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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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Optimization of binding affinities for compounds to their target protein is a primary objective in drug discovery. Herein we report on a collaborative study that evaluates a set of compounds binding to ROS1 kinase. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to rank the binding free energies. The predicted binding free energies from ESMACS simulations show good correlations with experimental data for subsets of the compounds. Consistent binding free energy differences are generated for TIES and ESMACS. Although an unexplained overestimation exists, we obtain excellent statistical rankings across the set of compounds from the TIES protocol, with a Pearson correlation coefficient of 0.90 between calculated and experimental activities.

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

Neural network representation of electronic structure from ab initio molecular dynamics

Despite their rich information content, electronic structure data amassed at high volumes in ab initio molecular dynamics simulations are generally under-utilized. Here we introduce a transferable high-fidelity neural network representation of such data in the form of tight-binding Hamiltonians for crystalline materials. This predictive representation of ab initio electronic structure, combined with machine-learning boosted molecular dynamics, enables efficient and accurate electronic evolution and sampling. When it is applied to a one-dimension charge-density wave material, carbyne, we are able to compute the spectral function and optical conductivity in the canonical ensemble. The spectral functions evaluated during soliton-antisoliton pair annihilation process reveal significant renormalization of low-energy edge modes due to retarded electron-lattice coupling beyond the Born–Oppenheimer limit. The availability of an efficient and reusable surrogate model for the electronic structure dynamical system will enable calculating many interesting physical properties, paving the way to previously inaccessible or challenging avenues in materials modeling.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

Advanced Semi-Supervised Learning with Uncertainty Estimation for Phase Identification in Distribution Systems

The integration of advanced metering infrastructure (AMI) into power distribution networks generates valuable data for tasks such as phase identification; however, the limited and unreliable availability of labeled data in the form of customer phase connectivity presents challenges. To address this issue, we propose a semi-supervised learning (SSL) framework that effectively leverages labeled and unlabeled data. Our approach incorporates self-training, label spreading, and Bayesian neural networks (BNNs) to enhance phase identification with AMI data. Our method uses an ensemble of multilayer perceptron classifiers in a self-training setup, iteratively adding high-confidence pseudo-labels to improve robustness. We also apply label spread to propagate labels based on data similarity, which enhances generalization across diverse distributions. In addition, we employ a BNNs with uncertainty estimation, boosting confidence in predictions and reducing phase identification errors. In our case study, we achieved approximately 98% +/- 0.08 accuracy with uncertainty using minimal and unreliable labeled data from a real U.S. utility, Duquesne Light Company. Our SSL approach, combined with uncertainty estimation, provides an efficient solution for phase identification in AMI data, ultimately improving the reliability of smart grid applications.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2026

Advanced Semi-Supervised Learning With Uncertainty Estimation for Phase Identification in Distribution Systems

The integration of advanced metering infrastructure (AMI) into power distribution networks generates valuable data for tasks such as phase identification; however, the limited and unreliable availability of labeled data in the form of customer phase connectivity presents challenges. To address this issue, we propose a semi-supervised learning (SSL) framework that effectively leverages labeled and unlabeled data. Our approach incorporates self-training, label spreading, and Bayesian neural networks (BNNs) to enhance phase identification with AMI data. Our method uses an ensemble of multilayer perceptron classifiers in a self-training setup, iteratively adding high-confidence pseudo-labels to improve robustness. We also apply label spread to propagate labels based on data similarity, which enhances generalization across diverse distributions. In addition, we employ a BNNs with uncertainty estimation, boosting confidence in predictions and reducing phase identification errors. In our case study, we achieved approximately 98% +/- 0.08 accuracy with uncertainty using minimal and unreliable labeled data from a real U.S. utility, Duquesne Light Company. Our SSL approach, combined with uncertainty estimation, provides an efficient solution for phase identification in AMI data, ultimately improving the reliability of smart grid applications.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

