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At least 1,117 records · Page 62
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Accelerating discrete dislocation dynamics simulations with graph neural networks

Discrete dislocation dynamics (DDD) is a widely employed computational method to study plasticity at the mesoscale that connects the motion of dislocation lines to the macroscopic response of crystalline materials. However, the computational cost of DDD simulations remains a bottleneck that limits its range of applicability. Here, we introduce a new DDD-GNN framework in which the expensive time-integration of dislocation motion is entirely substituted by a graph neural network (GNN) model trained on DDD trajectories. As a first application, we demonstrate the feasibility and potential of our method on a simple yet relevant model of a dislocation line gliding through an array of obstacles. We show that the DDD-GNN model is stable and reproduces very well unseen ground-truth DDD simulation responses for a range of straining rates and obstacle densities, without the need to explicitly compute nodal forces or dislocation mobilities during time-integration. Our approach opens new promising avenues to accelerate DDD simulations and to incorporate more complex dislocation motion behaviors.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Performance Evaluation of Comparative Vacuum Monitoring and Piezoelectric Sensors for Structural Health Monitoring of Rotorcraft Components

The costs associated with the increasing maintenance and surveillance needs of aging structures are rising at an unexpected rate. Multi-site fatigue damage, hidden cracks in hard-to-reach locations, disbonded joints, erosion, impact, and corrosion are among the major flaws encountered in today’s extensive fleet of aging aircraft and space vehicles. Aircraft maintenance and repairs represent about a quarter of a commercial fleet’s operating costs. The application of Structural Health Monitoring (SHM) systems using distributed sensor networks can reduce these costs by facilitating rapid and global assessments of structural integrity. The use of in-situ sensors for real-time health monitoring can overcome inspection impediments stemming from accessibility limitations, complex geometries, and the location and depth of hidden damage. Reliable, structural health monitoring systems can automatically process data, assess structural condition, and signal the need for human intervention. The ease of monitoring an entire on-board network of distributed sensors means that structural health assessments can occur more often, allowing operators to be even more vigilant with respect to flaw onset. SHM systems also allow for condition-based maintenance practices to be substituted for the current time-based or cycle-based maintenance approach thus optimizing maintenance labor. The Federal Aviation Administration has conducted a series of SHM validation and certification programs intended to comprehensively support the evolution and adoption of SHM practices into routine aircraft maintenance practices. This report presents one of those programs involving a Sandia Labs-aviation industry effort to move SHM into routine use for aircraft maintenance. The Airworthiness Assurance NDI Validation Center (AANC) at Sandia Labs, in conjunction with Sikorsky, Structural Monitoring Systems Ltd., Anodyne Electronics Manufacturing Corp., Acellent Technologies Inc., and the Federal Aviation Administration (FAA) carried out a trial validation and certification program to evaluate Comparative Vacuum Monitoring (CVM) and Piezoelectric Transducers (PZT) as a structural health monitoring solution to specific rotorcraft applications. Validation tasks were designed to address the SHM equipment, the health monitoring task, the resolution required, the sensor interrogation procedures, the conditions under which the monitoring will occur, the potential inspector population, adoption of CVM and PZT systems into rotorcraft maintenance programs and the document revisions necessary to allow for their routine use as an alternate means of performing periodic structural inspections. This program addressed formal SHM technology validation and certification issues so that the full spectrum of concerns, including design, deployment, performance and certification were appropriately considered. Sandia Labs designed, implemented, and analyzed the results from a focused and statistically relevant experimental effort to quantify the reliability of a CVM system applied to Sikorsky S-92 fuselage frame application and a PZT system applied to an S-92 main gearbox mount beam application. The applications included both local and global damage detection assessments. All factors that affect SHM sensitivity were included in this program: flaw size, shape, orientation and location relative to the sensors, as well as operational and environmental variables. Statistical methods were applied to performance data to derive Probability of Detection (POD) values for SHM sensors in a manner that agrees with current nondestructive inspection (NDI) validation requirements and is acceptable to both the aviation industry and regulatory bodies. The validation work completed in this program demonstrated the ability of both CVM and PZT SHM systems to detect cracks in rotorcraft components. It proved the ability to use final system response parameters to provide a Green Light/Red Light (“GO” – “NO GO”) decision on the presence of damage. In additional to quantifying the performance of each SHM system for the trial applications on the S-92 platform, this study also identified specific methods that can be used to optimize damage detection, guidance on deployment scenarios that can affect performance and considerations that must be made to properly apply CVM and PZT sensors. These results support the main goal of safely integrating SHM sensors into rotorcraft maintenance programs. Additional benefits from deploying rotorcraft Health and Usage Monitoring Systems (HUMS) may be realized when structural assessment data, collected by an SHM system, is also used to detect structural damage to compliment the operational environment monitoring. The use of in-situ sensors for health monitoring of rotorcraft structures can be a viable option for both flaw detection and maintenance planning activities. This formal SHM validation will allow aircraft manufacturers and airlines to confidently make informed decisions about the proper utilization of CVM and PZT technology. It will also streamline future regulatory actions and formal certification measures needed to assure the safe application of SHM solutions.

