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At least 757 records · Page 42

Abundance of Major Cell Wall Components in Natural Variants and Pedigrees of Populus trichocarpa

The rapid analysis of biopolymers including lignin and sugars in lignocellulosic biomass cell walls is essential for the analysis of the large sample populations needed for identifying heritable genetic variation in biomass feedstocks for biofuels and bioproducts. In this study, we reported the analysis of cell wall lignin content, syringyl/guaiacyl (S/G) ratio, as well as glucose and xylose content by high-throughput pyrolysis-molecular beam mass spectrometry (py-MBMS) for >3,600 samples derived from hundreds of accessions of Populus trichocarpa from natural populations, as well as pedigrees constructed from 14 parents (7 × 7). Partial Least Squares (PLS) regression models were built from the samples of known sugar composition previously determined by hydrolysis followed by nuclear magnetic resonance (NMR) analysis. Key spectral features positively correlated with glucose content consisted of m/z 126, 98, and 69, among others, deriving from pyrolyzates such as hydroxymethylfurfural, maltol, and other sugar-derived species. Xylose content positively correlated primarily with many lignin-derived ions and to a lesser degree with m/z 114, deriving from a lactone produced from xylose pyrolysis. Models were capable of predicting glucose and xylose contents with an average error of less than 4%, and accuracy was significantly improved over previously used methods. The differences in the models constructed from the two sample sets varied in training sample number, but the genetic and compositional uniformity of the pedigree set could be a potential driver in the slightly better performance of that model in comparison with the natural variants. Broad-sense heritability of glucose and xylose composition using these data was 0.32 and 0.34, respectively. In summary, we have demonstrated the use of a single high-throughput method to predict sugar and lignin composition in thousands of poplar samples to estimate the heritability and phenotypic plasticity of traits necessary to develop optimized feedstocks for bioenergy applications.

09 BIOMASS FUELS↗

SAXS Assistant: Automated SAXS analysis for structural discovery in biologics and polymeric nanoparticles

Small-angle x-ray scattering (SAXS) is a powerful technique for assessing macromolecular structure. High-throughput SAXS is limited by the time-consuming and, at times, subjective nature of SAXS data interpretation. Here, we present SAXS Assistant, a Python-based script that streamlines SAXS data analysis to extract features for machine learning (ML) and key structural parameters, including the Guinier radius of gyration (R g ), pair distance distribution function (PDDF)-derived R g , maximum particle dimension (D max ), and Kratky plots. The script builds upon BioXTAS RAW and validates reliability via Guinier/PDDF R g agreement, an important indicator of well-measured data sets. For assistance in D max estimation, a multilayer perceptron regressor was trained with 1940 data files from the Small Angle Scattering Biological Data Bank. The model achieved a test set performance R 2 = 0.90 and mean absolute error = 11.7 Å. Training exclusively with experimental data translates analyses from researchers, including experts in the field, to the ML model, which helps assess D max estimations from PDDF. Gaussian mixture model clustering was implemented to classify profiles into structural classes based on entries in the Small Angle Scattering Biological Data Bank. Users may therefore assess the similarity between experimental samples and known biomolecular shapes within the mapped repository entries. This probabilistic clustering aids in quantifying information from Kratky and generating shape-descriptive features. SAXS Assistant accelerates SAXS data analysis through enforced quality control, ML-ready outputs, and flags for low-confidence results. In addition to providing the ability to analyze large data sets at high throughput, this tool is versatile and may serve researchers in both biological and synthetic polymer research fields.

36 MATERIALS SCIENCE↗

Microscale thermophoresis as a powerful tool for screening glycosyltransferases involved in cell wall biosynthesis

