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DOE OSTI2022

Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization

Enhancing the thermostability of enzymes without impacting their catalytic function represents an important yet challenging goal in protein engineering and biocatalysis. We recently introduced a novel method for enzyme thermostabilization that relies on the computationally guided installation of genetically encoded thioether “staples” into a protein via cysteine alkylation with the noncanonical amino acid O-2-bromoethyl tyrosine (O2beY). Here, we demonstrate the functionality of an expanded set of electrophilic amino acids featuring chloroacetamido, acrylamido, and vinylsulfonamido side-chain groups for protein stapling using this strategy. Using a myoglobin-based cyclopropanase as a model enzyme, our studies show that covalent stapling with pchloroacetamido-phenylalanine (pCaaF) provides higher stapling efficiency and enhanced stability (thermodynamic and kinetic) compared to the other stapled variants and the parent protein. Interestingly, molecular simulations of conformational flexibility of the cross-links show that the pCaaF staple allows fewer energetically feasible conformers than the other staples, and this property may be a broader indicator of stability enhancement. Using this strategy, pCaaF-stapled variants with significantly enhanced stability against thermal denaturation (ΔT m ' = +27 °C) and temperature-induced heme loss (ΔT 50 = +30 °C) were obtained while maintaining high levels of catalytic activity and stereoselectivity. Crystallographic analyses of singly and doubly stapled variants provide key insights into the structural basis for stabilization, which includes both direct interactions of the staples with protein residues and indirect interactions through adjacent residues involved in heme binding. This work expands the toolbox of protein stapling strategies available for protein stabilization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Visualizing quasiparticles from quantum entanglement for general one-dimensional phases

In this work, we present a quantum information framework for the entanglement behavior of the low-energy quasiparticle (QP) excitations in various quantum phases in one-dimensional (1D) systems. We first establish an exact correspondence between the correlation matrix and the QP entanglement Hamiltonian for free fermions and find an extended in-gap state in the QP entanglement Hamiltonian as a consequence of the position uncertainty of the QP. A more general understanding of such an in-gap state can be extended to a Kramers theorem for the QP entanglement Hamiltonian, which also applies to strongly interacting systems. Further, we present a set of ubiquitous entanglement spectrum features, dubbed entanglement fragmentation, conditional mutual information, and measurement-induced nonlocal entanglement for QPs in 1D symmetry protected topological phases. Our result thus provides another framework to identify different phases of matter in terms of their QP entanglement.

1-dimensional spin chains↗

DOE OSTI2023

Two Large-Scale Meteorological Patterns are Associated with Short-Duration Dry Spells in the Northeastern United States

Large-scale meteorological pattern (LSMP)–based analysis is used in a novel way to understand meteorological conditions before and during short-duration dry spells over the northeastern United States. These LSMPs are useful to assess models and select better-performing models for future projections. Dry-spell events are identified from histograms of consecutive dry days below a daily precipitation threshold. Events lasting 12 days or longer, which correspond to ~10% of dry-spell events, are examined. The 500-hPa stream-function anomaly fields for the first 12 days of each event are time averaged, and k -means clustering is applied to isolate the dry-spell-related LSMPs. The first cluster has a strong low pressure anomaly over the Atlantic Ocean, southeast of the region, and is more common in winter and spring. The second cluster has strong high pressure over east-central North America and is most common during autumn. Over the region, both clusters have negative specific humidity anomalies, negative integrated vapor transport from the north, and subsidence associated with a midlatitude jet stream dipole structure that reinforces upper-level convergence. Subsidence is supported by cold-air advection in the first cluster and the location on the east side of the lower-level high pressure in the second cluster. Extratropical cyclone storm tracks are generally shifted southward of the region during the dry spells. Individual events lie on a continuum between two distinct clusters. These clusters have similar local, but different remote, properties. Although dry spells occur with greater frequency during drought months, most dry spells occur during nondrought months. Significance Statement: This study examines the large-scale weather patterns and meteorological conditions associated with dry-spell events lasting at least 2 weeks while affecting the northeastern United States. A statistical approach groups events together on the basis of similar atmospheric features. We find two distinct sets of patterns that we call large-scale meteorological patterns. These patterns reduce moisture, foster localized sinking, and shift the storm track southward along the Atlantic seaboard, all of which reduce precipitation. Besides greater understanding, knowing the meteorological patterns during short-term dryness in the region provides an important tool to assess how well atmospheric models reproduce these specific patterns. More dry spells occur in non-drought months than in drought months, which means that dry spells can occur without preexisting drought conditions.

