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At least 127 records · Page 7

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows. PHENIX – AFITT refinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentially difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows. PHENIX – AFITT refinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combining AFITT and the PHENIX software suite on a data set of 189 protein–ligand PDB structures are presented. Refinements using PHENIX – AFITT significantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. Finally, for the data presented, PHENIX – AFITT refinements result in more chemically accurate models for small-molecule ligands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Trust Model Measurements for the Energy Grid of Things

Information security is essential for the reliable operation of an Energy Grid of Things (EGoT). In addition to basic information security protocols as defined by published standards, there is a need for a monitoring function that measures the trustworthiness of the various actors participating in an EGoT. We describe in this paper the implementation and evaluation of a Distributed Trust Model that was developed specifically for monitoring communication within an EGoT. We then show how the model parameters are set using statistical measures for hypothesis testing.

Energy Grid of Things, EGoT, Smart Grid Security, ↗

Improving the Performance Scalability of the Community Atmosphere Model

The Community Atmosphere Model (CAM), which serves as the atmosphere component of the Community Climate System Model (CCSM), is the most computationally expensive CCSM component in typical configurations. On current and next-generation leadership class computing systems, the performance of CAM is tied to its parallel scalability. Improving performance scalability in CAM has been a challenge, due largely to algorithmic restrictions necessitated by the polar singularities in its latitude-longitude computational grid. Nevertheless, through a combination of exploiting additional parallelism, implementing improved communication protocols, and eliminating scalability bottlenecks, we have been able to more than double the maximum throughput rate of CAM on production platforms. We describe these improvements and present results on the Cray XT5 and IBM BG/P. The approaches taken are not specific to CAM and may inform similar scalability enhancement activities for other codes.

99 GENERAL AND MISCELLANEOUS↗

Electrodeposition of Nanostructured Copper on Gas Diffusion Layers as Electrocatalysts for Carbon Dioxide Reduction

The aim of the summer project was to immobilize copper nanostructures on gas diffusion layers to serve as electrocatalysts for the electrochemical reduction of CO 2 . Gas diffusion layers are typically bilayer structures consisting of a macro-porous backing material (carbon fiber paper) and a microporous, carbon-based layer (MPL). Classically, the copper catalysts are loaded on the microporous layer. Furthermore, the GDL is intrinsically hydrophobic due to polytetrafluoroethylene (PTFE)in its chemical composition, with the MPL having a more hydrophobic character due to its higher PTFE content. While beneficial for rendering the MPL impervious to electrolytes during actual CO 2 reduction, the hydrophobicity precludes sufficient wetting of the MPL layer, preventing conformal, uniformly distributed and strongly adhered deposits. A two electrode electrodeposition system was used to facilitate copper deposition. An implication of this system is the inability to ascertain or accurately modulate the cathodic over-potential. Hence, galvanostatic (current control) procedures are utilized for all deposition. To improve the wetting behavior of the MPL, the surface is subjected to surface pretreatment protocols prior to electrodeposition. In addition, as morphology of deposits play a role in their efficacy as catalysts in terms of selectivity and conversion, we systematically investigate the effects of different galvanostatic deposition procedures on copper morphology.

36 MATERIALS SCIENCE↗

Product Consistency Test and Vapor Hydration Test Comparisons of a Radioactive Hanford Waste Glass with its Non-Radioactive Simulant Glass

Product Consistency Tests (PCT) and Vapor Hydration Tests (VHT) were performed on a radioactive glass made from Hanford tank AP-107 waste (i.e., R-AP-107) and its non-radioactive equivalent glass made from simulated tank waste (i.e., S-AP-107). The radioactive and non-radioactive experiments were conducted in parallel with identical equipment, protocols, and staff to remove additional experimental uncertainties. PCT and VHT results are reported for all samples and are shown in Table S.1. Average normalized mass loss of B ( NL B ) and Na ( NL Na ) calculated from the three replicate test results for each glass with their respective standard deviations (SD) are presented for PCT results while individual VHT rates ( r VHT ) with their propagated errors ( σ r prop ) from individual thickness measurements on each sample are presented for the VHT results. Some VHT samples experienced more than 50% evaporation loss during the experiments. However, no visible alteration was detected on any VHT samples regardless on the amount of evaporation loss detected as shown in Table S.1.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Multilayer Electrodes with Metalized Polymer Current Collector for High-Energy Lithium-Ion Batteries with Extreme-Fast-Charging Capability