Characterizing the Reproducibility of Noisy Quantum Circuits

The ability of a quantum computer to reproduce or replicate the results of a quantum circuit is a key concern for verifying and validating applications of quantum computing. Statistical variations in circuit outcomes that arise from ill-characterized fluctuations in device noise may lead to computational errors and irreproducible results. While device characterization offers a direct assessment of noise, an outstanding concern is how such metrics bound the reproducibility of a given quantum circuit. Here, we first directly assess the reproducibility of a noisy quantum circuit, in terms of the Hellinger distance between the computational results, and then we show that device characterization offers an analytic bound on the observed variability. We validate the method using an ensemble of single qubit test circuits, executed on a superconducting transmon processor with well-characterized readout and gate error rates. The resulting description for circuit reproducibility, in terms of a composite device parameter, is confirmed to define an upper bound on the observed Hellinger distance, across the variable test circuits. This predictive correlation between circuit outcomes and device characterization offers an efficient method for assessing the reproducibility of noisy quantum circuits.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Current and Projected Future Distribution of Plant Community Types for the Southern Seward Peninsula, Alaska

Landscape scale maps of plant community distribution at 5 m resolution were developed for southern Seward Peninsula. A Random Forest based environmental niche model was developed using topographic and climate data sets. Models were trained for the 2010-2019 period and applied to develop plant community distributions for contemporary (2010-2019) period. Trained model was applied to project the plant community distributions under future climate. Using downscaled projections for RCP8.5 scenario from five climate models (CCSM4, GFDL-CM3, GISS-E2-R, IPSL-CM5A-LR, MRI-CGCM3) and multi-model mean, a six member ensemble of plant community distribution were developed for current decade (2010-2019) and for future decades (2020-2029, 2030-2039, 2040-2049, 2050-2059). Contains *.tif and *.sh files. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Machine Learning for Predicting Multipactor Susceptibility in Planar RF Structures

Multipactor discharge is a persistent challenge in high-power microwave (HPM) and accelerator systems, where secondary electron avalanches can cause heating, vacuum degradation, and failure. This work presents the first supervised machine learning (ML) framework for multipactor prediction, trained on high-fidelity 3D Particle-in-Cell (PIC) simulation data in planar geometries. The model maps operational, geometric, and material-dependent secondary electron yield (SEY) parameters to the time-averaged electron growth rate, enabling rapid reconstruction of susceptibility charts. Among the models evaluated, tree-based ensemble methods such as Random Forest and Extra Trees demonstrate superior generalization to unseen materials compared to neural networks such as multilayer perceptron (MLP). Performance metrics, including Intersection over Union (IoU), Structural Similarity Index Measure (SSIM), and Pearson correlation, show close agreement with simulation benchmarks. Principal Component Analysis attributes generalization limits to material feature-space disjointedness.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Modeling Liquid Water by Climbing up Jacob’s Ladder in Density Functional Theory Facilitated by Using Deep Neural Network Potentials

Within the framework of Kohn–Sham density functional theory (DFT), the ability to provide good predictions of water properties by employing a strongly constrained and appropriately normed (SCAN) functional has been extensively demonstrated in recent years. Here, we further advance the modeling of water by building a more accurate model on the fourth rung of Jacob’s ladder with the hybrid functional, SCAN0. In particular, we carry out both classical and Feynman path-integral molecular dynamics calculations of water with the SCAN0 functional and the isobaric–isothermal ensemble. To generate the equilibrated structure of water, a deep neural network potential is trained from the atomic potential energy surface based on ab initio data obtained from SCAN0 DFT calculations. For the electronic properties of water, a separate deep neural network potential is trained by using the Deep Wannier method based on the maximally localized Wannier functions of the equilibrated trajectory at the SCAN0 level. The structural, dynamic, and electric properties of water were analyzed. The hydrogen-bond structures, density, infrared spectra, diffusion coefficients, and dielectric constants of water, in the electronic ground state, are computed by using a large simulation box and long simulation time. For the properties involving electronic excitations, we apply the GW approximation within many-body perturbation theory to calculate the quasiparticle density of states and bandgap of water. Compared to the SCAN functional, mixing exact exchange mitigates the self-interaction error in the meta-generalized-gradient approximation and further softens liquid water toward the experimental direction. For most of the water properties, the SCAN0 functional shows a systematic improvement over the SCAN functional. However, some important discrepancies remain. The H-bond network predicted by the SCAN0 functional is still slightly overstructured compared to the experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Substrate-Mediated Evaporation and Stochastic Evolution of Supported Au Nanoparticles

