm{IH}$-$\mathrm{GAN}$: A conditional generative model for implicit surface-based inverse design of cellular structures

Variable-density cellular structures can overcome connectivity and manufacturability issues of topologically optimized structures, particularly those represented as discrete density maps. However, the optimization of such cellular structures is challenging due to the multiscale design problem. Past work addressing this problem generally either only optimizes the volume fraction of single-type unit cells but ignoring the effects of unit cell geometry on properties, or considers the geometry–property relation but builds this relation via heuristics. In contrast, we propose a simple yet more principled way to accurately model the property to geometry mapping using a conditional deep generative model, named Inverse Homogenization Generative Adversarial Network (IH-GAN). It learns the conditional distribution of unit cell geometries given properties and can realize the one-to-many mapping from properties to geometries. Here we further reduce the complexity of IH-GAN by using the implicit function parameterization to represent unit cell geometries. Results show that our method can 1) generate various unit cells that satisfy given material properties with high accuracy (R 2 -scores between target properties and properties of generated unit cells >98%) and 2) improve the optimized structural performance over the conventional variable-density single-type structure. In the minimum compliance example, our IH-GAN generated structure achieves a 79.7% reduction in concentrated stress and an extra 3.03% reduction in displacement. In the target deformation examples, our IH-GAN generated structure reduces the target matching error by 86.4% and 79.6% for two test cases, respectively. We also demonstrated that the connectivity issue for multi-type unit cells can be solved by transition layer blending.

42 ENGINEERING↗

A higher-order finite-element implementation of the nonlinear Fokker–Planck collision operator for charged particle collisions in a low density plasma

Collisions between particles in a low density plasma are described by the Fokker–Planck collision operator. In applications, this nonlinear integro-differential operator is often approximated by linearised or ad-hoc model operators due to computational cost and complexity. In this work, we present an implementation of the nonlinear Fokker–Planck collision operator written in terms of Rosenbluth potentials in the Rosenbluth–MacDonald–Judd (RMJ) form. The Rosenbluth potentials may be obtained either by direct integration or by solving partial differential equations (PDEs) similar to Poisson's equation: we optimise for performance and scalability by using sparse matrices to solve the relevant PDEs. We represent the distribution function using a tensor-product continuous-Galerkin finite-element representation and we derive and describe the implementation of the weak form of the collision operator. We present tests demonstrating a successful implementation using an explicit time integrator and we comment on the speed and accuracy of the operator. Finally, we speculate on the potential for applications in the current and next generation of kinetic plasma models.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Measurements of a LYSO crystal array from threshold to 100 MeV

We report measurements of ten custom-made high-homogeneity LYSO crystals. The investigation is motivated by the need for a compact, high-resolution, and fast electromagnetic calorimeter for a new rare pion decay experiment. Each 2.5 x 2.5 x 18 cm 3 crystal was first characterized for general light yield properties and then its longitudinal response uniformity and energy resolution were measured using low-energy gamma sources. The ten crystals were assembled as an array and subjected to a 30–100 MeV positron beam with excellent momentum definition. The energy and timing resolutions were measured as a function of energy, and the spatial resolution was determined at 70 MeV. An additional measurement using monoenergetic 17.6 MeV gammas produced through a p-Li resonance was later made after the photosensors used in positron testing were improved. Here, as an example of the results, the energy resolution at 70 MeV of (1.52 ± 0.03) % is more than two times better than reported results using previous generation LYSO crystals.

Electromagnetic calorimeter↗

Altermagnetism in the layered intercalated transition metal dichalcogenide CoNb 4 Se 8

Altermagnets (AMs) are a new class of magnetic materials that combine the beneficial spintronics properties of ferromagnets and antiferromagnets, garnering significant attention recently. Here, we have identified altermagnetism in a layered intercalated transition metal diselenide, CoNb 4 Se 8 , which crystallizes with an ordered sublattice of intercalated Co atoms between NbSe 2 layers. Single crystals are synthesized, and the structural characterizations are performed using single crystal diffraction and scanning tunneling microscopy. Magnetic measurements reveal easy-axis antiferromagnetism below 168 K. Density functional theory (DFT) calculations indicate that A-type antiferromagnetic ordering with easy-axis spin direction is the ground state, which is verified through single crystal neutron diffraction experiments. Electronic band structure calculations in this magnetic state display spin-split bands, confirming altermagnetism in this compound. The layered structure of CoNb 4 Se 8 presents a promising platform for testing various predicted properties associated with altermagnetism.

36 MATERIALS SCIENCE↗

Bayesian stability and force modeling for uncertain machining processes

Accurately simulating machining operations requires knowledge of the cutting force model and system frequency response. However, this data is collected using specialized instruments in an ex-situ manner. Bayesian statistical methods instead learn the system parameters using cutting test data, but to date, these approaches have only considered milling stability. This paper presents a physics-based Bayesian framework which incorporates both spindle power and milling stability. Initial probabilistic descriptions of the system parameters are propagated through a set of physics functions to form probabilistic predictions about the milling process. The system parameters are then updated using automatically selected cutting tests to reduce parameter uncertainty and identify more productive cutting conditions, where spindle power measurements are used to learn the cutting force model. The framework is demonstrated through both numerical and experimental case studies. Results show that the approach accurately identifies both the system natural frequency and cutting force model.