The pursuit of batteries capable of extreme fast charging (XFC), that also satisfy high energy and safety criteria, poses a significant challenge to current lithium-ion battery technologies. Additionally, the increasing demand for aluminum (Al) and copper (Cu) in electrification, and vehicle light weighting is driving these metals towards near-critical status in the medium term. This study introduced metalized polymer films by depositing an Al or Cu thin layer onto two sides of a polyethylene terephthalate (PET) film – named mPET/Al and mPET/Cu, as lightweight, cost-effective alternatives to traditional metal current collectors in LIBs. We have utilized current collectors that significantly reduce weight (by 73%), thickness (by 33%), and cost (by 85%) compared to traditional metal foil counterparts. We conducted an extensive evaluation of their mechanical and electrical properties, including in-plane and through-plane resistivities, affirming their suitability for the roll-to-roll battery manufacturing process. Additionally, a novel XFC testing protocol was employed to thoroughly assess the cells' (both half and full-cell) performance across various C-rates and under long-term tests. These advancements have the potential to enhance energy density to 280 Wh/kg at the electrode level under 10-minute charging at 6C. Through testing, including a novel XFC protocol across various C-rates and long-term cycling (up to 1000 cycles) in different cell configurations, we have demonstrated the superior performance of these metalized polymer films. Notably, mPET/Cu and mPET/Al foils exhibited comparable capacities to conventional cells under XFC, with the mPET cells showing a 27% improvement in energy density at 6C and maintaining significant energy density after 1000 cycles. This study underscored the potential of mPET foils to revolutionize the roll-to-roll battery manufacturing process and significantly advance the performance metrics of LIBs in EV applications. Moreover, our results suggest that there is potential to enhance the performance of mPET foils, especially mPET/Al, by optimizing the manufacturing process to achieve higher conductivity.

99 GENERAL AND MISCELLANEOUS↗

COVID-19 prevention at institutions of higher education, United States, 2020–2021: implementation of nonpharmaceutical interventions

Background, In early 2020, following the start of the coronavirus disease 2019 (COVID-19) pandemic, institutions of higher education (IHEs) across the United States rapidly pivoted to online learning to reduce the risk of on-campus virus transmission. We explored IHEs’ use of this and other nonpharmaceutical interventions (NPIs) during the subsequent pandemic-affected academic year 2020–2021. Methods, From December 2020 to June 2021, we collected publicly available data from official webpages of 847 IHEs, including all public (n = 547) and a stratified random sample of private four-year institutions (n = 300). Abstracted data included NPIs deployed during the academic year such as changes to the calendar, learning environment, housing, common areas, and dining; COVID-19 testing; and facemask protocols. We performed weighted analysis to assess congruence with the October 29, 2020, US Centers for Disease Control and Prevention (CDC) guidance for IHEs. For IHEs offering ≥50% of courses in person, we used weighted multivariable linear regression to explore the association between IHE characteristics and the summated number of implemented NPIs. Results, Overall, 20% of IHEs implemented all CDC-recommended NPIs. The most frequently utilized NPI was learning environment changes (91%), practiced as one or more of the following modalities: distance or hybrid learning opportunities (98%), 6-ft spacing (60%), and reduced class sizes (51%). Additionally, 88% of IHEs specified facemask protocols, 78% physically changed common areas, and 67% offered COVID-19 testing. Among the 33% of IHEs offering ≥50% of courses in person, having < 1000 students was associated with having implemented fewer NPIs than IHEs with ≥ 1000 students. Conclusions, Only 1 in 5 IHEs implemented all CDC recommendations, while a majority implemented a subset, most commonly changes to the classroom, facemask protocols, and COVID-19 testing. IHE enrollment size and location were associated with degree of NPI implementation. Additional research is needed to assess adherence to NPI implementation in IHE settings.