42 ENGINEERING↗
DOE OSTI2026

A Systematic Review on Coordinated Restoration Strategies for Power Distribution Grids

Power distribution grids are increasingly exposed to High-Impact Low-Probability (HILP) events, which cause widespread disruptions with severe societal and economic impacts. The growing complexity of modern grids, driven by the integration of distributed energy resources and smart grid technologies, has introduced new challenges to effective service restoration. While significant research has explored individual restoration strategies, such as network reconfiguration and microgrid formation, limited attention has been given to methods in which they can be effectively coordinated. Furthermore, the absence of systematic review papers addressing this issue hampers the development of cohesive restoration frameworks capable of addressing the operational complexities of modern grids. This paper presents a systematic review synthesizing existing knowledge on power grid restoration, identifying key limitations, and highlighting opportunities for coordinated strategies. By addressing research gaps and emphasizing the integration of diverse approaches, this study provides critical insights for advancing grid resiliency and recovery, offering a foundation for future research and practical applications in the face of HILP events.

Systematic review↗
DOE OSTI2022

Distributed deep learning training using silicon photonic switched architectures

The scaling trends of deep learning models and distributed training workloads are challenging network capacities in today’s datacenters and high-performance computing (HPC) systems. We propose a system architecture that leverages silicon photonic (SiP) switch-enabled server regrouping using bandwidth steering to tackle the challenges and accelerate distributed deep learning training. In addition, our proposed system architecture utilizes a highly integrated operating system-based SiP switch control scheme to reduce implementation complexity. To demonstrate the feasibility of our proposal, we built an experimental testbed with a SiP switch-enabled reconfigurable fat tree topology and evaluated the network performance of distributed ring all-reduce and parameter server workloads. The experimental results show up to 3.6× improvements over the static non-reconfigurable fat tree. Our large-scale simulation results show that server regrouping can deliver up to 2.3× flow throughput improvement for a 2× tapered fat tree and a further 11% improvement when higher-layer bandwidth steering is employed. The collective results show the potential of integrating SiP switches into datacenters and HPC systems to accelerate distributed deep learning training.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Tetris-inspired detector with neural network for radiation mapping

Abstract Radiation mapping has attracted widespread research attention and increased public concerns on environmental monitoring. Regarding materials and their configurations, radiation detectors have been developed to identify the position and strength of the radioactive sources. However, due to the complex mechanisms of radiation-matter interaction and data limitation, high-performance and low-cost radiation mapping is still challenging. Here, we present a radiation mapping framework using Tetris-inspired detector pixels. Applying inter-pixel padding for enhancing contrast between pixels and neural networks trained with Monte Carlo (MC) simulation data, a detector with as few as four pixels can achieve high-resolution directional prediction. A moving detector with Maximum a Posteriori (MAP) further achieved radiation position localization. Field testing with a simple detector has verified the capability of the MAP method for source localization. Our framework offers an avenue for high-quality radiation mapping with simple detector configurations and is anticipated to be deployed for real-world radiation detection.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Non-conformal interface-cohesive modeling with the shifted boundary method

