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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

Cryoelectron microscopy requires molecular modeling for refinement of structures. Ensemble models arrive at low free-energy molecular structures, but are computationally expensive and limited to resolving only small proteins. Here, we introduce CryoFold, a pipeline of molecular dynamics simulations that determines ensembles of protein structures by integrating density data of varying sparsity at 3–5 Å resolution with sequence information and coarse-grained topological knowledge of the protein folds. We present six examples, folding proteins between 72 and 2,000 residues, including large membrane and multi-domain systems, and results from two Electron Microscopy Data Bank (EMDB) competitions. Driven by data from a single state, CryoFold discovers ensembles of common low-energy models together with rare low-probability structures that capture the equilibrium distribution of proteins constrained by the density maps. Many of these conformations are experimentally validated and functionally relevant. We arrive at a set of best practices for data-guided protein folding that are controlled using a Python graphical user interface (GUI).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Improved Predictability of the Indian Ocean Dipole Using a Stochastic Dynamical Model Compared to the North American Multimodel Ensemble Forecast

This study assesses the predictive skill of eight North American Multimodel Ensemble (NMME) models in predicting the Indian Ocean dipole (IOD). We find that the forecasted ensemble-mean IOD–El Niño–Southern Oscillation (ENSO) relationship deteriorates away from the observed relationship with increasing lead time, which might be one reason that limits the IOD predictive skill in coupled models. We are able to improve the IOD predictive skill using a recently developed stochastic dynamical model (SDM) forced by forecasted ENSO conditions. The results are consistent with the previous result that operational IOD predictability beyond persistence at lead times beyond one season is mostly controlled by ENSO predictability and the signal-to-noise ratio of the Indo-Pacific climate system. The multimodel ensemble (MME) investigated here is found to be of superior skill compared to each individual model at most lead times. Importantly, the skill of the SDM IOD predictions forced with forecasted ENSO conditions were either similar or better than those of the MME IOD forecasts. Moreover, the SDM forced with observed ENSO conditions exhibits significantly higher IOD prediction skill than the MME at longer lead times, suggesting the large potential skill increase that could be achieved by improving operational ENSO forecasts. We find that both cold and warm biases of the predicted Niño-3.4 index may cause false alarms of negative and positive IOD events, respectively, in NMME models. Many false alarms for IOD forecasts at lead times longer than one season in the original forecasts disappear or are significantly reduced in the SDM forced by forecasted ENSO conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A combined ensemble-volume average homogenization method for lattice structures with defects under dynamic and static loading

In the study of lattices structures, both experiments and numerical simulations are often conducted with small samples. Using combined ensemble and volume averaging, this work introduces a method to extract a macroscopic constitutive response of a lattice material from numerical simulations performed in periodic domains. The domain size needed to obtain statistically accurate results is investigated. Similar to molecular dynamics, the concept of the virial stress is introduced after homogenized equations are derived using the ensemble averaging method. Under static conditions, the virial stress is shown to agree with the volume averaged solid stress. Using the homogenization method, constitutive relations for this stress can be obtained from systems with uniform strains. Application of such obtained constitutive relations to more general cases results in an error proportional to the square of the ratio between the lattice length scale and the macroscopic length scale. Taking advantage of this property, numerical simulations are performed in systems with a uniform gradient of the average velocity. The volume average method is then used to accelerate convergence when studying lattices with defects. To avoid the artificial numerical time scale from the size of a representative volume element divided by the wave speed, a numerical scheme is developed to enforce a spatially uniform velocity gradient within the computational domain while allowing fluctuations of the velocity or displacement to develop naturally. To account for probability distribution of lattice defects, the stress is calculated as the ensemble-volume averaged value. For dynamic systems, energy dissipation properties are also studied.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Evolution of highly multimodal Rayleigh–Taylor instabilities

Rayleigh–Taylor (RT) instabilities are important fluid instabilities that arise in inertial confinement fusion (ICF) capsule implosions, and many other contexts. Multi-mode coupling is observed in experiments and plays a substantial role in material mix from RT instabilities. In this work, we study the evolution of highly multimodal perturbations (power law distribution) that approximate those found at manufactured material interfaces. We use simulations of over 2000 different perturbations in the LANL code xRAGE to identify distinct phases in the processes of bubble growth and bubble merger which can be visualized in a 2D phase portrait with clear regimes of mode growth and decay. Our results show that the dynamic evolution of the instability strongly depends on the mode of the perturbations and mode interactions. The merger process accelerates bubble growth. A non-Markovian region and a transition of the instability from: (1) initial exponential growth to (2) linear growth and to (3) quadratic growth and asymptotic behavior, are clearly captured in the phase space. We have developed a quantitative model of bubble growth that reproduces the dynamic behavior of ensembles of perturbations. Implications for ICF capsules designed for robustness against instabilities are discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Scenario Storyline Discovery for Planning in Multi‐Actor Human‐Natural Systems Confronting Change