58 GEOSCIENCES↗

DOE OSTI2022

Reactor physics benchmark of Westinghouse PWR core design suite for high burnup/high enrichment fuel - Part 1: Pin and lattice

Westinghouse has performed a comprehensive set of code-to-code benchmark comparisons to corroborate application of its state-of-the-art NEXUS-based code suite to high burnup and high enrichment (HB/HE) fueled PWR core design and reload analysis. This paper focuses on analysis of the predictions for pin and lattice designs representative of HB/HE core reloads from the Westinghouse advanced lattice code PARAGON2, the Monte-Carlo code SERPENT2 and MPACT, the deterministic neutronic component of VERA. A companion paper presented at this conference analyzes results obtained with the Westinghouse ANC9 core simulator, using lattice data provided by PARAGON2 with the NEXUS cross-section methodology, and MPACT for 2D and 3D core configurations incorporating HB/HE fuel reloads to achieve cycle length extension to 24-month in high-power density PWRs. The results of the pin and lattice benchmark presented in this paper show that the neutronic predictions from PARAGON2 for HB/HE fueled PWRs are in remarkable agreement with predictions from both SERPENT2 and MPACT including for depletion to high fuel burnup values, and employing a set of challenging lattices which feature combined use of burnable absorbers to obtain the required reactivity hold-down to support PWR transition to HB/HE fuel and 24-month operational cycles. As corroborated by this analysis and the analysis contained in the companion paper, the Westinghouse NEXUS-based PWR core analysis package can be confidently applied by industry for design analysis of PWR core reloads adopting HB/HE fuel and properly support the industry commercialization plans for in-reactor deployment. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

DETECTING FIRE WITH MACHINE LEARNING-ENABLED VISUAL MONITORING FOR NUCLEAR POWER PLANT ENVIRONMENTS

Nuclear power plants are experiencing significant cost challenges to remain competitive with other energy-generation utilities. Unlike other industries, the cost of operation and maintenance activities is mostly attributed to workforce costs. To mitigate this, nuclear power plant stakeholders are increasingly interested in the development and deployment of machine learning methods to potentially automate or augment manually intensive tasks to reduce costs, especially for monitoring activities. One monitoring function that is visually demanding and that can occur frequently to meet the requirements of a fire protection program is visually monitoring an area for fire occurrence. Currently, fire watch activities consist of a worker physically stationed at a given location with the sole responsibility of observing a given area to ensure a fire is detected and mitigated promptly. This effort focused on the development and evaluation of a suitable deep convolutional neural network to classify individual video frames at a sub-second frequency for the occurrence of “fire” and “no fire” in varying industrial environments similar to nuclear power plants. It is believed that a trained neural network model could be integrated with existing facility video surveillance camera feeds to generate alerts when fire inferences occur in individual frames captured at sub-second temporal resolutions. Extensive effort was dedicated to identifying and curating suitable imagery training data representing varying environments and scene settings with and without flame features to maximize generalization in nuclear power plant environments. The data collection effort resulted in the aggregation of a large, labeled image library exceeding 12,000 images to support model training for diverse industrial environments. A deep neural network model incorporating parallel multi-scale capabilities was developed and trained to support accurate image-based detection of flame incidents of varying sizes and spectral feature properties within heterogeneous scenes. Analysis results show that the trained model can achieve high inference accuracy despite heterogeneous scene environments and components. Testing accuracy exceeded 95.0 percent with very low false positive and false negative inferences.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Standardization of ancillary installation tooling for SRF cavities at Fermilab

For assemblies of cavities in cleanrooms, single-use tooling systems are made for the alignment and installation of ancillary components such as couplers and bellows. To minimize the number of tooling sets created, a design has been created to standardize alignment features to allow for assembly of different components with one set of tooling. A prototype set of tooling has been developed to with the required degrees of freedom for multiple assemblies while minimizing deformation during the assembly process. Prototype designs have been created for PIP-II SSR2 and 650 Cavities and for AUP Crab Cavities. Using 3D printing, this tooling can be quickly adjusted to allow for different ancillary components. The development process and status of the design will be discussed.

