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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
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 OSTI2020

Validating first-principles molecular dynamics calculations of oxide/water interfaces with x-ray reflectivity data

Metal oxide/water interfaces play a crucial role in many electrochemical and photocatalytic processes, such as photoelectrochemical water splitting, the creation of fuel from sunlight, and electrochemical CO 2 reduction. First-principles electronic structure calculations can reveal unique insights into these processes, such as the role of the alignment of the oxide electronic energy levels with those of liquid water. An essential prerequisite for the success of such calculations is the ability to predict accurate structural models of these interfaces, which in turn requires careful experimental validation. Here we report a general, quantitative validation protocol for first-principles molecular dynamics simulations of oxide/aqueous interfaces. The approach makes direct comparisons of interfacial x-ray reflectivity (XR) signals from experimental measurements and those obtained from ab initio simulations with semilocal and van der Waals functionals. The protocol is demonstrated here for the case of the Al 2 O 3 (001)/water interface, one of the simplest oxide/water interfaces. We discuss the technical requirements needed for validation, including the choice of the density functional, the simulation cell size, and the optimal choice of the thermodynamic ensemble. Our results establish a general paradigm for the validation of structural models and interactions at solid/water interfaces derived from first-principles simulations. Furthermore, while there is qualitative agreement between the simulated structures and the experimental best-fit structure, direct comparisons of simulated and measured XR intensities show quantitative discrepancies that derive from both bulk regions (i.e., alumina and water) as well as the interfacial region, highlighting the need for accurate density functionals to properly describe interfacial interactions. Our results show that XR data are sensitive not only to the atomic structure (i.e., the atom locations) but also to the electron-density distributions in both the substrate and at the interface.

36 MATERIALS SCIENCE↗
DOE OSTI2023

From electronic structure to model application of key reactions for gasoline/alcohol combustion: Hydrogen-atom abstractions by $CH_3\dot{O}$ radical

H-atom abstraction by methoxy radical ($CH_3\dot{O}$) plays an important role in capturing the kinetics of reactions between gasoline components and alcohols. This study focuses on determining the reaction rates and thermodynamic properties of methoxy radical reactions with five gasoline fuel components: n-heptane, iso-octane, 1-hexene, cyclopentane and toluene. Electronic structure calculations were per-formed for all the stationary points with M06-2X/6 -311 ++ g(d,p) method. G3 composite method with atomization method is used for determining Δ f H 0 of all the closed shell and radical species, using which the necessary thermodynamic data of all the species was determined. Coupled cluster theory QCISD(T)/cc-pVXZ (where X = D and T) and Møller-Plesset perturbation theory MP2/cc-pVXZ (where X = D, T and Q) were used to calculate single point energies. Subsequently, rate constants for all hydrogen atom ab-straction channels have been performed using conventional transition state theory with unsymmetric tunneling corrections. A systematic comparison of rates for abstraction from different sites within the same species and same site from different species is done in order to get insights into this reaction class. Here, the computed thermodynamic properties and rate constants were incorporated into a recent gasoline mechanism to investigate the impact of the calculations performed in this work. A shift in predicted NTC (negative temperature coefficient) behavior and significant reduction in model reactivity is observed upon incorporating the rates calculated herein.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2020

Machine learning-based prediction of enzyme substrate scope: Application to bacterial nitrilases

Predicting the range of substrates accepted by an enzyme from its amino acid sequence is challenging. Although sequenc- and structure-based annotation approaches are often accurate for predicting broad categories of substrate specificity, they generally cannot predict which specific molecules will be accepted as substrates for a given enzyme, particularly within a class of closely related molecules. Combining targeted experimental activity data with structural modeling, ligand docking, and physicochemical properties of proteins and ligands with various machine learning models provides complementary information that can lead to accurate predictions of substrate scope for related enzymes. Here we describe such an approach that can predict the substrate scope of bacterial nitrilases, which catalyze the hydrolysis of nitrile compounds to the corresponding carboxylic acids and ammonia. Each of the four machine learning models (logistic regression, random forest, gradient-boosted decision trees, and support vector machines) performed similarly (average ROC = 0.9, average accuracy = ~82%) for predicting substrate scope for this dataset, although random forest offers some advantages. Finally, this approach is intended to be highly modular with respect to physicochemical property calculations and software used for structural modeling and docking.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

From electronic structure to model application of key reactions for gasoline/alcohol combustion: Hydrogen-atom abstraction by $CH_3O\dot{O}$ radicals