The accurate simulation of boundary- and interface-dominated problems on complex geometries remains challenging when boundary- or interface-fitted meshes are difficult to generate, particularly for curved boundaries, polycrystalline microstructures, and dense interface networks. The Shifted Boundary Method (SBM) alleviates this meshing burden by shifting the enforcement of boundary conditions from the true boundary to a nearby surrogate boundary and recovering the effect of the true boundary through geometric correction terms, thereby enabling standard finite element spaces on non-boundary-fitted meshes. In this report, we develop a general shiftedboundary and shifted-interface framework within the open-source MOOSE framework. We first present a general SBM implementation for complex geometries on non-boundary-fitted meshes. We then adopt the Shifted Interface Method (SIM) for internal interfaces and develop a unified shifted-interface treatment in which the interface law is enforced on a surrogate interface and the effect of the true interface is recovered through shifted jumps, fluxes, and tractions. This perspective brings scalar thermal-contact and vector-valued cohesive-zone mechanics into a single framework, the latter realized as the Shifted Cohesive Zone Method (SCZM) and coupled with history-dependent constitutive models from NEML2. We further extend the MOOSE mesh infrastructure to support cohesive-zone calculations on distributed meshes. The framework is verified and demonstrated through three progressive studies: Poisson’s equation on a smoothed starshaped domain, a manufactured thermal-contact problem on a non-interface-fitted mesh, and a two-dimensional polycrystalline representative volume element combining crystal plasticity with cohesive grain-boundary interfaces. Across these studies, the shifted formulations reproduce boundary- and interface-fitted reference solutions with high fidelity, indicating that the proposed framework provides an accurate and efficient route to boundary- and interface-dominated simulations on arbitrary geometries without requiring fitted meshes.

Yang, Cheng-Hau↗
DOE OSTI2025

Deployment of neural-network-based neutron microscopic cross sections in the Griffin reactor physics application

The capability to utilize neural networks to predict macroscopic and microscopic cross section parametric spaces has been developed for the Griffin reactor physics application. The LibTorch interface enables Griffin's MOOSE-based materials to interact with LibTorch-trained models, allowing for the evaluation of complex macroscopic or microscopic cross section spaces, which are then used to evaluate the neutronic properties of the Griffin finite element model. This study benchmarks traditional ISOXML-formatted tabulation libraries against neural network-based models for 279 nuclides on 20,160 grid points for zero-dimensional and two-dimensional reactor models. Benchmark metrics include the fundamental mode eigenvalue, fission and absorption rates, and various temperature coefficients of reactivity (isothermal, fuel, and moderator). From the perspective of storage space, the complete set of LibTorch models uses 11 MB on disk, compared to the 10 GB for the ISOXML multigroup library that covers the same grid space. For the two-dimensional performance case considered in Griffin, the Torch model uses 97% less RAM than the reference ISOXML dataset while runtime increases by a factor of 3 when using the LibTorch model compared to the ISOXML dataset with multi-linear interpolation. The LibTorch model consistently yields errors within 0.01% for most analyzed quantities except for the temperature coefficients of reactivity where the maximum discrepancies are up to 0.3 $\frac{pcm}{K}$. Due to the neural network attempting to best predict quantities with no regard for a positive or negative bias for any given quantity, predictions may experience random fluctuations, resulting in both positive and negative errors. Future work will entail both depletion and coupled transient analysis to determine the predictive capabilities of Griffin with neural network-based cross sections.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2020

A neural network for determination of latent dimensionality in Nonnegative Matrix Factorization

Non-negative Matrix Factorization (NMF) has proven to be a powerful unsupervised learning method for uncovering hidden features in complex and noisy datasets with applications in data mining, text recognition, dimension reduction, face recognition, anomaly detection, blind source separation, and many other fields. An important input for NMF is the latent dimensionality of the data, that is, the number of hidden features, K, present in the explored dataset. Unfortunately, and this quantity is rarely known a priori. The existing methods for determining latent dimensionality, such as Automatic Relevance Determination (ARD), are mostly heuristic and utilize different characteristics to estimate the number of hidden features. However, all of them require human presence to make a final determination of K. Here we utilize a supervised machine learning approach in combination with a recent method for model determination, called NMFk, to determine the number of hidden features automatically. NMFk performs a set of NMF simulations on an ensemble of matrices, obtained by bootstrapping the initial dataset, and estimates which K produces stable groups of latent features that reconstruct the initial dataset well. We then train a Multi-Layter Perceptron (MLP) classifier network to determine the correct number of latent features utilizing the statistics and characteristics of the NMF solution, obtained from NMFk. In order to train the MLP classifier, a training set of 58,660 matrices with predetermined latent features were factorized with NMFk. The MLP classifier in conjunction with NMFk maintains a greater than 95% success rate when applied to a held out test set. Additionally, when applied to two well-known benchmark datasets, the swimmer and MIT face data, NMFk/MLP correctly recovers the established number of hidden features. Finally, we compare the accuracy of our method to the ARD, AIC and Stability-based methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Exploring Classification of Topological Priors With Machine Learning for Feature Extraction