Narug, C. [Fermilab]↗

DOE OSTI2021

IMS Rapid Response FY21 Summary Report for: Integrating Patterned Probes with Four-Dimensional Scanning Transmission Electron Microscopy for Unrivaled Crystallographic Structure Determination in Nanomaterials

The initial goal of our 4-dimensional scanning transmission electron microscopy (4D-STEM)-based project was to develop strain resolution two orders of magnitude better than what is now currently possible with electron-based scattering techniques, all while collecting scattering information from 7 different tilt axes at one time [multi-beam electron diffraction (MBED)1 ] through the development of a new electron probe-forming aperture with non-circular features (patterned probes 2 ). We set out to accomplish this through a collaboration with Drs. Colin Ophus and Ben Savitsky at Lawrence Berkeley Laboratory (they are the world-leading experts in developing the complex computational codes required to perform orientation analysis and quantitative strain mapping on our 4D-STEM data sets. We are motivated to invest in this area as it will be the only technique sensitive enough to perform three- dimensional automated crystallographic orientation mapping (ACOM) and strain mapping for materials exposed to external stimulus (a focus of our larger efforts).

36 MATERIALS SCIENCE↗

DOE OSTI2024

Standardization of Ancillary Installation Tooling for SRF Cavities at Fermilab

For assemblies of cavities in cleanrooms, single-use tooling systems are made for the alignment and installation of ancillary components such as couplers and bellows. To try and minimize the amount of tooling sets used, a design has been created to standardize alignment features to allow for assembly of different components with one set of tooling. A prototype set of tooling has been developed to with the required degrees of freedom for multiple assemblies while minimizing deformation during the assembly process. Prototype designs have been created for PIP-II SSR2 and 650 Cavities and for AUP Crab Cavities. Using 3D printing, this tooling can be quickly adjusted to allow for different ancillary components. The development process and status of the design will be discussed.

Narug, Colin↗

DOE OSTI2025

Simple Integral Transport for Charged Particles

A short description of the simple integral transport (SIT) design, framework, and code is given. Explicit details are given for problems with spherical symmetry, as an explanation of the general features in context. This discussion sets up a simple calculation of alpha particle transport in inertial confinement fusion systems, as a proof of concept.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

A Case Study on Condenser Water Supply Temperature Optimization with a District Cooling Plant

District cooling (DC) continues to proliferate due to increasing global cooling demands and economies of scale benefits; however, most district-scale modeling has focused on heating, and to the best of our knowledge, researchers have yet to model cooling plants featuring waterside economizers in DC settings. With the popular Modelica Buildings library expanding its capabilities to district scale, this study is one of the first to demonstrate how the open-source models can be used for detailed energy and control analysis of a DC plant. For a real-world case study, we developed and calibrated high-fidelity models for a DC system central plant at a college campus in Colorado, USA, and we optimized the condenser water supply temperature (CWST) setpoint for a DC plant across multiple time horizons using the Optimization library in Dymola. Results indicate that annual CWST optimization saves 4.7% annual plant energy, with less than 1% of additional energy savings gained through daily optimization. This confirms previous studies' findings that high frequency CWST optimizations are not necessary for the studied system.