Scenarios have emerged as valuable tools in managing complex human-natural systems, but the traditional approach of limiting focus on a small number of predetermined scenarios can inadvertently miss consequential dynamics, extremes, and diverse stakeholder impacts. Exploratory modeling approaches have been developed to address these issues by exploring a wide range of possible futures and identifying those that yield consequential vulnerabilities. However, vulnerabilities are typically identified based on aggregate robustness measures that do not take full advantage of the richness of the underlying dynamics in the large ensembles of model simulations and can make it hard to identify key dynamics and/or storylines that can guide planning or further analyses. This study introduces the FRamework for Narrative Storylines and Impact Classification (FRNSIC; pronounced “forensic”): a scenario discovery framework that addresses these challenges by organizing and investigating consequential scenarios using hierarchical classification of diverse outcomes across actors, sectors, and scales, while also aiding in the selection of scenario storylines, based on system dynamics that drive consequential outcomes. We present an application of this framework to the Upper Colorado River Basin, focusing on decadal droughts and their water scarcity implications for the basin's diverse users and its obligations to downstream states through Lake Powell. We show how FRNSIC can explore alternative sets of impact metrics and drought dynamics and use them to identify drought scenario storylines, that can be used to inform future adaptation planning.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Mapping the global distribution of C 4 vegetation using observations and optimality theory

Plants with the C 4 photosynthesis pathway typically respond to climate change differently from more common C 3 -type plants, due to their distinct anatomical and biochemical characteristics. These different responses are expected to drive changes in global C 4 and C 3 vegetation distributions. However, current C 4 vegetation distribution models may not predict this response as they do not capture multiple interacting factors and often lack observational constraints. Here, we used global observations of plant photosynthetic pathways, satellite remote sensing, and photosynthetic optimality theory to produce an observation-constrained global map of C 4 vegetation. We find that global C 4 vegetation coverage decreased from 17.7% to 17.1% of the land surface during 2001 to 2019. This was the net result of a reduction in C 4 natural grass cover due to elevated CO 2 favoring C 3 -type photosynthesis, and an increase in C 4 crop cover, mainly from corn (maize) expansion. Using an emergent constraint approach, we estimated that C 4 vegetation contributed 19.5% of global photosynthetic carbon assimilation, a value within the range of previous estimates (18–23%) but higher than the ensemble mean of dynamic global vegetation models (14 ± 13%; mean ± one standard deviation). Our study sheds insight on the critical and underappreciated role of C 4 plants in the contemporary global carbon cycle.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG 1 antibody

Subcutaneous injection is the preferred route of administration for many antibody therapeutics for reasons that include its speed and convenience. However, the small volume limit (typically ≤2 mL) for subcutaneous delivery often necessitates antibody formulations at high concentrations (commonly ≥100 mg/mL), which may lead to physicochemical problems. For example, antibodies with large hydrophobic or charged patches can be prone to self-interaction giving rise to high viscosity. Here, we combined X-ray crystallography with computational modeling to predict regions of an anti-glucagon receptor (GCGR) IgG 1 antibody prone to self-interaction. An extensive mutational analysis was undertaken of the complementarity-determining region residues residing in hydrophobic surface patches predicted by spatial aggregation propensity, in conjunction with residue-level solvent accessibility, averaged over conformational ensembles from molecular dynamics simulations. Dynamic light scattering (DLS) was used as a medium throughput screen for self-interaction of ~200 anti-GCGR IgG 1 variants. A negative correlation was found between the viscosity determined at high concentration (180 mg/mL) and the DLS interaction parameter measured at low concentration (2–10 mg/mL). Additionally, anti-GCGR variants were readily identified with reduced viscosity and antigen-binding affinity within a few fold of the parent antibody, with no identified impact on overall developability. The methods described here may be useful in the optimization of other antibodies to facilitate their therapeutic administration at high concentration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Quantum turbulence, superfluidity, non-Markovian dynamics, and wave function thermalization

While quantum turbulence has been addressed both experimentally (predominantly for superfluid He 4 and He 3 ) and theoretically, the dynamics of various ensembles of quantized vortices has been followed in time only until the vortices have decayed into phonons. How this “thermalization” is achieved is still an unaddressed and thus an unelucidated question. The unitary Fermi gas (UFG) is a unique quantum system, which has no classical counterpart and is of relevance to neutron stars, cold atoms, condensed-matter and nuclear many-body systems. The non-Markovian evolution of an isolated UFG is put in evidence and its entire nonequilibrium evolution can be studied theoretically within a unified theoretical framework. The initial lattice of quantum vortices and antivortices evolves through a couple of vortex tangles and excitation of Kelvin waves, where vortices cross and reconnect, until very slowly thermalization sets in. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Quantification of Sub-Pixel Dynamics in High-Speed Neutron Imaging