42 ENGINEERING↗

Enhancing the performance of solvent-borne poly(ethyl methacrylate) coatings for high-power laser applications via low-temperature drying

Organic polymers are a versatile class of materials employed in a broad range of optical coating applications. However, their use as coatings in high-power laser applications, particularly in the UV spectral region, has been limited in scope due to their relatively low laser-induced damage thresholds (LIDTs), which decrease further with exposure to multiple pulses. This study explores the effect of post-deposition drying temperature and residual solvent on the LIDT of solvent-borne polymer coatings. In this work, poly(ethyl methacrylate) (PEMA) coatings were deposited by first spin coating solutions of PEMA (dissolved in 2,2,2-trichloroethanol (TCE)) onto fused silica substrates, then baking at temperatures of either 130°C (soft-bake) or 180°C (hard-bake). Analysis of the two coatings revealed that the soft-bake coating retained a significant amount of TCE within the polymer matrix, which functioned to plasticize the coating and reduce internal stress. The laser-induced damage resistance of the two coatings was evaluated using 351-nm, 1-ns laser pulses. The testing protocols included single-pulse (1-on-1), 1-pulse ramp (R-on-1), and a 1000-pulse ramp (1000R-on-1) test. The results showed that the plasticized, soft-bake coating exhibits a significantly increased LIDT, especially for multipulse irradiation conditions.

36 MATERIALS SCIENCE↗

Hardware Specification and Reference Design for the Low-Cost, Interoperable, User-Centric, Supervisory Controller Kit for Small and Medium Size Commercial Buildings

Commercial buildings are responsible for approximately 20 percent of the total United States energy consumption and greenhouse gas emissions. Over 85 percent of these buildings lack building automation systems to manage the various building systems they have. Many of these buildings are small (< 50,000 square feet), underserved, and use rooftop units (RTUs) for heating, ventilation, and air-conditioning needs. Because these buildings lack proper control systems, they have several operational deficiencies that lead to excess energy consumption. Studies have shown that managing the RTU’s heating and cooling setpoints, schedules, setbacks, and optimal start times can result in 20 to 25 percent reduction in electricity consumption in small and medium commercial buildings (SMBs). In addition, improving the demand flexibility of these buildings will result in additional cost savings for the building owner. To address the needs of the SMBs, the Department of Energy’s Building Technologies Office jointly funded Pacific Northwest National Laboratory (PNNL) and Oak Ridge National Laboratory (ORNL) to design, develop, test, and validate a low-cost, interoperable, user-centric, retrofit supervisory controller kit (SC-SMB) that can be used to continuously optimize energy consumption and deliver demand flexibility of SMBs, including all-electric buildings, and provide a means for maximizing decarbonization benefits. The team also includes industry partners Edo and Intellimation. Previously, the team drafted an SC-SMB system specification document (Goodman et al. 2023). This document describes a reference design of a low-cost supervisory control system for SMBs, including the various hardware components, software system, and an example implementation of the reference design. The final release of the reference design is planned for December 2025. Section 2.0 of the report documents the relevant building types that the SC-SMB system is suitable for. Section 3.0 documents the various hardware components, their function, cost, whether they are off-the-shelve, support standard communication, etc., and the software system. An example deployment in a 10,000-sf building with six rooftop units, a hot water heater, solar, and storage is described in Section 4.0. The planned next steps are described in Section 5.0, and references are listed in Section 6.0.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

PBE-HIL (Powering the Blue Economy Hardware-in-the-Loop models) [SWR-25-37]

Powering the Blue Economy Hardware-in-the-Loop models (PBE-HIL) is a repository of Power Hardware-in-the-loop models developed for typical Powering the Blue Economy market loads and power requirements. The HIL models were developed to be as generic and functional as possible, meaning that the user can easily configure these models to represent their unique PBE design. These PBE load and power requirement HIL models can then be used to inform marine energy converter (MEC) and power electronics design, as well as be used in laboratory testing using HIL equipment, leading to improved understanding of MEC performance and lower risk prior to open-water MEC deployment.