In many scientific endeavors, increasingly abstract representations of data allow for new interpretive methodologies and conceptualization of phenomena. For example, moving from raw imaged pixels to segmented and reconstructed objects allows researchers new insights and means to direct their studies toward relevant areas. Thus, the development of new and improved methods for segmentation remains an active area of research. With advances in machine learning and neural networks, scientists have been focused on employing deep neural networks such as U-Net to obtain pixel-level segmentations, namely, defining associations between pixels and corresponding/referent objects and gathering those objects afterward. Topological analysis, such as the use of the Morse-Smale complex to encode regions of uniform gradient flow behavior, offers an alternative approach: first, create geometric priors, and then apply machine learning to classify. This approach is empirically motivated since phenomena of interest often appear as subsets of topological priors in many applications. Using topological elements not only reduces the learning space but also introduces the ability to use learnable geometries and connectivity to aid the classification of the segmentation target. Here, in this article, we describe an approach to creating learnable topological elements, explore the application of ML techniques to classification tasks in a number of areas, and demonstrate this approach as a viable alternative to pixel-level classification, with similar accuracy, improved execution time, and requiring marginal training data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Biobased Semi-Interpenetrating Polymer Networks of Poly(ε-caprolactone) and Epoxidized Soybean Oil with Nanoscale Morphology, Shape-Memory Effect, and Biocompatibility

Creating biobased polymer blends with outstanding properties, nanoscale morphology, shape-memory capability, and biocompatibility is very crucial and requires a fundamental understanding of the phase behavior, macromolecular structure, and biological compatibility of the polymer blends with living cells. It is very critical to understand the complex relationships among the polymer structure, morphology, and performance of multifunctional smart materials under conditions that they are likely to encounter during use, particularly in biomedical applications. Biobased semi-interpenetrating polymer networks of poly(ε-caprolactone) and epoxidized soybean oil with nanoscale morphology have been successfully synthesized via in situ cationic polymerization and compatibilization in a homogeneous solution. Varies analytical and characterization techniques, such as Fourier transform infrared spectroscopy, differential scanning calorimetry, dynamic mechanical analysis, transmission electron microscopy, X-ray scattering, cell toxicity, and shape-memory effects (SMEs), have been employed to understand the structure–properties relationship of these smart, biobased nanostructured polymer blends. The synthesized nano blends were nontoxic or biocompatible and supported attachment of human vein endothelial cells, showing their potential use in biomedical applications. The current versatile, low-cost strategy for synthesizing the nanoscale morphology of semi-interpenetrating polymer networks with SMEs and biocompatibility should be widely applicable for polymer systems. This study is also considered as a continuation to our efforts in the area of biobased polymers to develop innovative technologies to transform natural resources into smart multifunctional materials for a wide range of applications, including coatings, adhesives, and medical devices.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Universal progression of structure and dynamics in colloidal nanocrystal gels during salt-accelerated aging

Controlling the structure and function of colloidal gels requires a detailed understanding of how the various components govern network formation and aging. In particular, molecular additives like salts are widely used to tune interparticle interactions, yet their influence on gelation pathways in complex systems such as colloidal nanocrystal gels remains inadequately understood. Here, we investigate how noncoordinating salts modulate the evolution of gels formed using chemically linked tin-doped indium oxide nanocrystals. Through combined structural, dynamic, and kinetic analyses, we demonstrate that increasing salt concentration accelerates gelation. When rescaled by salt-dependent characteristic times, the evolution collapses onto universal trajectories, revealing a time-salt superposition principle. The universality extends across length scales, suggesting a consistent salt-dependent mechanism that controls both local structuring and macroscopic network formation. This observed salt modulation of structure and dynamics provides a predictive basis for controlling the kinetics of nonequilibrium nanocrystal gel assembly, enhancing the rational design of functional nanomaterials with tunable properties.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Attention-based 3D – convolutional neural network model for mechanical property predictions using visible light images in metal additive manufacturing

