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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A Multicontinuum-Theory-Based Approach to the Analysis of Fiber-Reinforced Polymer Composites with Degraded Stiffness and Strength Properties Due to Moisture Absorption

Marine energy generation technologies such as wave and tidal power have great potential in meeting the need for renewable energy in the years ahead. Yet, many challenges remain associated with marine-based systems because of the corrosive environment. Conventional materials like metals are subject to rapid corrosive breakdown, crippling the lifespan of structures in such environments. Fiber-reinforced polymer composites offer an appealing alternative in their strength and corrosion resistance, but can experience degradation of mechanical properties as a result of moisture absorption. An investigation is conducted to test the application of a technique for micromechanical analysis of composites, known as multicontinuum theory and demonstrated in past works, as a mechanism for predicting the effects of prolonged moisture absorption on the performance of fiber-reinforced composites. Experimental tensile tests are performed on composite coupons with and without prolonged exposure to a salt water solution to obtain stiffness and strength properties. Multicontinuum theory is applied in conjunction with micromechanical modeling to deduce the effects of moisture absorption on the behavior of constituent materials within the composites. The results are consistent with experimental observations when guided by known mechanisms and trends from previous studies, indicating multicontinuum theory as a potentially effective tool in predicting the long-term performance of composites in marine environments.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Improving Trustworthiness of Data-Driven Power Grid Contingency Analysis With Bayesian Residual Graph Neural Networks

The evolving energy landscape requires novel tools to efficiently perform contingency analysis and reliability assessment of power grids, potentially in real-time. The high computational cost of traditional power flow solvers limits their applicability in practice. Machine learning (ML) surrogates such as deep neural networks (NNs) accelerate power flow solvers computations, enabling high-order contingency analysis and real-time decision-making by learning highly nonlinear functions and integrating grid topology via graph architectures. However, (graph) NNs lack predictive power away from training data and do not provide predictive confidence estimates. Here, we present a Bayesian residual graph NN that integrates knowledge from low-fidelity data via residual training and embeds granular quantification of uncertainties, improving trustworthiness critical for high-consequence decision-making. Applying Bayesian concepts to NNs is challenging due to the high-dimensionality of both the parameter space, complicating derivation of a meaningful prior, and the output space in large grid systems, requiring enhanced techniques to assess the predicted high-dimensional uncertainties. Our contributions include: (1) Deriving a prior for fully connected and graph NNs that leverages low-fidelity data to guide mean predictions and appropriately control prior predictive uncertainty. (2) Integrating this prior within an ensembling with anchoring scheme for efficient approximate posterior inference. (3) Deriving enhanced metrics to assess accuracy of both the mean and uncertainty predictions in high dimensions, appropriately accounting for correlations propagated through graph layers. The resulting Bayesian residual graph NN is tested on a contingency analysis task for 14-bus and 118-bus grids.

24 - POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

Summary of LWRS Research in Addressing RPV Research Gaps in NRC EMDA Report

Reactor Pressure Vessels (RPVs) are critical components in nuclear reactors, housing the reactor core and coolant under extreme conditions of temperature, pressure, and radiation. These harsh environments contribute to the degradation of RPV materials over time, presenting challenges for extending reactor operations beyond their original design lifespans. The NRC Expanded Materials Degradation Assessment (EMDA) report volume 3 have been instrumental in guiding research to support extending the operational life of light water reactors (LWRs) up to 80 years. It provides a comprehensive framework to address technical challenges related to aging and degradation mechanisms in RPVs. The LWRS program has played a key role in advancing this research, supporting projects such as the UCSB ATR-2 Experiment, material testing from Zion and Palisades reactors, and the development of advanced mini-compact tension testing techniques. These efforts have been crucial in identifying and addressing gaps in our understanding of RPV aging, contributing to the successful subsequent license renewals of eight LWR units in the U.S. The EMDA report volume 3, built on the Phenomena Identification and Ranking Table (PIRT) analysis from earlier versions of the EPRI Materials Degradation Matrix (MDM) and Issue Management Tables (IMTs), provides a detailed assessment of RPV degradation mechanisms. However, as EPRI has updated the MDM and IMT, it is important to revisit research priorities and methodologies to reflect these changes. The revised MDM and IMT may introduce new factors affecting long-term RPV performance and safety, highlighting the need for continued research and updated guidance to ensure the reliable and safe operation of reactors beyond 80 years.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