Here, we use in situ transmission electron microscopy with automated tracking to study supported gold nanoparticles (NPs) during high-temperature vacuum annealing. The average mass loss per NP is governed by a flat, nearly size-independent substrate-mediated evaporation profile. On top of this mean shrinkage, individual NPs show significant fluctuations in apparent growth or shrinkage, and NP volume follows a random-walk-like trajectory. To rationalize both the ensemble-mean behavior and the particle-resolved variability, we develop a self-consistent theory that couples substrate-mediated evaporation to collective 2D Ostwald-type mass exchange through a shared adatom field, described in terms of a renormalized screening length and background concentration. In the experimentally relevant regime, the theory predicts an approximately size-independent mean shrinkage rate and clarifies how net mass loss suppresses classical coarsening. Superimposed on this deterministic drift, we quantify stochastic volume trajectories and capture their fluctuation spectrum with a minimal Langevin description consistent with intermittent adatom attachment and detachment events. In addition, we characterize the lateral diffusive motion of NPs, which is responsible for their coalescence. Altogether, our results highlight that stochasticity is intrinsic at the nanoscale and that predicting the evolution of supported NPs at early and intermediate times requires a unified framework combining substrate-mediated evaporation, collective mass exchange, and stochastic fluctuations.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Assessing the Sensitivity of the Tropical Cyclone Boundary Layer to the Parameterization of Momentum Flux in the Community Earth System Model

Recent studies have demonstrated that high-resolution (~25 km) Earth System Models (ESMs) have the potential to skillfully predict tropical cyclone (TC) occurrence and intensity. However, biases in ESM TCs still exist, largely due to the need to parameterize processes such as boundary layer (PBL) turbulence. Building on past studies, we hypothesize that the depiction of the TC PBL in ESMs is sensitive to the configuration of the PBL parameterization scheme, and that the targeted perturbation of tunable parameters can reduce biases. The Morris one-at-a-time (MOAT) method is implemented to assess the sensitivity of the TC PBL to tunable parameters in the PBL scheme in an idealized configuration of the Community Atmosphere Model, version 6 (CAM6). The MOAT method objectively identifies several parameters in an experimental version of the Cloud Layers Unified by Binormals (CLUBB) scheme that appreciably influence the structure of the TC PBL. We then perturb the parameters identified by the MOAT method within a suite of CAM6 ensemble simulations and find a reduction in model biases compared to observations and a high-resolution, cloud-resolving model. Importantly, we demonstrate that the high-sensitivity parameters are tied to PBL processes that reduce turbulent mixing and effective eddy diffusivity, and that in CAM6 these parameters alter the TC PBL in a manner consistent with past modeling studies. In this way, we provide an initial identification of process-based input parameters that, when altered, have the potential to improve TC predictions by ESMs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