59 BASIC BIOLOGICAL SCIENCES↗

MasQiTT

SAND2025-03471O MasQiTT software is a proof-of-concept code that implements the Secure MQTT protocol. It demonstrates a publish/subscribe model of message passing within a network where the publishers can encrypt messages according to a topic and the subscribers can decrypt those messages. The example code shows an example of deployment of an end-to-end system that includes certificate authority and key management in addition to basic implementation of the protocol. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Fisher, Andrew [Sandia National Lab. (SNL-CA), Liv↗

Cyclic moisture reactivation of calcium sorbents for long duration thermochemical energy storage

The transition to a flexible and reliable energy infrastructure, using electro-thermal energy generation technologies such as geothermal, concentrated solar power, and nuclear, usually demands simultaneous advancement of thermal energy storage (TES) to support on-demand electricity generation and industrial applications while mitigating the inherent intermittency of renewable energy sources and power outages from direct energy generation. Among TES technologies, thermochemical energy storage (TCES) based on calcium looping emerges as a compelling high-power energy storage candidate due to its high reaction enthalpy, compatibility with elevated operating temperatures, and abundance of low-cost materials. However, the long-term durability of calcium-based sorbents for TCES is hindered by surface sintering and particle aggregation, leading to performance degradation over repeated thermal cycles. This study explores a moisture hydration-based strategy to regenerate a degraded calcium sorbent and mitigate performance degradation for long duration TCES. The addition of moisture transforms calcium oxide into calcium hydroxide and produces intercalation water layers, associated with a regenerated surface area and reduced calcium oxide crystallite size. Both these effects are beneficial in restoring the sorbents' reactivity for carbonization. Additionally, an optimized hydration-assisted reactivation protocol balances the recovered energy storage capacity with heating penalty required for moisture removal from hydrated samples, resulting in an enhanced energy storage capacity up to 176% compared to benchmark sorbents that undergo cycling without reactivation after 60 cycles. In conclusion, these results highlight the potential of hydration-assisted reactivation to enhance the long-term performance of TCES, providing an effective pathway to advancing electro-thermal storage technologies.

36 MATERIALS SCIENCE↗

System architecture and method of processing data therein

A system architecture encoded on a non-transitory computer readable medium, the system architecture includes a first protocol. The first protocol is configured to receive a plurality of outputs from an ICS used in controlling an industrial system. The first protocol is configured to receive a plurality of inputs from a physical module. The physical module includes at least one of a component, a sensor, or the ICS. Additionally, the system architecture includes a second protocol, wherein the second protocol is configured to validate the plurality of inputs from the first protocol. Moreover, the system architectures includes a third protocol, wherein the third protocol is configured to validate the plurality of outputs from the first protocol. Further, the system architecture includes a fourth protocol, wherein the fourth protocol is configured to manage the ICS based on the second protocol and the third protocol.

Abdel-Khalik, Hany S.↗

System architecture and method of processing data therein

A system architecture encoded on a non-transitory computer readable medium, the system architecture includes a first protocol. The first protocol is configured to receive a plurality of outputs from an ICS used in controlling an industrial system. The first protocol is configured to receive a plurality of inputs from a physical module. The physical module includes at least one of a component, a sensor, or the ICS. Additionally, the system architecture includes a second protocol, wherein the second protocol is configured to validate the plurality of inputs from the first protocol. Moreover, the system architectures includes a third protocol, wherein the third protocol is configured to validate the plurality of outputs from the first protocol. Further, the system architecture includes a fourth protocol, wherein the fourth protocol is configured to manage the ICS based on the second protocol and the third protocol.

Abdel-Khalik, Hany S.↗

Degrees of Rate Control in Interconnected Reaction Networks

Overall reactions in interconnected networks exhibit net, forward, and reverse rates that are governed by both constitutive elementary steps in the pathway of interest and branching elementary steps that lead to alternative products. Accordingly, steps in branching pathways exhibit negative net, forward, and reverse degrees of rate control, as they reduce reaction flux to the desired product. We here contextualize the forward and reverse degrees of rate control in terms of kinetic resistances (inverse of rates) and leverage the additive nature of kinetic resistance to decouple kinetic driving forces contributed by constitutive elementary steps and branching points (nodal species) in interconnected networks. Regardless of the network connectivity, forward and reverse degrees of rate control are shown to converge at equilibrium. Away from equilibrium, we identify two critical features of interconnected networks: stoichiometric regularity─condition where all stoichiometric numbers are unity─and pathway symmetry around nodal species─condition where branching pathways share the same rate constants, stoichiometry, and species concentrations/activities─that result in (i) equal forward, reverse, and consequently net degrees of rate control and (ii) forward and reverse degrees of rate control that exhibit constant offsets, respectively, across all extents of reaction. Furthermore, our discourse further provides a mathematical description for the influence of stoichiometric irregularity and pathway asymmetry on forward and reverse degrees of rate control. Altogether, the presented work details the effects of network (inter)connectivity and stoichiometry on reaction kinetics and, in doing so, establishes general protocols for capturing these effects as additive terms in the formulation of forward and reverse degrees of rate control.