FAIR Data and Interpretable AI Framework for Architectured Metamaterials (Final Report)

This research program established a transformative framework for the discovery and design of mechanical metamaterials, which are architected structures engineered to control physical phenomena like sound and vibration in ways natural materials cannot. To overcome the traditional reliance on trial-and-error, the project developed an interpretable Artificial Intelligence (AI) framework that moves beyond "black box" models to reveal the specific geometric patterns—such as "unit-cell templates"—that govern a material’s performance. A major breakthrough was the development of a hierarchical design method, which allows a single material to block vibrations across multiple frequency ranges simultaneously by layering patterns at different scales without them interfering with one another. This was further expanded to include irregular, graph-based designs that use spanning tree algorithms to ensure structural connectivity while allowing for customized, direction-dependent properties like stiffness and acoustic impedance. Beyond design, the project addressed the practicalities of real-world production by developing uncertainty quantification techniques that account for manufacturing defects and material variability, reducing the need for expensive physical testing by orders of magnitude. To speed up the discovery process, the team implemented Gaussian Process Regression and other surrogate models that provide accurate performance predictions at a fraction of the traditional computational cost. The AI-generated designs were successfully validated through fabrication of physical samples and wave propagation experiments, confirming their ability to accurately guide or reflect waves as predicted. By contributing these tools and high-quality FAIR benchmark datasets to the wider scientific community, this work provides a scalable foundation for advancing technologies in aerospace vibration control, medical imaging, and noise reduction.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Creep Behavior and Phase Equilibria in Model Precipitate Strengthened Alumina-Forming Austenitic Alloys

Abstract Creep-rupture behavior and microstructural response in alumina-forming austenitic (AFA) alloys with two different precipitation strengthening mechanisms, “Laves-phase + M 23 C 6 carbide” and “coherent L1 2 γ′-Ni 3 (Al,Ti),” were explored as “model” cases of multi-phase, multi-scale heat-resistant AFA alloys for 650–750°C use. These alloys will be used to guide and verify computational alloy design and life-prediction modeling under an on-going eXtremeMAT project through the Office of Fossil Energy and Carbon Management, US Department of Energy. Computational thermodynamics were used to design and predict the amounts of strengthening and deteriorating secondary phases at 750°C. Creep-rupture lives of the alloys tested at 750°C and 100 MPa were in a range of 4000–9000 h, and the microstructure at the gage/grip after creep-rupture testing was compared with isothermally aged alloys for 1500 h, as well as the calculated phases. Detailed microstructure characterization includes phase identification, volume fraction measurement, and compositional analysis, which were correlated with the creep-rupture properties. High-temperature oxidation resistance was also screened and compared with commercial, chromia-forming heat-resistant steels. These model alloys also provide the basis for further design and optimization of next generation AFA alloys with improved creep resistance.

36 MATERIALS SCIENCE↗
DOE OSTI2020

The impact of the fiducial cosmology assumption on BAO distance scale measurements

ABSTRACT Standard analysis pipelines for measurements of Baryon Acoustic Oscillations (BAO) in galaxy surveys make use of a fiducial cosmological model to guide the data compression required to transform from observed redshifts and angles to the measured angular and radial BAO peak positions. In order to remove any dependence on the fiducial cosmology from the results, all models compared to the data should mimic the compression and its dependence on the fiducial model. In practice, approximations are made when testing models: (1) There is assumed to be no residual dependence on the fiducial cosmology after reconstruction, (2) differences in the distance–redshift relationship are assumed to match a linear scaling, and (3) differences in clustering between true and fiducial models are assumed to be removed by the free parameters used to null the non-BAO signal. We test these approximations using the current standard measurement procedure with a set of halo catalogues from the aemulus suite of N-body simulations, which span a range of wCDM cosmological models. We focus on reconstruction of the primordial BAO and locating the BAO. For the range of wCDM cosmologies covered by the aemulus suite, we find no evidence for systematic errors in the measured BAO shift parameters α∥ and α⊥ to $\lt 0.1\%$. However, the measured errors $\sigma _{\alpha _{\parallel }}$ and $\sigma _{\alpha _{\bot }}$ show a notable absolute increase by up to +0.001 and +0.002, respectively, in the case that the fiducial cosmology does not match the truth. These effects on the inferred BAO scale will be important, given the precision of measurements expected from future surveys including DESI, Euclid, and WFIRST.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Deep Reinforcement Learning Based Volt-VAR Optimization in Smart Distribution Systems