Additive manufacturing (AM), while commonly used for rapid prototyping and creating components with complex geometries, has not been widely adopted for critical applications across the aerospace, automotive, defense, energy, and medical industries. This is, in part, due to the challenges of controlling flaws and uncertainty in the mechanical behavior of additively manufactured components. In recent years, there has been an increase in research aimed at predicting the final mechanical properties of additively manufactured components during the printing process. To address these issues, a 3D-CNN model was trained using low-cost in situ visible-light camera data, anomaly classifications, and the chosen process parameters to predict the ultimate tensile strength (UTS), yield strength (YS), total elongation (TE), and uniform elongation (UE). The 3D-CNN layers of the model employed attention mechanisms to prioritize features in the data, thereby improving prediction accuracy. Furthermore, the effect of each process parameter and anomaly class is investigated using attention-based dynamic sigmoid weighted gates to interpret the influence each class has on the final prediction. Different combinations of the in situ data were fed into the 3D-CNN, with varying amounts of image layers, to determine the ideal combination for predicting mechanical properties in situ. Here, the 3D-CNN model achieved mean absolute percentage errors (MAPE) below 5% for both UTS and YS while using only a single camera input and under half of the available image layers.

36 MATERIALS SCIENCE↗
DOE OSTI2026

PopGNN: Graph Neural Network-Based Flexible Future Population Forecasting Model

Accurate population forecasts is important to plan critical infrastructure and services, from housing and education to healthcare and transport. However, traditional population prediction studies have only employed traditional machine learning models limited to capture complex spatial interdependencies and patterns. Althogh recently computer vision-based framework was introduced with with promising accuracy, it has critical limitations for real-world planning applications: it function only at fixed spatial resolutions, restricting their use in diverse boundaries such as census tracts, neighborhoods, or administrative zones. Therefore, this study suggests a Graph Neural Network (GNN)-based population prediction framework, called PopGNN. This model recorded remarkable performance compared with state-of-the-art models and traditional baseline models in the grid and administrative boundaries. Furthermore, our framework achieved comparable predictive accuracy to a computer vision-based model in both the South Korea and Tennessee case studies. Consequently, this study is valuable in that a single model can provide accurate population forecasts that address diverse planning demands, ranging from granular grid-level estimates for precise service allocation and facility location planning to aggregate administrative-level forecasts for macro-scale regional policy and resource distribution.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Localization of proteins involved in the biogenesis and repair of the photosynthetic apparatus to thylakoid subdomains in Arabidopsis

Abstract Thylakoid membranes in chloroplasts and cyanobacteria harbor the multisubunit protein complexes that catalyze the light reactions of photosynthesis. In plant chloroplasts, the thylakoid membrane system comprises a highly organized network with several subcompartments that differ in composition and morphology: grana stacks, unstacked stromal lamellae, and grana margins at the interface between stacked and unstacked regions. The localization of components of the photosynthetic apparatus among these subcompartments has been well characterized. However, less is known about the localization of proteins involved in the biogenesis and repair of the photosynthetic apparatus, the partitioning of proteins between two recently resolved components of the traditional margin fraction (refined margins and curvature), and the effects of light on these features. In this study, we analyzed the partitioning of numerous thylakoid biogenesis and repair factors among grana, curvature, refined margin, and stromal lamellae fractions of Arabidopsis thylakoid membranes, comparing the results from illuminated and dark‐adapted plants. Several proteins previously shown to localize to a margin fraction partitioned in varying ways among the resolved curvature and refined margin fractions. For example, the ALB3 insertase and FtsH protease involved in photosystem II (PSII) repair were concentrated in the refined margin fraction, whereas TAT translocon subunits and proteins involved in early steps in photosystem assembly were concentrated in the curvature fraction. By contrast, two photosystem assembly factors that facilitate late assembly steps were depleted from the curvature fraction. The enrichment of the PSII subunit OE23/PsbP in the curvature fraction set it apart from other PSII subunits, supporting the previous conjecture that OE23/PsbP assists in PSII biogenesis and/or repair. The PSII assembly factor PAM68 partitioned differently among thylakoid fractions from dark‐adapted plants and illuminated plants and was the only analyzed protein to convincingly do so. These results demonstrate an unanticipated spatial heterogeneity of photosystem biogenesis and repair functions in thylakoid membranes and reveal the curvature fraction to be a focal point of early photosystem biogenesis.