10 SYNTHETIC FUELS↗

Investigation into image quality and dose for different patient geometries with multiple cone-beam CT systems

Purpose: To provide quantitative and qualitative image quality metrics and imaging dose for modern Varian On-board Imager (OBI) (ver. 1.5) and Elekta X-ray Volume Imager (XVI) (ver. 4.5R) cone-beam computed tomography (CBCT) systems in a clinical adaptive radiation therapy environment by accounting for varying patient thickness. Methods: Image quality measurements were acquired with Catphan 504 phantom (nominal diameter and with additional 10 cm thickness) for OBI and XVI systems and compared to planning CT (pCT) (GE LightSpeed). Various clinical protocols were analyzed for the OBI and XVI systems and analyzed using image quality metrics, including spatial resolution, low contrast detectability, uniformity, and HU sensitivity. Imaging dose measurements were acquired in Wellhofer Scanditronix i'mRT phantom at nominal phantom diameter and with additional 4 cm phantom diameter using GafChromic XRQA2 film. Calibration curves were generated using previously published in-air Air Kerma calibration method. Results: The OBI system full trajectory scans exhibited very little dependence on phantom thickness for accurate HU calculation, while half-trajectory scans with full-fan filter exhibited dependence of HU calculation on phantom thickness. The contrast-to-noise ratio (CNR) for the OBI scans decreased with additional phantom thickness. The uniformity of Head protocol scan was most significantly affected with additional phantom thickness. The spatial resolution and CNR compared favorably with pCT, while the uniformity of the OBI system was slightly inferior to pCT. The OBI scan protocol dose levels for nominal phantom thickness at the central portion of the phantom were 2.61, 0.72, and 1.88 cGy, and for additional phantom thickness were 1.95, 0.48, and 1.52 cGy, for the Pelvis, Thorax, and Spotlight protocols, respectively. The XVI system scans exhibited dependence on phantom thickness for accurate HU calculation regardless of trajectory. The CNR for the XVI scans decreased with additional phantom thickness. The uniformity of the XVI scans was significantly dependent on the selection of the proper FOV setting for all phantom geometries. The spatial resolution, CNR, and uniformity for XVI were lower than values measured for pCT. The XVI scan protocol dose levels at the central portion of the phantom for nominal phantom thickness were 2.14, 2.15, and 0.33 cGy, and for additional phantom thickness were 1.56, 1.68, and 0.21 cGy, for the Pelvis M20, Chest M20, and Prostate Seed S10 scan protocols, respectively. Conclusions: The OBI system offered comparable spatial resolution and CNR results to the results for pCT. Full trajectory scans with the OBI system need little-to-no correction for HU calculation based on HU stability with changing phantom thickness. The XVI system offered lower spatial resolution and CNR results than pCT. In addition, the HU calculation for all scan protocols was dependent on the phantom thickness. The uniformity for each CBCT system was inferior to that of pCT for each phantom geometry. The dose for each system and scan protocol in the interior of the phantom tended to decrease by approximately 25% with 4 cm additional phantom thickness.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Lead Research and Development Activity for DOE's High Temperature, Low Relative Humidity Membrane Program (Topic 2)

The Department of Energy’s High Temperature, Low Relative Humidity Membrane Program was begun in 2006 with the Florida Solar Energy Center (FSEC) as the lead organization. During the first three years of the program, FSEC was tasked with developing non-Nafion® proton exchange membranes with improved conductivity for fuel cells. Additionally, FSEC was responsible for developing protocols for the measurement of in-plane conductivity, providing conductivity measurements for the other funded teams, developing a method for through-plane conductivity and organizing and holding semiannual meetings of the High Temperature Membrane Working Group (HTMWG). The FSEC membrane research focused on the development of supported poly[perfluorosulfonic acid] (PFSA) – Teflon membranes and a hydrocarbon membrane, sulfonated poly(ether ether ketone). The fourth generation of the PFSA membrane (designated FSEC-4) came close to, but did not meet, the Go/No-Go milestone of 0.1 S/cm at 50% relative humidity at 120 °C. In-plane conductivity of membranes provided by the funded teams was measured and reported to the teams and DOE. Late in the third year of the program, DOE used this data and other factors to decide upon the teams to continue in the program. The teams that continued provided promising membranes to FSEC for development of membrane electrode assemblies (MEAs) that could be tested in an operating fuel cell. FSEC worked closely with each team to provide customized support. A logic flow chart was developed and discussed before MEA fabrication or any testing began. Of the five teams supported, by the end of the project, membranes from two of the teams were easily manufactured into MEAs and successfully characterized for performance. One of these teams exceeded performance targets, while the other requires further optimization. An additional team developed a membrane that shows great promise for significantly reducing membrane costs and increasing membrane lifetime.