This paper develops a model-free volt-VAR optimization (VVO) algorithm via multi-agent deep reinforcement learning (DRL) in unbalanced distribution systems. This method is novel since we cast the VVO problem in distribution networks to an intelligent deep Q-network (DQN) framework, which avoids solving a specific optimization model directly when facing time-varying operating conditions in the systems. We consider statuses/ratios of switchable capacitors, voltage regulators, and smart inverters installed at distributed generators as the action variables of the agents. A delicately designed reward function guides these agents to interact with the distribution system, in the direction of reinforcing voltage regulation and power loss reduction simultaneously. The forward-backward sweep method for radial three-phase distribution systems provides accurate power flow results within a few iterations to the DRL environment. The proposed method realizes the dual goals for VVO. We test this algorithm on the unbalanced IEEE 13-bus and 123-bus systems. Numerical simulations validate the excellent performance of this method in voltage regulation and power loss reduction.

41 EE - Solar Energy Technologies Office (EE-4S)↗
DOE OSTI2023

Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome

Metaproteomics, a method for untargeted, high-throughput identification of proteins in complex samples, provides functional information about microbial communities and can tie functions to specific taxa. Metaproteomics often generates less data than other omics techniques, but analytical workflows can be improved to increase usable data in metaproteomic outputs. Identification of peptides in the metaproteomic analysis is performed by comparing mass spectra of sample peptides to a reference database of protein sequences. Although these protein databases are an integral part of the metaproteomic analysis, few studies have explored how database composition impacts peptide identification. Here, we used cervicovaginal lavage (CVL) samples from a study of bacterial vaginosis (BV) to compare the performance of databases built using six different strategies. We evaluated broad versus sample-matched databases, as well as databases populated with proteins translated from metagenomic sequencing of the same samples versus sequences from public repositories. Smaller sample-matched databases performed significantly better, driven by the statistical constraints on large databases. Additionally, large databases attributed up to 34% of significant bacterial hits to taxa absent from the sample, as determined orthogonally by 16S rRNA gene sequencing. We also tested a set of hybrid databases which included bacterial proteins from NCBI RefSeq and translated bacterial genes from the samples. These hybrid databases had the best overall performance, identifying 1,068 unique human and 1,418 unique bacterial proteins, ~30% more than a database populated with proteins from typical vaginal bacteria and fungi. Our findings can help guide the optimal identification of proteins while maintaining statistical power for reaching biological conclusions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Real-Time Health Monitoring for Gas Turbine Components Using Online Learning and High-Dimensional Data

Capital-intensive turbomachinery, such as gas turbines and combined cycle plants, are constantly being monitored for performance anomalies, faults, and physical degradation. Although these power-generating assets are equipped with hundreds of sensors, existing monitoring tools can only handle moderate-sized data. As a result, only a handful of aggregate metrics are used to monitor machine health. At the same time, developing advanced tools suitable for large datasets have been restricted by the lack of appropriate data. The objective of this proposal was to demonstrate a Big Data analytics framework for fault detection and diagnosis in gas turbine applications. We develop a predictive analytics framework methodology guided by these experimental data, industrial data from our collaborators, and physics-based models with engineering domain knowledge. Our analytics framework consists of four key components (1) a data curation process that addresses data storage, data quality assessments, and integrity checks, (2) a feature engineering component that utilizes statistical methods and transformation algorithms guided by physics-based models to extract high-fidelity fault features that can be leveraged for fault detection and classifying fault severities, (3) a Machine Learning-based fault detection and diagnostics algorithms for detecting operational and hardware faults in the combustion and the turbines section. We utilize two industry-class gas turbine component test rigs to generate first of its kind data for critical gas turbine faults with varying severity levels. Advanced gas turbine test facilities will be interrogated using state-of-the-art instrumentation techniques to build fault signatures and data trends for key combustor and turbine faults. Data generated from a combustor test rig (Georgia Tech) and a turbine test rig (Penn State) during both normal operation and with seeded faults serve as the basis for the Big Data sets. The test conditions in the two test facilities include common, critical events that occur in the operation. Utilizing the combustor test rig, we examine two common combustor faults: lean blowout and centerbody degradation. For the turbine section we develop analytic models for monitoring cooling faults in the gas turbine