chiller plant↗

DOE OSTI2021

DESC DC2 Data Release Note

In preparation for cosmological analyses of the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST), the LSST Dark Energy Science Collaboration (LSST DESC) has created a 300 deg$^2$ simulated survey as part of an effort called Data Challenge 2 (DC2). The DC2 simulated sky survey, in six optical bands with observations following a reference LSST observing cadence, was processed with the LSST Science Pipelines (19.0.0). In this Note, we describe the public data release of the resulting object catalogs for the coadded images of five years of simulated observations along with associated truth catalogs. We include a brief description of the major features of the available data sets. To enable convenient access to the data products, we have developed a web portal connected to Globus data services. We describe how to access the data and provide example Jupyter Notebooks in Python to aid first interactions with the data. We welcome feedback and questions about the data release via a GitHub repository.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Light-Duty Vehicle Trip Classification Using One-Class Novelty Detection and Exhaustive Feature Extraction

Travel mode classification within travel survey data sets, especially light-duty vehicle (LDV) trips, is foundational, though nontrivial, to emerging mobility systems, travel behavior analysis, and fuel consumption estimation. Current travel mode detection approaches require well-sampled and balanced data sets with ground truth travel mode labels. The detection approaches are rarely applied and validated on large-scale, real-world data sets, which may not satisfy the dataset requirements. This work proposes an LDV trip detection model as a supplement to current travel mode detection methods, for the case when the training set is highly (and/or completely) unbalanced, to the extent that classical machine-learning approaches become difficult or impossible to deploy. The proposed model uses a novelty detection technique - one-class support vector machines (OCSVMs) - and a novel exhaustive feature extraction (EFE) technique on continuous time series data (i.e., Global Positioning System [GPS] speed profiles) for single-mode trip trajectories. Training and validation of the model are conducted on a large-scale, real-world data set. The proposed method accurately identifies LDV trips from a broad set of multimodal trips by leveraging a wealth of preexisting in-vehicle GPS travel data. Additional sensitivity analysis sheds light on the optimal training size and feature selection, which will benefit applications limited by highly imbalanced data. The paper also discusses performance comparison with regular machine-learning approaches, the model's robustness, and the potential to extend the proposed model to multi-modal trip prediction.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2025

ARCH: Large-scale knowledge graph via aggregated narrative codified health records analysis

Objective: Electronic health record (EHR) systems contain a wealth of clinical data stored as both codified data and free-text narrative notes (NLP). The complexity of EHR presents challenges in feature representation, information extraction, and uncertainty quantification. Here, to address these challenges, we proposed an efficient Aggregated naRrative Codified Health (ARCH) records analysis to generate a large-scale knowledge graph (KG) for a comprehensive set of EHR codified and narrative features. Methods: Using data from 12.5 million Veterans Affairs patients, ARCH first derives embedding vectors and generates similarities along with associated p-values to measure the strength of relatedness between clinical features with statistical certainty quantification. Next, ARCH performs a sparse embedding regression to remove indirect linkage between features to build a sparse KG. Finally, ARCH was validated on various clinical tasks, including detecting known relationships between entity pairs, predicting drug side effects, disease phenotyping, as well as sub-typing Alzheimer’s disease patients. Results: ARCH produces high-quality clinical embeddings and KG for over 60,000 codified and narrative EHR concepts. The KG and embeddings are visualized in the R-shiny powered web-API.3 ARCH achieved high accuracy in detecting EHR concept relationships, with AUCs of 0.926 (codified) and 0.861 (NLP) for similar EHR concepts, and 0.810 (codified) and 0.843 (NLP) for related pairs. It detected drug side effects with a 0.723 AUC, which improved to 0.826 after fine-tuning. Using both codified and NLP features, the detection power increased significantly. Compared to other methods, ARCH has superior accuracy and enhances weakly supervised phenotyping algorithms’ performance. Notably, it successfully categorized Alzheimer’s patients into two subgroups with varying mortality rates. Conclusion: The proposed ARCH algorithm generates large-scale high-quality semantic representations and knowledge graph for both codified and NLP EHR features, useful for a wide range of predictive modeling tasks.