08 HYDROGEN↗

Radiopaque Resists for Two-Photon Lithography To Enable Submicron 3D Imaging of Polymer Parts via X-ray Computed Tomography

Two-photon lithography (TPL) is a high-resolution additive manufacturing (AM) technique capable of producing arbitrarily complex three-dimensional (3D) microstructures with features 2–3 orders of magnitude finer than human hair. This process finds numerous applications as a direct route toward the fabrication of novel optical and mechanical metamaterials, miniaturized optics, microfluidics, biological scaffolds, and various other intricate 3D parts. As TPL matures, metrology and inspection become a crucial step in the manufacturing process to ensure that the geometric form of the end product meets design specifications. X-ray-based computed tomography (CT) is a nondestructive technique that can provide this inspection capability for the evaluation of complex internal 3D structure. However, polymeric photoresists commonly used for TPL, as well as other forms of stereolithography, poorly attenuate X-rays due to the low atomic number (Z) of their constituent elements and therefore appear relatively transparent during imaging. We present the development of optically clear yet radiopaque photoresists for enhanced contrast under X-ray CT. We have synthesized iodinated acrylate monomers to formulate high-Z photoresist materials that are capable of forming 3D microstructures with sub-150 nm features. In addition, we have developed a formulation protocol to match the refractive index of the photoresists to the immersion medium of the objective lens so as to enable dip-in laser lithography, a direct laser writing technique for producing millimeter-tall structures. Our radiopaque photopolymer then resists increase X-ray attenuation by a factor of more than 10 times without sacrificing the sub-150 nm feature resolution or the millimeter-scale part height. Thus, our resists can successfully replace existing photopolymers to generate AM parts that are suitable for inspection via X-ray CT. By providing the “feedstock” for radiopaque AM parts, our resist formulation is expected to play a critical role in enabling fabrication of functional polymer parts to tight design tolerances.

36 MATERIALS SCIENCE↗

Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications

Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts, and they hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies-for example, repeated terminator and insulator sequences-that complicate recombination-based assembly. We and others have recently developed DNA assembly methods, which we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly assembled constructs, or into high-quality combinatorial libraries in only 2-3 d. If the DNA parts must be generated from scratch, an additional 2-5 d are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques.

Torella, JP↗

Quantification of birefringence readily measures the level of muscle damage in zebrafish

Highlights: Black-Right-Pointing-Pointer Report of an unbiased quantification of the birefringence of muscle of fish larvae. Black-Right-Pointing-Pointer Quantification method readily identifies level of overall muscle damage. Black-Right-Pointing-Pointer Compare zebrafish muscle mutants for level of phenotype severity. Black-Right-Pointing-Pointer Proposed tool to survey treatments that aim to ameliorate muscular dystrophy. -- Abstract: Muscular dystrophies are a group of genetic disorders that progressively weaken and degenerate muscle. Many zebrafish models for human muscular dystrophies have been generated and analysed, including dystrophin-deficient zebrafish mutants dmd that model Duchenne Muscular Dystrophy. Under polarised light the zebrafish muscle can be detected as a bright area in an otherwise dark background. This light effect, called birefringence, results from the diffraction of polarised light through the pseudo-crystalline array of the muscle sarcomeres. Muscle damage, as seen in zebrafish models for muscular dystrophies, can readily be detected by a reduction in the birefringence. Therefore, birefringence is a very sensitive indicator of overall muscle integrity within larval zebrafish. Unbiased documentation of the birefringence followed by densitometric measurement enables the quantification of the birefringence of zebrafish larvae. Thereby, the overall level of muscle integrity can be detected, allowing the identification and categorisation of zebrafish muscle mutants. In addition, we propose that the establish protocol can be used to analyse treatments aimed at ameliorating dystrophic zebrafish models.

60 APPLIED LIFE SCIENCES↗