03 NATURAL GAS↗
DOE OSTI2024

Complete Development of Critical Capabilities for TRISO Fission Product Source Term Calculations and Quantify Mechanisms for Pd Penetration of SiC

Overall fission product (FP) release will be an important consideration for the licensing and deployment of advanced reactors utilizing tristructural isotropic (TRISO) fuels. This work focuses on enhancing and applying the BISON models needed to predict FP transport within TRISO particles and particle failure probability, both of which factor directly into release predictions. Specifically, this report details (1) the development of the models needed to predict palladium (Pd) conservation at the engineering scale and the application of those models to characterize Pd fluxes for input into a mechanistic multiscale model for Pd penetration; (2) the refinement of sorption mass transfer models and the development of models for trapping in porous layers, which were applied and compared to particle scans from AGR-2 to provide proof of concept for a method of particle-scale validation that may reduce uncertainties compared to compact-scale validation using data from integral effects tests; (3) the development of a failure-statistics-informed, mesh-independent methodology for applying smeared cracking, enabling further study of the localized multiphysics behaviors associated with cascading particle failure mechanisms; and (4) the preliminary characterization of those coupled multiphysics particle failure behaviors using smeared, nonretentive diffusivities to provide a baseline for future study and to guide ongoing engineering applications.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Real-Time Health Monitoring for Gas Turbine Components Using Online Learning and High-Dimensional Data (Final Report)

Capital-intensive turbomachinery, such as gas turbines and combined cycle plants, are constantly being monitored for performance anomalies, faults, and physical degradation. Although these power-generating assets are equipped with hundreds of sensors, existing monitoring tools can only handle moderate-sized data. As a result, only a handful of aggregate metrics are used to monitor machine health. At the same time, developing advanced tools suitable for large datasets have been restricted by the lack of appropriate data. The objective of this proposal was to demonstrate a Big Data analytics framework for fault detection and diagnosis in gas turbine applications. We develop a predictive analytics framework methodology guided by these experimental data, industrial data from our collaborators, and physics-based models with engineering domain knowledge. Our analytics framework consists of four key components: (1) a data curation process that addresses data storage, data quality assessments, and integrity checks, (2) a feature engineering component that utilizes statistical methods and transformation algorithms guided by physics-based models to extract high-fidelity fault features that can be leveraged for fault detection and classifying fault severities, (3) a Machine Learning-based fault detection and diagnostics algorithms for detecting operational and hardware faults in the combustion and the turbines section. We utilize two industry-class gas turbine component test rigs to generate first of its kind data for critical gas turbine faults with varying severity levels. Advanced gas turbine test facilities will be interrogated using state-of-the-art instrumentation techniques to build fault signatures and data trends for key combustor and turbine faults. Data generated from a combustor test rig (Georgia Tech) and a turbine test rig (Penn State) during both normal operation and with seeded faults serve as the basis for the Big Data sets. The test conditions in the two test facilities include common, critical events that occur in the operation. Utilizing the combustor test rig, we examine two common combustor faults: lean blowout and centerbody degradation. For the turbine section we develop analytic models for monitoring cooling faults in the gas turbine.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2025

Development of Innovative Non-Concentrated Alloy (NCA) Fuel Cladding for Advanced Nuclear Reactors