GEFSv12 High- and Low-Skill Day-10 Tornado Forecasts

Abstract On average, modern numerical weather prediction forecasts for daily tornado frequency exhibit no skill beyond day 10. However, in this extended-range lead window, there are particular model cycles that have exceptionally high forecast skill for tornadoes because of their ability to correctly simulate the future synoptic pattern. Here, model initial conditions that produced a more skillful forecast for tornadoes over the United States were exploited while also highlighting potential causes for low-skill cycles within the Global Ensemble Forecasting System, version 12 (GEFSv12). There were 88 high-skill and 91 low-skill forecasts in which the verifying day-10 synoptic pattern for tornado conditions revealed a western U.S. thermal trough and an eastern U.S. thermal ridge, a favorable configuration for tornadic storm occurrence. Initial conditions for high skill forecasts tended to exhibit warmer sea surface temperatures throughout the tropical Pacific Ocean and Gulf of Mexico, an active Madden–Julian oscillation, and significant modulation of Earth-relative atmospheric angular momentum. Low-skill forecasts were often initialized during La Niña and negative Pacific decadal oscillation conditions. Significant atmospheric blocking over eastern Russia—in which the GEFSv12 overforecast the duration and characteristics of the downstream flow—was a common physical process associated with low-skill forecasts. This work helps to increase our understanding of the common causes of high- or low-skill extended-range tornado forecasts and could serve as a helpful tool for operational forecasters. Significance Statement This research provides a framework for the anticipation of a more (or less) skillful 10-day tornado forecast in an operational numerical weather prediction system. High-skill forecasts were associated with substantial tropical convection and warm sea surface temperature throughout the Pacific Ocean and Gulf of Mexico, whereas the underlying cause of low-skill forecasts were typically associated with a blocking anticyclone over eastern Russia. These findings are important because they permit increased or decreased confidence in a long-range forecast of tornado occurrence based on a dynamical prediction system.

Meteorology & Atmospheric Sciences↗
DOE OSTI2023

Multifidelity validation of digital surrogates using variable-density turbulent mixing models

In this study, ensembles of experimental data are presented and utilized to compare and validate two models used in the simulation of variable-density (Atwood = 0.22), compressible turbulent mixing. Though models of this kind (Reynolds averaged NavierStokes and large-eddy simulations) have been validated extensively with more canonical flows in previous studies, here the present approach offers novelty in the complexity of the geometry, the ensemble-based validation, and the uniformity of the computational framework on which the models are tested. Moreover, all experimental and computational tasks were completed by the authors which has led to a tightly coupled experimental configuration with its “digital twin.” The experimental divergent-shock-tube facility and its data acquisition methods are described and replicated in simulation space. A 2D Euler model which neglects the turbulent mixing at the interface is optimized to experimental data using a Gaussian process. This model then serves as the basis for both the 2D RANS and 3D LES studies that make comparisons to the mixing-layer data from the experiment. A relatively simple RANS model is shown to produce good agreement with experimental data only at late flow development times. The LES ensembles generally show good agreement with experimental data but display sensitivity to the characterization of initial conditions. Resolution-dependent behavior is also observed for certain higher-order statistics of interest. Overall, the LES model successfully captures the effects of divergent geometry, compressibility, and combined nonlinear instabilities inherent to the problem. The successful prediction of mixing width and its growth rate highlight the existence of three distinct regimes in the development of the instability, each with similarities to previously studied instabilities.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Tropical High Cloud Feedback Relationships to Climate Sensitivity

Clouds constitute a large portion of uncertainty in predictions of equilibrium climate sensitivity (ECS). While low cloud feedbacks have been the focus of intermodel studies due to their high variability among global climate models, tropical high cloud feedbacks also exhibit considerable uncertainty. Here, we apply the cloud radiative kernel technique of Zelinka et al. to 22 models across the CMIP5 and CMIP6 ensembles to survey tropical high cloud feedbacks and analyze their relationship to ECS. We find that the net high cloud feedback and its altitude and optical depth feedback components are significantly positively correlated with ECS in the tropical mean. On the other hand, the tropical mean high cloud amount feedback is not correlated with ECS. These relationships are most pronounced outside of areas of strong climatological ascent, suggesting the importance of thin cirrus feedbacks. Finally, we explore connections between high cloud feedbacks, climate sensitivity, and mean state high cloud properties. In general, high ECS models are cloudier in the upper troposphere but have a thinner high cloud population. Furthermore, we find that having more thin cirrus in the mean state relates to more positive high cloud altitude and optical depth feedbacks, and it either amplifies or dampens the high cloud amount feedback depending on the large-scale dynamical regime (amplifying in descent and dampening in ascent). In summary, our analysis highlights the importance of tropical high cloud feedbacks for driving intermodel spread in ECS and suggests that mean state high cloud characteristics might provide a unique opportunity for observationally constraining high cloud feedbacks.