The high penetration depth of neutrons through many metals and other common materials makes neutron imaging an attractive method for non-destructively probing the internal structure and dynamics of objects or systems that may not be accessible by conventional means, such as X-ray or optical imaging. While neutron imaging has been demonstrated to achieve a spatial resolution below 10 μm and temporal resolution below 10 μs, the relatively low flux of neutron sources and the limitations of existing neutron detectors have, until now, dictated that these cannot be achieved simultaneously, which substantially restricts the applicability of neutron imaging to many fields of research that could otherwise benefit from its unique capabilities. In this work, we present an attenuation modeling approach to the quantification of sub-pixel dynamics in cyclic ensemble neutron image sequences of an automotive gasoline direct injector at a 5 μs time scale with a spatial noise floor in the order of 5 μm.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Information-Guided Dynamic Nuclear Polarization

A spin ensemble in thermal equilibrium continuously undergoes random fluctuations analogous to those observed in Brownian motion, a process known as spin noise. Here, we investigate the dynamics of a system comprising a spin-1 paramagnetic center and a hyperfine-coupled spin-1/2 nucleus in the vicinity of a level crossing. We theoretically show that nuclear spins polarize efficiently under the combined action of thermal fluctuations and a closed-loop feedback protocol. The latter articulates periodic observations of the electronic magnetization and radio-frequency pulses connecting hybrid states with opposite nuclear spin alignment. Since nuclear polarization emerges from electronic spin fluctuations, not spin order, this microwave-free technique generically benefits from warmer, not colder, operation temperatures. Furthermore, because the spin dynamics at play near a level crossing is rather insensitive to the absolute value of the magnetic field, our work promises opportunities for high-field dynamic nuclear polarization, which is difficult to attain through present methods.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Global fire modelling and control attributions based on the ensemble machine learning and satellite observations

Contemporary fire dynamics is one of the most complex and least understood land surface phenomena. Global fire controls related to climate, vegetation, and anthropogenic activity are usually intertwined, and difficult to disentangle in a quantitative way. Here, we leveraged an ensemble of five machine learning (ML) models and multiple satellite-based observations to conduct global fire modeling for three fire metrics (burned area, fire number, and fire size), and quantified driving mechanisms underlying annual fire changes in a spatially resolved manner for the period 2003–2019. Ensemble learning is a meta-approach that combines multiple ML predictions to improve accuracy, robustness, and generalization performance. We found that the optimized ensemble ML well reproduced annual dynamics of global burned area (R 2 = 0.90, P < 0.001), total fire numbers (R 2 = 0.86, P < 0.001), and averaged fire size (R 2 = 0.70, P < 0.001). Additionally, the ensemble ML captured key spatial patterns of multi-year mean magnitudes, annual variabilities, anomalies, and trends for different fire metrics. Our ML-based fire attributions further highlighted the dominant role of enhanced anthropogenic activity in reducing global burned area (–1.9 Mha/yr, P < 0.01), followed by climate control (–1.3 Mha/yr, P < 0.01) and insignificant positive vegetation control (0.4 Mha/yr, P = 0.60). Spatially, climate dominated a much larger burned area (53.7%) than human (23.4%) or vegetation control (22.9%); however, the counteracting effects from regional wetting and drying trends weakened the net climate impacts on global burned area. The fire number and fire size exhibited similar spatial control patterns with burned area; globally, however, fire number tended to be more affected by climate while fire size more influenced by human activities. Overall, our study confirmed the feasibility and efficiency of ensemble ML in global fire modeling and subsequent control attributions, providing a better understanding of contemporary fire regimes and contributing to robust fire projections in a changing environment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

BEAM (Battery Ensemble ANN Modeler) [SWR-19-69]

Dynamic losses of batteries can be a nonlinear function of the operational state of the battery. This package trains an Ensemble of Artificial Neural Networks on battery operational data to model the dynamic losses as a function of the operational state of charge and the active power set point. The package can also be used to return the dynamic battery losses which will be incurred as the battery operates if fed some operational profile.