Background: Identification and characterization of key enzymes associated with cell wall biosynthesis and modification is fundamental to gain insights into cell wall dynamics. However, it is a challenge that activity assays of glycosyltransferases are very low throughput and acceptor substrates are generally not available. Results: We optimized and validated microscale thermophoresis (MST) to achieve high throughput screening for glycosyltransferase substrates. MST is a powerful method for the quantitative analysis of protein-ligand interactions with low sample consumption. The technique is based on the motion of molecules along local temperature gradients, measured by fluorescence changes. We expressed glycosyltransferases as YFP-fusion proteins in tobacco and optimized the MST method to allow the determination of substrate binding affinity without purification of the target protein from the cell lysate. The application of this MST method to the β-1,4-galactosyltransferase AtGALS1 validated the capability to screen both nucleotide-sugar donor substrates and acceptor substrates. We also expanded the application to members of glycosyltransferase family GT61 in sorghum for substrate screening and function prediction. Conclusions: This method is rapid and sensitive to allow determination of both donor and acceptor substrates of glycosyltransferases. MST enables high throughput screening of glycosyltransferases for likely substrates, which will narrow down their in vivo function and help to select candidates for further studies. Additionally, this method gives insight into biochemical mechanism of glycosyltransferase function.

59 BASIC BIOLOGICAL SCIENCES↗

Computation-guided discovery of coating materials to stabilize the interface between lithium garnet solid electrolyte and high-energy cathodes for all-solid-state lithium batteries

All-solid-state batteries with a lithium metal anode, enabled by lithium garnet solid electrolytes such as Li 7 La 3 Zr 2 O 12 (LLZO), are a promising next-generation energy-storage technology. The further development of all-solid-state battery requires the integration of high-energy cathodes such as LiNi 1-x-y Mn x Co y O 2 (NMC) with the garnet solid electrolyte with stable and low-resistance interfaces, which requires a coating layer to stabilize the interface during high-temperature sintering and electrochemical cycling. In order to guide the future development of interfacial coatings, we perform high-throughput thermodynamic analyses based on first-principles computation to investigate the stability of LLZO garnet and high-energy NMC cathodes with a wide range of materials chemistries. Here our study reveals the factors governing the materials stability with LLZO garnet and NMC cathodes, and identifies the mechanisms of good coating layers stable with LLZO and NMC. In addition to classifying known coating layers, our study provides detailed guiding charts and multiple new materials systems as promising coatings for stabilizing LLZO—NMC interfaces to enable high-energy-density garnet-based all-solid-state batteries. Our demonstrated computation scheme and high-throughput analyses are generally applicable to investigate and screen coating materials for stabilizing interfaces in energy-related applications.

25 ENERGY STORAGE↗

Rahasak—Scalable blockchain architecture for enterprise applications

Blockchain-based decentralized infrastructure has been adapted in various industries to handle the sensitive data in a privacy-preserving manner without trusting third parties. However, integrating state-of-the-art blockchain platforms with the scalable, enterprise-level applications result in several challenges. Current blockchain platforms do not support high transaction throughput, lack high scalability, and cannot provide real-time transaction processing and back-pressure operation handling in high transaction throughput applications(e.g Big data, IoT). In this paper, we propose a novel permissioned blockchain platform “Rahasak” for highly scalable, enterprise applications. Rahasak blockchain adopts the Apache Kafka-based consensus on top of a “Validate-Execute-Group” blockchain architecture to handle realtime transaction execution on the blockchain. The architecture is equipped with a functional programming and actor-based smart contract platform that enables concurrent execution of transactions in the blockchain. Rahasak supports high transaction throughput, high scalability, concurrent transaction execution, data analytics features. Finally, with Rahasak, we make blockchain more scalable, secure, structured and meaningful for further data analytics.

97 MATHEMATICS AND COMPUTING↗

Phase stabilization and oxidation of a continuous composition spread multi-principal element (AlFeNiTiVZr) 1-x Cr x alloy

Multi-Principal Element Alloys (MPEA) have been hypothesized to maintain a stable single alloy phase and resist corrosion at high temperatures, which are desirable in various functional applications, including material of turbine blades. However, studies into oxidation resistant alloys have been constrained to individual MPEA systems or a limited selection of compositions within those systems. Here, High-Throughput Experimental (HTE) techniques were utilized to rapidly assess phase stability and resistance to oxidation of an (AlFeNiTiVZr) 1-x Cr x continuous composition spread (CCS) thin-film alloy system. High-throughput synchrotron diffraction and Raman spectroscopy were used to identify phases, especially high symmetry structures and oxides, as a function of annealing time and composition. The formation of two distinct phase regions, R 1 and R 2 , across the CCS was observed. One of these phase regions, R 2 , exhibited a stable high symmetry BCC-like phase at Cr concentrations greater than 25.4 at%, and grew a passivating mixed metal surface oxide; whereas, the R 1 phase region, decomposed on oxidation to multiple oxides and reacted with the substrate to form silicides. The passivating mixed metal oxide layer appears to prevent destabilization of the (AlFeNiTiVZr) 1-x Cr x MPEA BCC solid solution. Furthermore, at longer annealing times the passivating phase was seen only above 29.2 at% Cr. High Cr-doped (AlFeNiTiVZr) 1-x Cr x appear to be a good candidate for high temperature, oxidation-resistant structural alloys.