As the nuclear energy sector advances toward next-generation reactors, the need for high-performance fuel cladding materials has become increasingly urgent. Traditional alloys like zirconium and stainless steel are reaching their performance limits under higher temperatures, more corrosive coolants, and extended irradiation. This report presents the development of a new class of fuel cladding materials based on Non-Concentrated Alloys (NCAs) ? multi-element systems designed to deliver enhanced mechanical strength, corrosion resistance, and radiation tolerance. Through a combination of computational modeling (Computer Coupling of Phase Diagrams and Thermochemistry: CALPHAD), simulation-guided alloy selection, and experimental fabrication via arc melting and spark plasma sintering (SPS), three strategic alloy design paths were explored: (1) FeCrAl-based NCAs, (2) refractory-lean neutron-efficient alloys, and (3) equimolar high-entropy compositions. Microstructural analysis confirmed the formation of stable body-centered cubic BCC_A2 phases, while mechanical testing demonstrated hardness values significantly exceeding those of conventional cladding materials. The results highlight the tunability of NCA systems and their potential for balancing strength and ductility ? a critical consideration for in-reactor performance. Looking forward, future work will focus on thermomechanical optimization, CALPHAD refinement, and benchmarking against industry standards to enable scalable deployment. This work not only advances the science of nuclear materials but also supports broader goals in nuclear safety, performance, and nuclear energy innovation.

36 - MATERIALS SCIENCE↗
DOE OSTI2023

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Quantifying particle movement in a spout-fluidized bed with irregular feedstock morphology

Here, the spout-bed fluidization behavior of nonspherical, 140 μm SiC feedstock was quantified via particle image velocimetry for varying gas distributor geometries. A bench-scale, room-temperature fluidization setup was assembled to model a 50 mm fluidized bed chemical vapor deposition (FB-CVD) system, and fluidized bed motion was captured using a high-speed camera. Modular tips with varying inlet geometries were 3D printed and tested on the bench-scale rig using identical feedstock and gas flow rates in the range of 3.0–9.0 L/min. Fluidization behavior was quantified by extracting parameters of the bed velocity, frequency, dead time, and other measurements, which were ranked for each inlet geometry configuration tested. The results from this work demonstrate that changing the path of inlet gas flow can significantly change the hydrodynamics within a spout-fluidized bed under identical feedstock, loading, and flow rate conditions, potentially enabling experimental control of particle fluidization behavior for a given condition. Moreover, composite rankings of fluidization behavior for unique distributor geometries hold potential to guide the design of FB-CVD experiments for various engineering and scientific applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Hydrodynamic Test Requirements Process Improvements

Hydrodynamic testing at Los Alamos National Laboratory would benefit from a process improvement for the requirements process. Cameo was used as a digital solution for requirements management to allow Lead Engineers to track requirements more effectively. This was identified as a process improvement throughout this Capstone project. This report includes a project proposal, business case, literature review, methodology, project plan, data analysis, decision-making report, financial analysis report, discussion, and conclusion. Initially, this project focused on figuring out a solution for the hydrotest requirement process improvements. The scope narrowed to focus on the use of Cameo for requirement capture and management. During this Capstone, four tests had digital models produced for requirements management in Cameo. The initial model was the baseline, with core requirements used across the tests. Commonalities in tests were used and the core requirements allowed for process efficiencies. In the data analysis, it was seen that overall, the implementation of using Cameo for requirements resulted in a decreasing trend for both schedule and normalized cost. Tests have different complexity levels which is also a factor in how long the requirements process will take. Additional data is needed to continue analyzing process improvements. Through decisionmaking and financial analysis, the recommendation was to use Cameo for requirements process improvement. Multiple experts provided feedback for requirements that were then captured within models. Numerous tangible and intangible benefits were identified with this process improvement. For return on investment, the metric of success was schedule reduction, which was overall seen. Four tests were analyzed, so future analysis will be needed. There is also not a great financial risk because the main cost would be purchasing more licenses. Individuals must generate requirements whether using this software or not. Overall, training is needed to help improve the skillsets of Lead Engineers but is already being supported on a regular frequency. A desktop guide was started associated with explaining the process, however, it is a work in progress. The team plans on adding additional information in the digital models to help status when requirements are met using verification methods and artifacts. From working on this project an improved understanding of Cameo and requirements was the result. There are future opportunities to extend the usage for requirements management and progress will continue after this project.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2026

Pennsylvania and Delaware Energy Code Field Studies (Final Technical Report (FTR)