Bryce, Richard↗
DOE OSTI2026

Enhanced accuracy through ensembling of randomly initialized auto-regressive models for dynamical systems

Computational mechanics simulations using traditional finite element methods (FEM) require prohibitively expensive computational resources for real-time engineering applications, design optimization, and digital twin implementations. While machine learning (ML) surrogate models offer significant computational speedups, autoregressive ML models for time-dependent mechanical systems suffer from error accumulation that compromises long-term prediction reliability - a critical concern for engineering applications where accuracy over extended time horizons is essential for safety and performance assessments. Here, we propose a deep ensemble framework specifically designed to address this challenge in computational mechanics applications, where multiple ML surrogate models with random weight initializations are trained in parallel and their predictions aggregated during inference. This approach leverages statistical diversity to maximize information gain from a fixed set of training data and to mitigate error propagation, while maintaining the computational efficiency that makes ML surrogates attractive for engineering practice. We validate the framework on three representative problems spanning critical areas of computational mechanics: stress field evolution in heterogeneous microstructures under complex loading (relevant to advanced materials design and composite analysis), planetary-scale shallow water dynamics (applicable to environmental and geotechnical engineering), and Gray-Scott reaction-diffusion systems (relevant to mass transport and chemical process engineering). Across all test cases, the ensemble approach demonstrates consistent error reduction of 15-33% compared to individual models. The codes for this work are available on GitHub (https://github.com/Graham-Brady-Research-Group/AutoregressiveEnsemble_SpatioTemporal_Evolution).

autoregressive prediction↗
DOE OSTI2021

Deconstructing the Local Intermolecular Ordering and Dynamics of Liquid Chloroform and Bromoform

Local intermolecular structure and dynamics of the polar molecular liquids chloroform and bromoform are studied by molecular dynamics simulation. Structural distribution functions, including 1- and 2-D pair correlations and dipole contour plots allow direct comparison and show agreement with recent analyses of diffraction experiments. Studies of the haloforms’ reorientational dynamics and longevity of structural features resulting from intermolecular interaction extend previous work toward deeper understanding of the factors controlling these features. Analyses of ensemble average structures and dynamical properties isolate mass, electrostatics, and steric packing as driving forces or contributing factors for the observed ordering and dynamics.

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

Nonlinear Ensemble Filtering with Diffusion Models: Application to the Surface Quasigeostrophic Dynamics

The intersection between classical data assimilation methods and novel machine learning techniques has attracted significant interest in recent years. Here, we explore another promising solution in which diffusion models are used to formulate a robust nonlinear ensemble filter for sequential data assimilation. Unlike standard machine learning methods, the proposed ensemble score filter (EnSF) is completely training free and can efficiently generate a set of analysis ensemble members. Here, in this study, we apply the EnSF to a surface quasigeostrophic model and compare its performance against the popular local ensemble transform Kalman filter (LETKF), which makes Gaussian assumptions in the analysis step. Numerical tests demonstrate that EnSF maintains stable performance in the absence of localization and for a variety of experimental settings. We find that while LETKF maintains optimal performance in the case of linear observations of the entire state and a perfect model, EnSF shows improvements over LETKF when nonlinear observations are assimilated and the system is subject to unexpected model errors. A spectral decomposition of the analysis results in this nonlinear observation regime shows that the largest improvements over LETKF occur at large scales (small wavenumbers), where LETKF lacks sufficient ensemble spread. Overall, this initial application of EnSF to a geophysical model of intermediate complexity motivates further development of the algorithm for more realistic problems.

Artificial intelligence↗
DOE OSTI2022

Learning emergent partial differential equations in a learned emergent space

We propose an approach to learn effective evolution equations for large systems of interacting agents. This is demonstrated on two examples, a well-studied system of coupled normal form oscillators and a biologically motivated example of coupled Hodgkin-Huxley-like neurons. For such types of systems there is no obvious space coordinate in which to learn effective evolution laws in the form of partial differential equations. In our approach, we accomplish this by learning embedding coordinates from the time series data of the system using manifold learning as a first step. In these emergent coordinates, we then show how one can learn effective partial differential equations, using neural networks, that do not only reproduce the dynamics of the oscillator ensemble, but also capture the collective bifurcations when system parameters vary. The proposed approach thus integrates the automatic, data-driven extraction of emergent space coordinates parametrizing the agent dynamics, with machine-learning assisted identification of an emergent PDE description of the dynamics in this parametrization.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Spatially-resolved dynamic sampling of different phasic magnetic resonances of nanoparticle ensembles in a magnetotactic bacterium Magnetospirillum magnetotacticum

Abstract Nanoscaled magnetic particle ensembles are promising building blocks for realizing magnon based binary logic. Element-specific real-space monitoring of magnetic resonance modes with sampling rates in the GHz regime is imperative for the experimental verification of future complex magnonic devices. Here we present the observation of different phasic magnetic resonance modes using the element-specific technique of time-resolved scanning transmission x-ray microscopy within a chain of dipolarly coupled Fe 3 O 4 nanoparticles (40–50 nm particle size) inside a single cell of a magnetotactic bacterium Magnetospirillum magnetotacticum . The particles are probed with 25 nm resolution at the Fe L 3 x-ray absorption edge in response to a microwave excitation of 4.07 GHz. A plethora of resonance modes is observed within multiple particle segments oscillating in- and out-of-phase, well resembled by micromagnetic simulations.

time-resolved scanning transmission x-ray microsco↗