Labuschagne, Hannes [National Renewable Energy Lab↗

Heat Transfer in Void Generating Foam Decomposition: Further Development

Continued development of the additive conductivity material model, used to simulate changes in heat transfer that occurs in void generating foam decomposition, has resulted in an improved model and new features. The previous version of the model was calibrated against the Aria Bulk Fluid Element (BFE) solution and proposed a third-order polynomial correction term best captured the increased heat transfer due to voids in the foam. An investigation of the Fuego Conjugate Heat Transfer (CHT) and Aria BFE solutions at several geometries revealed the CHT solution and BFE solution had differing behavior across length scales, especially at smaller scales. Five calibration studies, using the Fuego CHT as the calibration data, were carried out with polynomial functions of 4-th, 3-rd, 2-nd, 1-st and 0-th orders to determine the best correction function that generalized well across length scales. Each polynomial function was calibrated/trained on six different sized geometries and then tested on three uniquely sized geometries. This study revealed that the 1-st order additive conductivity model performed the best. A new feature of void formation scaling was implemented to more realistically capture the heat transfer as voids are created. A scaling term was added to the model to activate the conductivity correction as decomposition progresses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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↗

Analytical noise bias correction for precise weak lensing shear inference

Noise bias is a significant source of systematic error in weak gravitational lensing measurements that must be corrected to satisfy the stringent standards of modern imaging surveys in the era of precision cosmology. This paper reviews the analytical noise bias correction method and provides analytical derivations demonstrating that we can recover shear to its second order using the ‘renoising’ noise bias correction approach introduced by METACALIBRATION. We implement this analytical noise bias correction within the AnaCal shear estimation framework and propose several enhancements to the noise bias correction algorithm. We evaluate the improved AnaCal using simulations designed to replicate Rubin Legacy Survey of Space and Time (LSST) imaging data. These simulations feature semi-realistic galaxies and stars, complete with representative distributions of magnitudes and Galactic spatial density. We conduct tests under various observational challenges, including cosmic rays, defective CCD columns, bright star saturation, bleed trails, and spatially variable point spread functions. Our results indicate a multiplicative bias in weak lensing shear recovery of less than a few tenths of a per cent, meeting LSST Dark Energy Science Collaboration requirements without requiring calibration from external image simulations. Additionally, our algorithm achieves rapid processing, handling one galaxy in less than a millisecond.

79 ASTRONOMY AND ASTROPHYSICS↗

Development of Next-Generation Additive Chemistry for Direct Air Capture Sorbents (CRADA Final Report)

Introducing antioxidant additives into amine-based DAC sorbents can extend their lifetime. These sorbents are readily prepared by physically mixing additives with amines, a straightforward approach using commercially available materials. Advancing this strategy requires understanding how additives function under varying conditions, especially humidity. This project aims to reveal how humidity and additive chemistry influence oxidative degradation of PEI-based sorbents, levereging LLNL’s expertise in physics-based computational modeling, and Global Thermostat (GT)’s expertise in materials synthesis, characterization, and degradation kinetics testing, to gain fundamental insights into the chemistries and mechanisms of PEI oxidative degradation, and develop design principles that enhance sorbent durability.

36 MATERIALS SCIENCE↗

A Computational Framework to design 3D stiffness gradient acoustic metamaterials for impedance matching

Acoustic waves play a crucial role in various applications, including medical imaging, non-destructive testing, and sonar systems. One of the significant challenges in these applications is impedance matching, which is essential for minimizing reflections and maximizing the transfer of acoustic energy between different media. Acoustic metamaterials offer a promising solution to this challenge. In addition to impedance control, gradient stiffness can enhance structural efficiency and enable spatial control of wave propagation, making it a valuable feature in acoustic metamaterial design. In this pa- per, we present our developed computational method to design 3D stiffness gradient acoustic metamaterials for impedance matching. The key steps in our approach include generating initial designs using a periodic covariance function to provide unit cells that are both periodic on the boundaries and randomly formed inside the unit cell. Furthermore, we integrated manufacturing constraints into the design process, ensuring that the structures are interconnected for fabrication. We propose two computational optimization algorithms: GenUnit, based on a non-dominated sorting genetic algorithm (NSGA-II), and MLMatch, which leverages differentiable machine learning. The two approaches are not separate contributions but complementary com- ponents of a unified framework. GenUnit requires no training data and directly interfaces with physics-based simulations, making it highly accurate but slower for large-scale exploration. In contrast, MLMatch is data-hungry during training but, once trained, enables near-instantaneous inference and broad design-space coverage. Together, they form a hybrid strategy: ML- Match rapidly explores the global design space, and GenUnit provides local refinement with high-fidelity accuracy. This balance between training cost, inference time, and precision is the motivation for including both methods in the same study. We applied this dual-algorithm framework to generate two metallic-based metamaterial designs that match the acoustic impedance of water while exhibiting a controlled gradient in stiffness (from stiff to soft). The stiffness gradient is particularly advantageous in applications where one side of the structure must interface with soft or sensitive surfaces, such as human tissue or delicate components. Here, this work paves the way for improved materials in various acoustic applications, particularly in ultrasound devices, by providing better impedance.

Metamaterial↗

Iterative HOMER with uncertainties

We present iHOMER, an iterative version of the HOMER method to extract Lund fragmentation functions from experimental data. Through iterations, we address the information gap between latent and observable phase spaces and systematically remove bias. To quantify uncertainties on the inferred weights, we use a combination of Bayesian neural networks and uncertainty-aware regression. We find that the combination of iterations and uncertainty quantification produces well-calibrated weights that accurately reproduce the data distribution. A parametric closure test shows that the iteratively learned fragmentation function is compatible with the true fragmentation function.

Butter, Anja [Heidelberg Univ. (Germany); Sorbonne↗