36 MATERIALS SCIENCE↗

Constructing a Testing Application for GWMS

Many of Fermilab’s High Energy Physics experiments require High Throughput Computing to carry out simulations, data reconstruction, and data analysis. Glidein Workflow Management System (GWMS) is a tool that distributes High Throughput Computing. The purpose of GWMS is to provide convenient access to Grid resources and sites. GWMS is coupled to HTCondor. HTCondor is the workload management system that is used for scheduling and job control. Users submit jobs to a local HTCondor queue and GWMS will make sure the job will run on one of the many remote resources.

Neely-Brown, LeRayah↗

TransPlatformer

We propose TransPlatformer for translating toxicogenomics from one platform to another. Transcriptomic profiling has evolved through multiple generations of technology, from microarrays (e.g., Affymetrix, CodeLink) to more recent high-throughput sequencing and targeted panels such as S1500+. Microarrays, which dominated gene expression studies in the early 2000s, provided affordable and high-throughput transcript quantification but suffered from cross-hybridization issues and limited dynamic range . RNA-Seq, introduced in the late 2000s, revolutionized transcriptomics by enabling unbiased and comprehensive gene expression analysis, albeit at higher costs and computational demands . Despite advances, many studies rely on historical microarray data, necessitating the translation of legacy data into modern platforms to ensure continuity and comparability. This translation is complicated by factors such as platform-specific probe design, differences in transcript coverage, and batch effects . Existing methods for cross-platform mapping include statistical normalization, machine learning models, and biological anchoring approaches. The ability to translate transcriptomic data between platforms has broad implications, including enhanced meta-analyses, improved toxicological modeling, and better integration of historical datasets with contemporary research. TransPlatformer seeks to contribute to this effort by evaluating translation methodologies and proposing novel strategies to improve cross-platform gene expression harmonization. In this repository there are code examples for TransPlatformer implementation

Cong, Guojing↗

Multilevel analysis between Physcomitrium patens and Mortierellaceae endophytes explores potential long‐standing interaction among land plants and fungi

SUMMARY The model moss species Physcomitrium patens has long been used for studying divergence of land plants spanning from bryophytes to angiosperms. In addition to its phylogenetic relationships, the limited number of differential tissues, and comparable morphology to the earliest embryophytes provide a system to represent basic plant architecture. Based on plant–fungal interactions today, it is hypothesized these kingdoms have a long‐standing relationship, predating plant terrestrialization. Mortierellaceae have origins diverging from other land fungi paralleling bryophyte divergence, are related to arbuscular mycorrhizal fungi but are free‐living, observed to interact with plants, and can be found in moss microbiomes globally. Due to their parallel origins, we assess here how two Mortierellaceae species, Linnemannia elongata and Benniella erionia , interact with P. patens in coculture. We also assess how Mollicute ‐related or Burkholderia ‐related endobacterial symbionts (MRE or BRE) of these fungi impact plant response. Coculture interactions are investigated through high‐throughput phenomics, microscopy, RNA‐sequencing, differential expression profiling, gene ontology enrichment, and comparisons among 99 other P. patens transcriptomic studies. Here we present new high‐throughput approaches for measuring P. patens growth, identify novel expression of over 800 genes that are not expressed on traditional agar media, identify subtle interactions between P. patens and Mortierellaceae, and observe changes to plant–fungal interactions dependent on whether MRE or BRE are present. Our study provides insights into how plants and fungal partners may have interacted based on their communications observed today as well as identifying L. elongata and B. erionia as modern fungal endophytes with P. patens .