Chotewutmontri, Prakitchai↗
DOE OSTI2020

A machine learning approach to fracture mechanics problems

Analytical and empirical solutions to engineering problems are usually preferred because of their convenience in applications. However, they are not always accessible in complex problems. A new class of solutions, based on machine learning (ML) models such as regression trees and neural networks (NNs), are proposed and their feasibility and value are demonstrated through the analysis of fracture toughness measurements. It is found that both solutions based on regression trees and NNs can provide accurate results for the specific problem, but NN-based solutions outperform regression-tree-based solutions in terms of their simplicity. Here this example demonstrates that ML solutions are a major improvement over analytical and empirical solutions in terms of both reliable functionality and rapid deployment. When analytical solutions are not available, the use of ML solutions can overcome the limitations of empirical solutions and substantially change the way that engineering problems are solved.

36 MATERIALS SCIENCE↗
DOE OSTI2025

HydroEcoLSTM: A Python package with graphical user interface for hydro-ecological modeling with long short-term memory neural network

Machine learning (ML) is emerging as a promising tool for modeling hydro-ecological processes due to the increasing availability of large environmental data. However, the use of ML requires sufficient programming knowledge due to a lack of a graphical user interface (GUI). In this study, we introduced a GUI package, named HydroEcoLSTM, with the long short-term memory network (LSTM) as the core model, that allows non-ML experts to utilize their domain knowledge to construct complex ML models. We demonstrated the functionalities of HydroEcoLSTM with two practical examples, including (1) predictions of streamflow in both gauged and ungauged catchments and (2) predictions of multiple outputs (i.e., streamflow and isotope transport from two catchments). The simulation results obtained in both case experiments are satisfactory. In the first example, the average Nash–Sutcliffe Efficiency (NSE) for streamflow simulation during the testing period is 0.79 while the application of the trained model in two assumed ungauged catchments also achieves the average NSE of 0.68. In the second example, the average NSE for streamflow and instream isotope simulation during the testing period is 0.71. Ultimately, applications of HydroEcoLSTM with real-world examples demonstrate its potential use for practical applications and research without requiring extensive coding skills.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Fracture Characterization Via AI‐Assisted Analysis of Temperature Logs

Abstract Fractures control fluid flow, mass transport, and heat transfer in a geothermal reservoir. This makes accurate characterization of fracture networks a prerequisite for optimal design and control of a reservoir's exploitation. We develop a deep‐learning procedure to identify fracture locations via interpretation of temporally and spatially continuous downhole temperature measurements. A long short‐term memory fully convolutional network (LSTM‐FCN) is used both to capture long‐term dependencies in sequential temperature data and to distill local features around fractures. A wellbore and fractured‐reservoir thermal model is established to generate temperature data for network training. The trained LSTM‐FCN exhibits a unique ability to detect multiple fractures intersecting a borehole. We use the LSTM‐FCN algorithm to evaluate the effectiveness of different‐stage wellbore temperature measurements on fracture detection in a complex fractured system. Our experiments reveal that the use of various‐stage temperature information as an input feature set improves the robustness of fracture detection to noise interference. This study indicates the practical feasibility of obtaining accurate fracture‐network reconstructions from temperature signals, at reasonable computational cost.

Yang, Xiaoyu↗
DOE OSTI2022

AF2Complex predicts direct physical interactions in multimeric proteins with deep learning

Abstract Accurate descriptions of protein-protein interactions are essential for understanding biological systems. Remarkably accurate atomic structures have been recently computed for individual proteins by AlphaFold2 (AF2). Here, we demonstrate that the same neural network models from AF2 developed for single protein sequences can be adapted to predict the structures of multimeric protein complexes without retraining. In contrast to common approaches, our method, AF2Complex, does not require paired multiple sequence alignments. It achieves higher accuracy than some complex protein-protein docking strategies and provides a significant improvement over AF-Multimer, a development of AlphaFold for multimeric proteins. Moreover, we introduce metrics for predicting direct protein-protein interactions between arbitrary protein pairs and validate AF2Complex on some challenging benchmark sets and the E. coli proteome. Lastly, using the cytochrome c biogenesis system I as an example, we present high-confidence models of three sought-after assemblies formed by eight members of this system.

59 BASIC BIOLOGICAL SCIENCES↗