Electronic health records↗

DOE OSTI2023

Predicting variable gene content in Escherichia coli using conserved genes

Having the ability to predict the protein-encoding gene content of an incomplete genome or metagenome-assembled genome is important for a variety of bioinformatic tasks. In this study, as a proof of concept, we built machine learning classifiers for predicting variable gene content in Escherichia coli genomes using only the nucleotide k-mers from a set of 100 conserved genes as features. Protein families were used to define orthologs, and a single classifier was built for predicting the presence or absence of each protein family occurring in 10%–90% of all E. coli genomes. The resulting set of 3,259 extreme gradient boosting classifiers had a per-genome average macro F1 score of 0.944 [0.943–0.945, 95% CI]. We show that the F1 scores are stable across multi-locus sequence types and that the trend can be recapitulated by sampling a smaller number of core genes or diverse input genomes. Surprisingly, the presence or absence of poorly annotated proteins, including “hypothetical proteins” was accurately predicted (F1 = 0.902 [0.898–0.906, 95% CI]). Models for proteins with horizontal gene transfer-related functions had slightly lower F1 scores but were still accurate (F1s = 0.895, 0.872, 0.824, and 0.841 for transposon, phage, plasmid, and antimicrobial resistance-related functions, respectively). Finally, using a holdout set of 419 diverse E. coli genomes that were isolated from freshwater environmental sources, we observed an average per-genome F1 score of 0.880 [0.876–0.883, 95% CI], demonstrating the extensibility of the models. Overall, this study provides a framework for predicting variable gene content using a limited amount of input sequence data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

QuantumScents: Quantum-Mechanical Properties for 3.5k Olfactory Molecules

Quantitative structure–odor relationships are critically important for studies related to the function of olfaction. Current literature data sets contain expert-labeled molecules but lack feature data. This paper introduces QuantumScents, a quantum mechanics augmented derivative of the Leffingwell data set. QuantumScents contains 3.5k structurally and chemically diverse molecules ranging from 2 to 30 heavy atoms (CNOS) and their corresponding 3D coordinates, total PBE0 energy, molecular dipole moment, and per-atom Hirshfeld charges, dipoles, and ratios. The authors demonstrate that Hirshfeld charges and ratios contain sufficient information to perform molecular classification by training a Message Passing Neural Network with chemprop (Heid, E.; et al. ChemRxiv, 2023, DOI: 10.26434/chemrxiv-2023-3zcfl) to predict scent labels. Finally, the QuantumScents data set is freely available on Zenodo along with the authors’ code, example models, and data set generation workflow (https://zenodo.org/doi/10.5281/zenodo.8239853).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Computational framework for modeling of physical process

Techniques, systems, and devices are described for providing a computational frame for estimating high-dimensional stochastic behaviors. In one exemplary aspect, a method for performing numerical estimation includes receiving a set of measurements of a stochastic behavior. The set of correlated measurements follows a non-standard probability distribution and is non-linearly correlated. Also, a non-linear relationship exists between a set of system variables that describes the stochastic behavior and a corresponding set of measurements. The method includes determining, based on the set of measurements, a numerical model of the stochastic behavior. The numerical model comprises a feature space comprising non-correlated features corresponding to the stochastic behavior. The non-correlated features have a dimensionality of M and the set of measurements has a dimensionality of N, M being smaller than N. The method includes generating a set of approximated system variables corresponding to the set of measurements based on the numerical model.

Chen, Xiao↗

DOE OSTI2024

Computational framework for modeling of physical process

Chen, Xiao↗

DOE OSTI2023

Method for rapid development of additive manufacturing parameter set

An apparatus includes a control system that defines a test part having multiple features of multiple feature types. The control system controls an additive manufacturing (AM) machine to print multiple copies of the test part, with each copy being printed according to a respective set of values used as printing parameters. A measurement system obtains a computed tomography (CT) image of each of the copies of the test part. An analysis system, for each of the plurality of feature types, analyzes the CT images to identify a selected set of values for the printing parameters. The analysis system identifies a portion of the CT image related to a first feature and assesses its density based on an average grayscale value. The AM machine is then controlled to print production parts according to, for each feature type of the production parts, the selected set of values for the printing parameters.

Bhattad, Pradeep↗