Led by Northeast Energy Efficiency Partnerships (NEEP) in partnership with Performance Systems Development (PSD), the project aimed to conduct energy code compliance field studies for single-family residential buildings in Pennsylvania and Delaware, as well as multifamily and commercial buildings in Pennsylvania. Using U.S. Department of Energy (DOE) approved methodologies, trained field teams conducted on-site observations and testing to document compliance with key energy efficiency measures, including building envelope insulation, air sealing, duct leakage, windows, and mechanical systems. Data from these studies would then be analyzed to identify construction trends and compliance gaps. The goals included published baseline data for each study, and a training roadmap tailored to each state’s needs. This roadmap would have guided outreach and training for builders, code officials, and other stakeholders on the specific code requirements that offered the greatest opportunity for improvement.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers

Abstract Motivation Deep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accuracy of predicting quaternary structures of protein complexes consisting of multiple chains is still relatively low due to lack of advanced deep learning methods in the field. Because interchain residue–residue contacts can be used as distance restraints to guide quaternary structure modeling, here we develop a deep dilated convolutional residual network method (DRCon) to predict interchain residue–residue contacts in homodimers from residue–residue co-evolutionary signals derived from multiple sequence alignments of monomers, intrachain residue–residue contacts of monomers extracted from true/predicted tertiary structures or predicted by deep learning, and other sequence and structural features. Results Tested on three homodimer test datasets (Homo_std dataset, DeepHomo dataset and CASP-CAPRI dataset), the precision of DRCon for top L/5 interchain contact predictions (L: length of monomer in a homodimer) is 43.46%, 47.10% and 33.50% respectively at 6 Å contact threshold, which is substantially better than DeepHomo and DNCON2_inter and similar to Glinter. Moreover, our experiments demonstrate that using predicted tertiary structure or intrachain contacts of monomers in the unbound state as input, DRCon still performs well, even though its accuracy is lower than using true tertiary structures in the bound state are used as input. Finally, our case study shows that good interchain contact predictions can be used to build high-accuracy quaternary structure models of homodimers. Availability and implementation The source code of DRCon is available at https://github.com/jianlin-cheng/DRCon. The datasets are available at https://zenodo.org/record/5998532#.YgF70vXMKsB. Supplementary information Supplementary data are available at Bioinformatics online.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Developing Multi-Gene CRISPRa/I Programs to Accelerate DBTL Cycles in ABF Hosts Engineered for Chemical Production (CRADA 468)

Bacterial metabolism is comprised of large and complex gene networks that can produce valuable chemical products. Sophisticated organism engineering efforts are required to optimize production of high-value compounds from these networks. In principle, synthetic multi-gene transcriptional programs could be constructed to reengineer these networks for efficient industrial chemical production. In practice, however, our incomplete ability to understand and model the underlying networks, combined with our limited ability to predictably control the expression of multiple genes makes achieving this goal difficult. To overcome these challenges, we will combine new CRISPR-Cas multi-gene expression programs with computational modeling, machine learning, and multi-omics data to enhance the efficacy of design-build-test-learn (DBTL) cycles. For industrially promising microorganisms in early stages of development, creating technologies for rapidly engineering complex multi-gene programs could be transformative for accelerating data- and model-driven strain design. New CRISPR-Cas tools allow programmable gene activation (CRISPRa) or repression (CRISPRi) at multiple genes simultaneously, using the catalytically inactive Cas9 protein (dCas9) with guide RNAs that recognize DNA targets through predictable Watson-Crick base pairing. To enable accelerated DBTL cycles, we will combine these technologies with advanced Agile BioFoundry (ABF) capabilities for multi-omics data collection and machine learning. We will demonstrate the immediate applicability of these tools by rapidly improving the production of an industrial aromatic in multiple ABF organisms. We recently identified and optimized new transcriptional activators that can be linked to programmable CRISPR-Cas DNA binding domains to activate gene expression in E. coli. We can now use these CRISPRa tools as generalizable trans-acting regulators for combinatorial multi-gene expression tuning that can be easily transferred to new pathways and networks without additional genome engineering. We anticipate these tools will also transfer to new hosts. We have recently found that CRISPRa systems developed in E. coli can be readily ported to Pseudomonas putida, suggesting that multi-gene CRISPRa/i programs for diverse ABF organisms may be within reach.

59 BASIC BIOLOGICAL SCIENCES↗