59 BASIC BIOLOGICAL SCIENCES↗

High gas throughput SOLPS-ITER simulations extending the ITER database to strong detachment

Abstract SOLPS-ITER simulations performed for Q DT = 10, P SOL = 100 MW burning plasmas on ITER extend the existing database to high values of separatrix averaged neon impurity concentration (⟨ c Ne ⟩ ≈ 6%) and divertor neutral pressure (⟨ p div ⟩ > 25 Pa) in order to determine the heat flux mitigation capability of these scenarios and whether strongly detached states are accessible. In the existing database of ITER simulations, the level of detachment was limited to cases where the integral ion flux to the outer target was greater than 80% of the value at rollover, with the impurity radiation localized near the target. With the possibility of narrow heat flux channels and increased deposited power due to tile shaping, it is important to explore operation at a higher degree of detachment. Two series of simulations were explored to extend the database of SOLPS simulations. By increasing the deuterium and neon puff rates proportionally, the peak divertor energy flux ( q ⊥,max ) is decreased from 5 to 3 MW m −2 while ⟨ p div ⟩ increased from 11 to 27 Pa. By increasing only the neon puff, q ⊥, max can be reduced to <1MW m −2 while ⟨ p div ⟩ is maintained at ∼ 11 Pa. As the neon puff level is increased, the position of the impurity radiation peak is shifted towards the X-point. At the highest neon puff levels with steady-state solutions, the electron temperature is reduced below 1 eV across 50 cm of each divertor target. The new cases extend previously observed tight relationships in power and momentum loss factors to low electron temperature improving their utility for highly detached regimes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Picturing the future of food

Abstract High‐throughput phenotyping (HTP) has emerged as one of the most exciting and rapidly evolving spaces within plant science. The successful application of phenotyping technologies will facilitate increases in agricultural productivity. High‐throughput phenotyping research is interdisciplinary and may involve biologists, engineers, mathematicians, physicists, and computer scientists. Here we describe the need for additional interest in HTP and offer a primer for those looking to engage with the HTP community. This is a high‐level overview of HTP technologies and analysis methodologies, which highlights recent progress in applying HTP to foundational research, identification of biotic and abiotic stress, breeding and crop improvement, and commercial and production processes. We also point to the opportunities and challenges associated with incorporating HTP across food production to sustainably meet the current and future global food supply requirements.

59 BASIC BIOLOGICAL SCIENCES↗

A flexible and scalable scheme for mixing computed formation energies from different levels of theory

Abstract Computational materials discovery efforts are enabled by large databases of properties derived from high-throughput density functional theory (DFT), which now contain millions of calculations at the generalized gradient approximation (GGA) level of theory. It is now feasible to carry out high-throughput calculations using more accurate methods, such as meta-GGA DFT; however recomputing an entire database with a higher-fidelity method would not effectively leverage the enormous investment of computational resources embodied in existing (GGA) calculations. Instead, we propose here a general procedure by which higher-fidelity, low-coverage calculations (e.g., meta-GGA calculations for selected chemical systems) can be combined with lower-fidelity, high-coverage calculations (e.g., an existing database of GGA calculations) in a robust and scalable manner. We then use legacy PBE(+ U ) GGA calculations and new r 2 SCAN meta-GGA calculations from the Materials Project database to demonstrate that our scheme improves solid and aqueous phase stability predictions, and discuss practical considerations for its implementation.

36 MATERIALS SCIENCE↗

Screening and Validation of Molecular Targeted Radiosensitizers

The development of molecular targeted drugs with radiation and chemotherapy is critically important for improving the outcomes of patients with hard-to-treat, potentially curable cancers. However, too many preclinical studies have not translated into successful radiation oncology trials. Major contributing factors to this insufficiency include poor reproducibility of preclinical data, inadequate preclinical modeling of intertumoral genomic heterogeneity that influences treatment sensitivity in the clinic, and a reliance on tumor growth delay instead of local control (TCD50) endpoints. There exists an urgent need to overcome these barriers to facilitate successful clinical translation of targeted radiosensitizers. To this end, we have used 3-dimensional (3D) cell culture assays to better model tumor behavior in vivo. Examples of successful prediction of in vivo effects with these 3D assays include radiosensitization of head and neck cancers by inhibiting epidermal growth factor receptor or focal adhesion kinase signaling, and radioresistance associated with oncogenic mutation of KRAS. To address the issue of tumor heterogeneity, we leveraged institutional resources that allow high-throughput 3D screening of radiation combinations with small-molecule inhibitors across genomically characterized cell lines from lung, head and neck, and pancreatic cancers. This high-throughput screen is expected to uncover genomic biomarkers that will inform the successful clinical translation of targeted agents from the National Cancer Institute Cancer Therapy Evaluation Program portfolio and other sources. Screening “hits” need to be subjected to refinement studies that include clonogenic assays, addition of disease-specific chemotherapeutics, target/biomarker validation, and integration of patient-derived tumor models. The chemoradiosensitizing activities of the most promising drugs should be confirmed in TCD50 assays in xenograft models with or without relevant biomarker and using clinically relevant radiation fractionation. We predict that appropriately validated and biomarker-directed targeted therapies will have a higher likelihood than past efforts of being successfully incorporated into the standard management of hard-to-treat tumors.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