Hydrogen atom abstraction by methyl peroxy ($CH_3O\dot{O}$) radicals can play an important role in gasoline/ethanol interacting chemistry for fuels that produce high concentrations of methyl radicals. Detailed kinetic reactions for hydrogen atom abstraction by $CH_3O\dot{O}$ radicals from the components of FGF-LLNL (a gasoline surrogate) including cyclopentane, toluene, 1-hexene, n -heptane, and isooctane have been systematically studied in this work. Here, the M06-2X/6-311 ++ G(d,p) level of theory was used to obtain the optimized structure and vibrational frequency for all stationary points and the low-frequency torsional modes. The 1-D hindered rotor treatment for low-frequency torsional modes was treated at M06-2X/6-31G level of theory. The UCCSD(T)-F12a/cc-pVDZ-F12 and QCISD(T)/CBS level of theory were used to calculate single point energies for all species. High pressure limiting rate constants for all hydrogen atom abstraction channels were performed using conventional transition state theory with unsymmetric tunneling corrections. Individual rate constants are reported in the temperature range from 298.15 to 2000 K. Our computed results show that the abstraction of allylic hydrogen atoms from 1-hexene is the fastest at low temperatures. When the temperature increases, the hydrogen atom abstraction reaction channel at the primary alkyl site gradually becomes dominant. Thermodynamics properties for all stable species and high-pressure limiting rate constants for each reaction pathway obtained in this work were incorporated into the latest gasoline surrogate/ethanol model to investigate the influence of the rate constants calculated here on model predicted ignition delay times.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2023

A small-box approach to the local crystal structure of Y 3 NbO 7

The local crystal structure of Y 3 NbO 7 was probed using neutron total scattering. Five different structural models were fit to the experimental pair distribution function of this material up to 15 Å. Fits of defect fluorite (Fm$\overline{3}$m), pyrochlore (Fd$\overline{3}$m), and orthorhombic C weberite models (C222 1 ) were attempted based on prior structural investigations of Y 3 NbO 7 and related fluorite-based materials. Orthorhombic P weberite (P222 1 ) and monoclinic weberite models (P112 1 ) were derived via symmetry reduction of the orthorhombic C weberite structure. All models except monoclinic weberite failed to reproduce the experimental pair distribution function. Misfits were clearly visible for peaks arising from atom pairs within the first coordination shell (defect fluorite and pyrochlore) and beyond (orthorhombic C and P weberite). By contrast, monoclinic weberite (γ ≈ 91.8°) provided an excellent fit, with no major misfits observed. This unit cell features distorted YO 8 dodecahedra, YO 7 monocapped octahedra, and NbO 6 octahedra as building blocks. Comparison between the topologies of the cationic and anionic substructures in monoclinic weberite and its parent orthorhombic C structure revealed displacements of the metal atoms along the [100] direction and a less compact spatial distribution of oxygen atoms along the a axis. In conclusion, the monoclinic weberite model presented herein may serve as a starting point to revisit structural modeling of fluorite-based materials with challenging local structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Self-consistent description of the halo nature of 31 Ne with continuum and pairing correlations

Here a relativistic structure model has previously been used to predict a halo structure for 31 Ne, consistent with halo signatures from measured reaction cross sections of Ne isotopes bombarding Carbon targets. However, previous attempts to calculate those cross sections with reaction models were missing contributions from resonances and pairing correlations in their structure input. Use a reaction model with our relativistic fully microscopic structure model input to predict these cross sections and momentum distributions and analyze for possible halo signatures. Structure input for exotic Ne isotopes were obtained via the analytical continuation of the coupling constant (ACCC) method based on the relativistic mean field (RMF) theory with Bardeen - Cooper - Schrieffer (BCS) pairing approximation, the RAB approach. Total reaction cross sections, one-neutron removal cross sections, and momentum distributions of breakup reaction products were calculated with a Glauber model using our relativistic structure input. Our predictions of total reaction and one-neutron removal cross sections of 31 Ne on a Carbon target were significantly enhanced compared with those of neighboring Neon isotopes, agreeing with measurements at 240 MeV/nucleon and consistent with a single neutron halo. Furthermore, our calculations of the inclusive longitudinal momentum distribution of the 30 Ne and valence neutron residues from the 31 Ne breakup reaction indicate a dilute density distribution in coordinate space, another halo signature. We give a full description of the halo nature of 31 Ne that includes a self-consistent use of pairing and continuum contributions that makes predictions consistent with reaction cross section measurements. This approach can be utilized to determine the halo structure of other exotic nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Multidimensional Modeling of Mixture Formation in a Hydrogen-Fueled Heavy-Duty Optical Engine With Direct Injection

Hydrogen (H 2 ), as a carbon-free fuel, is considered as one of the most promising solutions to reduce the carbon footprint of hard-to-decarbonize energy and transportation sectors. As such, hydrogen-fueled internal combustion engines (H 2 ICEs) have recently been receiving increasing attention, particularly in applications such as on-road/off-road heavy-duty transport and combined heat and power. The direct injection (DI) of gaseous hydrogen into the combustion chamber offers great potential for achieving high power density and high engine efficiency, while mitigating the risk of backfire and reducing pre-ignition. However, the numerical simulation of H 2 DI system remains a formidable challenge associated with the high computational cost of reproducing compressible supersonic flow and shocks in narrow injector passages and in near-nozzle regions. In general, there is a lack of well-established and validated practices for the modeling of high-pressure H 2 DI in large-bore engines. Here, to this end, this study focuses on computational fluid dynamics (CFD) modeling of the mixture formation process in a heavy-duty optical engine employing a medium-pressure H 2 DI system. Both large eddy simulations (LES) and Reynolds Averaged Navier–Stokes (RANS) simulations are performed and evaluated against optical data. Gaseous hydrogen is injected into the combustion chamber via a centrally located outward opening hollow-cone injector at a pressure of 40 bar. Simulations are carried out for two injection timings, namely, −120 and −60 °CA. The numerical predictions for H 2 distribution in different horizontal and vertical planes during the compression stroke are systematically compared against optical data obtained through planar laser-induced fluorescence (PLIF) measurements. Overall, the LES approach using the Dynamic Structure model is found to have good predictive capabilities for the early jet penetration in terms of length and shape, as well as the later H 2 distributions. However, the unsteady RANS approach with the renormalization group $k - ϵ$ model, which is widely used by industry to model heavy-duty ICEs, significantly underpredicts the H 2 mixing, even at similar mesh resolution to that used in LES. These results indicate that there is a need for the improvement of mixing submodels within the RANS approach when applied to H 2 DI simulations.