atmosphere↗
DOE OSTI2021

Multi-scale Multi-physics Scientific Machine Learning for Water Cycle Extreme Events Identification, Labelling, Representation, and Characterization

Impacts of climate are usually felt through extreme events such as droughts, floods, thunderstorms, windstorms, wildfires, and so on, that are intimately tied to the water cycle. Predicting the frequency and severity of extreme events under climate change remains a significant challenge; meanwhile, the mechanisms and impacts of these extremes are far from well understood. There are several major science challenges: (1) Lack of labelled extreme events data and missing standards in defining extremes; (2) Computational demand of high-resolution ensemble climate modeling; (3) Modeling the multiscale multi-physics hierarchical structure of compound extremes; (4) Lack of understanding of mechanisms of extreme events; (5) Large uncertainty in extreme events impacts on infrastructure; (6) Subjective assessment of weather-related risk from seasonal to multi-decadal time scales and lack of metrics for risk assessment and mitigation control.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

CRADA Final Report: CRADA Number NFE-22-09330 with General Fusion

General Fusion is developing a magnetized target fusion (MTF) approach that involves compressing an initial magnetically confined plasma inside a cavity formed in liquid metal. This approach builds from concepts initially developed under the Linus program at the U.S. Naval Research Laboratory and combines it with advances from compact toroid experiment (CTX) and sustained spheromak plasma experiment (SSPX) in compact toroid plasmas and coaxial Marshall gun systems. Modeling the tokamak during compression is central to designing a successful MTF device. The plasma is formed by coaxial helicity injection in the General Fusion device. Immediately after formation, the plasma has a diverted tokamak configuration with a single null. As the wall moves inwards, the plasma is repelled from the conducting surface and driven inwards by currents induced by its magnetic field in the liquid metal wall. As the liquid metal closes (or bridges) the opening of the coaxial plasma injector, the magnetic field topology alters to remove the null. Due to this, the plasma moves from a diverted to a wall-limited configuration. The liquid metal liner continues to close in and change shape, reducing in radius by a factor of ten at the peak of plasma compression. A model of the MTF plasma must be able to handle this continually varying geometry, and to be predictive, it must faithfully include the real imperfections arising in the process. In this project, we pursued a Monte Carlo approach to closures for MHD by computing kinetic electron trajectories in an MHD plasma background from simulations of GF devices. This requires enhancing the capabilities of the KORC-T code for running large ensembles of kinetic trajectories by porting it to GPU architectures and enabling workflows for large ensembles on OLCF machines. With these capabilities, it is possible to produce a large library of kinetic calculations of electron orbits evolving in plasma configurations spanning the magnetic configurations and plasma density profiles, including non-axisymmetry, arising in the General Fusion’s existing PI3 spherical tokamak device. Using ensembles will capture particles passing a single point in space in a given magnetic configuration, and the entire dataset will cover a range of global magnetic field geometries. By sampling around many starting points, this dataset will capture the spatial dependence of the plasma parameters. From this large dataset, it is possible to produce a reduced model for the kinetic effects not captured in MHD.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Scalable deep learning for watershed model calibration