High Performing Inverted Flexible Perovskite Solar Cells via Solution Phase Deposition of Yttrium-Doped SnO 2 Directly on Perovskite

Solution processing of flexible perovskite solar cells (f-PSCs) provides an avenue for scalable, high-throughput printing of lightweight, scalable, and cost-effective flexible solar cells. However, the deposition of fully solution-processed metal oxide charge transport layers on perovskites has been limited by solvent incompatibilities and high processing temperatures for metal oxide nanoparticles. In this study, we present high-performance, inverted f-PSCs from the direct deposition of yttrium doped SnO 2 nanoparticles functionalized with acetate on top of perovskite as an ink in anhydrous ethanol via blade coating. Yttrium doping improved device performance by improving the charge extraction leading with a decreased series resistance leading to improvements in the open-circuit voltage and fill factor. Furthermore, the champion power conversion efficiency for 0.1 cm 2 devices increased from 14.3% for undoped SnO 2 to 18.2% with 2% Y:SnO 2 doping, which is unprecedented for f-PSCs on ITO-PET substrate employing SnO 2 as an ETL.

14 SOLAR ENERGY↗

CRAGE-mediated insertion of fluorescent chromosomal markers for accurate and scalable measurement of co-culture dynamics in Escherichia coli

Monitoring population dynamics in co-culture is necessary in engineering microbial consortia involved in distributed metabolic processes or biosensing applications. However, it remains difficult to measure strain-specific growth dynamics in high-throughput formats. This is especially vexing in plate-based functional screens leveraging whole-cell biosensors to detect specific metabolic signals. Here, we develop an experimental high-throughput co-culture system to measure and model the relationship between fluorescence and cell abundance, combining chassis-independent recombinase-assisted genome engineering (CRAGE) and whole-cell biosensing with a PemrR-green fluorescent protein (GFP) monoaromatic reporter used in plate-based functional screening. CRAGE was used to construct Escherichia coli EPI300 strains constitutively expressing red fluorescent protein (RFP) and the relationship between RFP expression and optical density (OD600) was determined throughout the EPI300 growth cycle. A linear equation describing the increase of normalized RFP fluorescence during deceleration phase was derived and used to predict biosensor strain dynamics in co-culture. Measured and predicted values were compared using flow cytometric detection methods. Induction of the biosensor lead to increased GFP fluorescence normalized to biosensor cell abundance, as expected, but a significant decrease in relative abundance of the biosensor strain in co-culture and a decrease in bulk GFP fluorescence. Taken together, these results highlight sensitivity of population dynamics to variations in metabolic activity in co-culture and the potential effect of these dynamics on the performance of functional screens in plate-based formats. The engineered strains and model used to evaluate these dynamics provide a framework for optimizing growth of synthetic co-cultures used in screening, testing and pathway engineering applications.

59 BASIC BIOLOGICAL SCIENCES↗

Report Outlining Computed Tomography Strategy and Microscopy Approach to Qualifying AM 316 Materials

This report is part of work package CR-22OR0406012, Automated, High-Throughput Materials Characterization Techniques , under the Advanced Materials and Manufacturing Technologies program (AMMT). The project’s primary objective is to leverage our AI-based rapid and high-throughput automated characterization framework to qualify additively manufactured 316 materials comprehensively, focusing on optimizing the additive manufacturing process and evaluating the performance of 3D-printed stainless steel components. This report outlines our strategy for leveraging the automated characterization process for qualifying 316H materials.