LES↗
DOE OSTI2024

Operando pair distribution function analysis of nanocrystalline functional materials: the case of TiO 2 -bronze nanocrystals in Li-ion battery electrodes

Structural modelling of operando pair distribution function (PDF) data of complex functional materials can be highly challenging. To aid the understanding of complex operando PDF data, this article demonstrates a toolbox for PDF analysis. The tools include denoising using principal component analysis together with the structureMining , similarityMapping and nmfMapping apps available through the online service `PDF in the cloud' ( PDFitc , https://pdfitc.org/). The toolbox is used for both ex situ and operando PDF data for 3 nm TiO 2 -bronze nanocrystals, which function as the active electrode material in a Li-ion battery. The tools enable structural modelling of the ex situ and operando PDF data, revealing two pristine TiO 2 phases (bronze and anatase) and two lithiated Li x TiO 2 phases (lithiated versions of bronze and anatase), and the phase evolution during galvanostatic cycling is characterized.

Chemistry↗
DOE OSTI2023

Accelerating crystal structure determination with iterative AlphaFold prediction

Experimental structure determination can be accelerated with artificial intelligence (AI)-based structure-prediction methods such as AlphaFold . Here, an automatic procedure requiring only sequence information and crystallographic data is presented that uses AlphaFold predictions to produce an electron-density map and a structural model. Iterating through cycles of structure prediction is a key element of this procedure: a predicted model rebuilt in one cycle is used as a template for prediction in the next cycle. This procedure was applied to X-ray data for 215 structures released by the Protein Data Bank in a recent six-month period. In 87% of cases our procedure yielded a model with at least 50% of C α atoms matching those in the deposited models within 2 Å. Predictions from the iterative template-guided prediction procedure were more accurate than those obtained without templates. It is concluded that AlphaFold predictions obtained based on sequence information alone are usually accurate enough to solve the crystallographic phase problem with molecular replacement, and a general strategy for macromolecular structure determination that includes AI-based prediction both as a starting point and as a method of model optimization is suggested.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Comparison of structurally diverse simulation models for prediction of epidemic outcomes caused by a long-distance dispersed pathogen

Long-distance dispersal (LDD) pathogens pose substantial challenges for epidemic control due to their ability to generate new infection foci at great distances. While various modeling approaches have been developed to understand and manage such outbreaks, little work has compared how models of different structures behave under shared conditions. Here, in this study, we compare four structurally distinct epidemiological models — EPIMUL, GEMF, PoPS, and Warwick — each adapted to simulate the spread of wheat stripe rust (WSR), a wind-dispersed LDD pathogen, under identical epidemiological parameters and dispersal kernel. Using data from a controlled field experiment, we evaluate the ability of each model to replicate disease prevalence under nine intervention scenarios that vary in timing and culling area. While the models differ substantially in design — ranging from spatial grid-based to network-based and raster-based frameworks — the shared dispersal kernel allowed for close alignment in their predictions. All models accurately captured general epidemic trends, particularly the strong effect of early intervention on disease suppression. We qualitatively compared their behavioral responses across scenarios and also evaluated an ensemble prediction by averaging across model outputs. Our findings highlight how integrating shared epidemiological components into distinct modeling frameworks can improve consistency and accuracy, while reinforcing the importance of early culling in managing LDD pathogen outbreaks.

Dispersal kernel↗
DOE OSTI2021

The Climate Response to Emissions Reductions Due to COVID-19: Initial Results From CovidMIP

Many nations responded to the COVID-19 pandemic by restricting travel and other activities during 2020, resulting in temporarily reduced emissions of CO 2 , other greenhouse gases and ozone and aerosol precursors. We perform a coordinated Intercomparison, CovidMIP, of Earth System model simulations to assess the impact on climate of these emissions reductions. Eleven models performed multiple initial-condition ensembles to produce over 280 simulations spanning both initial condition and model structural uncertainty. We find model consensus on reduced aerosol amounts (particularly over East Asia) and associated increases in surface shortwave radiation levels. However, any impact on near-surface temperature or rainfall during 2020-2024 is extremely small and is not detectable in this initial analysis. Regional analyses on a finer scale, and closer attention to extremes (especially linked to changes in atmospheric composition and air quality) are required to test the impact of COVID-19-related emission reductions on near-term climate.

54 ENVIRONMENTAL SCIENCES↗