Watershed models such as the Soil and Water Assessment Tool (SWAT) consist of high-dimensional physical and empirical parameters. These parameters often need to be estimated/calibrated through inverse modeling to produce reliable predictions on hydrological fluxes and states. Existing parameter estimation methods can be time consuming, inefficient, and computationally expensive for high-dimensional problems. In this paper, we present an accurate and robust method to calibrate the SWAT model (i.e., 20 parameters) using scalable deep learning (DL). We developed inverse models based on convolutional neural networks (CNN) to assimilate observed streamflow data and estimate the SWAT model parameters. Scalable hyperparameter tuning is performed using high-performance computing resources to identify the top 50 optimal neural network architectures. We used ensemble SWAT simulations to train, validate, and test the CNN models. We estimated the parameters of the SWAT model using observed streamflow data and assessed the impact of measurement errors on SWAT model calibration. We tested and validated the proposed scalable DL methodology on the American River Watershed, located in the Pacific Northwest-based Yakima River basin. Our results show that the CNN-based calibration is better than two popular parameter estimation methods (i.e., the generalized likelihood uncertainty estimation [GLUE] and the dynamically dimensioned search [DDS], which is a global optimization algorithm). For the set of parameters that are sensitive to the observations, our proposed method yields narrower ranges than the GLUE method but broader ranges than values produced using the DDS method within the sampling range even under high relative observational errors. The SWAT model calibration performance using the CNNs, GLUE, and DDS methods are compared using R 2 and a set of efficiency metrics, including Nash-Sutcliffe, logarithmic Nash-Sutcliffe, Kling-Gupta, modified Kling-Gupta, and non-parametric Kling-Gupta scores, computed on the observed and simulated watershed responses. The best CNN-based calibrated set has scores of 0.71, 0.75, 0.85, 0.85, 0.86, and 0.91. The best DDS-based calibrated set has scores of 0.62, 0.69, 0.8, 0.77, 0.79, and 0.82. The best GLUE-based calibrated set has scores of 0.56, 0.58, 0.71, 0.7, 0.71, and 0.8. The scores above show that the CNN-based calibration leads to more accurate low and high streamflow predictions than the GLUE and DDS sets. Our research demonstrates that the proposed method has high potential to improve our current practice in calibrating large-scale integrated hydrologic models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Pervasive alterations to snow-dominated ecosystem functions under climate change

Climate change projections consistently demonstrate that warming temperatures and dwindling seasonal snowpack will elicit cascading effects on ecosystem function and water resource availability. Despite this consensus, little is known about potential changes in the variability of ecohydrological conditions, which is also required to inform climate change adaptation and mitigation strategies. Considering potential changes in ecohydrological variability is critical to evaluating the emergence of trends, assessing the likelihood of extreme events such as floods and droughts, and identifying when tipping points may be reached that fundamentally alter ecohydrological function. Using a single-model Large Ensemble with sophisticated terrestrial ecosystem representation, we characterize projected changes in the mean state and variability of ecohydrological processes in historically snow-dominated regions of the Northern Hemisphere. Widespread snowpack reductions, earlier snowmelt timing, longer growing seasons, drier soils, and increased fire risk are projected for this century under a high-emissions scenario. In addition to these changes in the mean state, increased variability in winter snowmelt will increase growing-season water deficits and increase the stochasticity of runoff. Thus, with warming, declining snowpack loses its dependable buffering capacity so that runoff quantity and timing more closely reflect the episodic characteristics of precipitation. This results in a declining predictability of annual runoff from maximum snow water equivalent, which has critical implications for ecosystem stress and water resource management. So our results suggest that there is a strong likelihood of pervasive alterations to ecohydrological function that may be expected with climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

Targeted protein degradation (TPD) is a promising approach in drug discovery for degrading proteins implicated in diseases. A key step in this process is the formation of a ternary complex where a heterobifunctional molecule induces proximity of an E3 ligase to a protein of interest (POI), thus facilitating ubiquitin transfer to the POI. In this work, we characterize 3 steps in the TPD process. (1) We simulate the ternary complex formation of SMARCA2 bromodomain and VHL E3 ligase by combining hydrogen-deuterium exchange mass spectrometry with weighted ensemble molecular dynamics (MD). (2) We characterize the conformational heterogeneity of the ternary complex using Hamiltonian replica exchange simulations and small-angle X-ray scattering. (3) We assess the ubiquitination of the POI in the context of the full Cullin-RING Ligase, confirming experimental ubiquitinomics results. Differences in degradation efficiency can be explained by the proximity of lysine residues on the POI relative to ubiquitin.

59 BASIC BIOLOGICAL SCIENCES↗