36 MATERIALS SCIENCE↗

Higher Throughput, Lower Cost Processing of Flexible Perovskite Solar Cells by Photonic Curing

The objectives of this SETO project are to explore whether photonic curing can be used to perform annealing in perovskite solar cell (PSC) fabrication, and if so, whether it can enable high-throughput PSC manufacturing. The successful outcome of the project will reduce manufacturing cost towards realizing the SETO goal of the Levelized cost of electricity (LCOE) $0.03/kWh by 2030. The project is a collaboration between Hsu’s group at the University of Texas at Dallas (UTD) and NovaCentrix, an Austin TX based company that pioneered the PulseForge® photonic curing tools and has expertise in applying this technology to printed electronics. Thin-film synthesis typically involves a thermal annealing step to convert from precursors to final material phases, to obtain the desired crystalline phase, or to improve materials structural or electrical properties. However, thermal annealing typically requires high temperatures that are incompatible with inexpensive plastic substrates and annealing times lasting tens-to-hundreds of minutes, making it incompatible with roll-to-roll (R2R) manufacturing at a desirable web speed. Photonic curing uses a flash Xe lamp to deliver short (20 µs to 100 ms) but high intensity (up to 50 kW/cm 2 ) pulses of broadband light (200 – 1500 nm) to the sample. It has been successfully applied to sinter printed metal nanoparticle inks into conductive patterns. This project aimed to extend the applications of photonic curing to convert halide perovskite films and transparent metal oxide transport layers. Despite the interruption by COVID-19, we have achieved significant accomplishments to establish photonic curing as a viable technology for the high-throughput manufacturing of PSCs. (1) We demonstrated that photonic curing can convert both metal oxide transport layer and halide perovskite absorber in the PSCs and successfully made flexible PSCs on Corning Willow glass® (WG)/ indium tin oxide (ITO) substrates without any thermal annealing steps. These photonically cured devices achieve performance comparable to conventional thermally annealed devices but were fabricated with a total processing time reduced by six orders of magnitude. We also show that photonic curing can achieve desirable web speed (up to 26 m/min) and large-area uniformity. (2) By establishing photonic curing processing phase spaces for the perovskite, we show that the longer pulses are more forgiving in small variation in the photonic curing conditions, making it more suitable for R2R manufacturing. (3) Our results clearly illustrated the importance of improving mechanical and optical properties of transparent electrodes on flexible substrates. (4) We also performed fundamental studies that elucidate the interactions between perovskite absorber and metal oxide transport layer that can undermine the PSC stability. Five refereed journal papers in top journals (ACS Energy Letters, npj Flexible Electronics, ACS Applied Energy Materials, Materials Advances, and Frontiers in Energy Research), one conference proceeding (PVSC-47), six conference presentations (PVSC and Materials Research Society meetings), and a Ph.D. dissertation (Trey B. Daunis) were produced under this project. Energy Materials Corporation (EMC) has forecast that with a 1.5 m wide web moving at a web speed of 30 m/min, R2R processing of PSC could provide up to 4 GW/year for a single R2R assembly line. Replacing thermal annealing with photonic curing, as demonstrated by the accomplishments of this project, is necessary to realize such an energy production goal.

14 SOLAR ENERGY↗

Thermal Image Processing for Feature Extraction from Encapsulated Phase Change Materials

Encapsulated inorganic particles with high melting points (>300 °C) are desired as high-temperature Phase Change Materials (PCMs) for next-generation Latent Heat Thermal Energy Storage (LHTES) systems. One of the many challenges during the development of PCMs is to achieve a high throughput that in turn depends on accurately modeling the relation between process parameters and geometric & thermal properties of the PCMs particle. During the production of the PCMs, a high-speed infrared camera is used to acquire images of the encapsulated material under controlled illumination conditions. This research article focuses on the development of image processing techniques for both geometric and thermal feature extraction during the development of the PCMs. A user-friendly GUI has been designed in MATLAB and preliminary experimental results have demonstrated that the method is fast, accurate and reliable for a high throughput production. The extracted features will be used to develop Machine Learning (ML) models to predict the geometric and thermal properties of the PCM based on the process parameter settings. The ML model will accelerate the search for the optimized process settings to boost the throughput of the production.

25 ENERGY STORAGE↗