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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The Generality of the GUGA MRCI Approach in COLUMBUS for Treating Complex Quantum Chemistry

The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying out all of these calculations effectively is the availability of an efficient parallel code for the CI step. Configuration spaces of several billion in size now can be treated quite routinely on standard parallel computer clusters. Emerging developments in COLUMBUS, including the all configuration mean energy multiconfiguration self-consistent field method and the graphically contracted function method, promise to allow practically unlimited configuration space dimensions. Spin density based on the GUGA approach, analytic spin-orbit energy gradients, possibilities for local electron correlation MR calculations, development of general interfaces for nonadiabatic dynamics, and MRCI linear vibronic coupling models conclude this overview.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Selective One-Dimensional 13 C– 13 C Spin-Diffusion Solid-State Nuclear Magnetic Resonance Methods to Probe Spatial Arrangements in Biopolymers Including Plant Cell Walls, Peptides, and Spider Silk

Two-dimensional (2D) and 3D through-space 13 C– 13 C homonuclear spin-diffusion techniques are powerful solid-state nuclear magnetic resonance (NMR) tools for extracting structural information from 13 C-enriched biomolecules, but necessarily long acquisition times restrict their applications. In this work, we explore the broad utility and underutilized power of a chemical shift-selective one-dimensional (1D) version of a 2D 13 C– 13 C spin-diffusion solid-state NMR technique. The method, which is called 1D dipolar-assisted rotational resonance (DARR) difference, is applied to a variety of biomaterials including lignocellulosic plant cell walls, microcrystalline peptide fMLF, and black widow dragline spider silk. 1D 13 C– 13 C spin-diffusion methods described here apply in select cases in which the 1D 13 C solid-state NMR spectrum displays chemical shift-resolved moieties. Furthermore, this is analogous to the selective 1D nuclear Overhauser effect spectroscopy (NOESY) experiment utilized in liquid-state NMR as a faster (1D instead of 2D) and often less ambiguous (direct sampling of the time domain data, coupled with increased signal averaging) alternative to 2D NOESY. Selective 1D 13 C– 13 C spin-diffusion methods are more time-efficient than their 2D counterparts such as proton-driven spin diffusion (PDSD) and dipolar-assisted rotational resonance. The additional time gained enables measurements of 13 C– 13 C spin-diffusion buildup curves and extraction of spin-diffusion time constants TSD, yielding detailed structural information. Specifically, selective 1D DARR difference buildup curves applied to 13 C-enriched hybrid poplar woody stems confirm strong spatial interaction between lignin and acetylated xylan polymers within poplar plant secondary cell walls, and an interpolymer distance of ~0.45–0.5 nm was estimated. Additionally, Tyr/Gly long-range correlations were observed on isotopically enriched black widow spider dragline silks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Revealing the Predominant Surface Facets of Rough Cu Electrodes under Electrochemical Conditions

Metal electrodes with rough surfaces are frequently found to convert CO or CO 2 to hydrocarbons and oxygenates with high selectivity and at high reaction rates in comparison with their smooth counterparts. The atomic-level morphology of a rough electrode is likely one key factor responsible for its comparatively high catalytic selectivity and activity. However, few methods are capable of probing the atomic-level structure of rough metal electrodes under electrocatalytic conditions. As a result, the nuances in the atomic-level surface morphology that control the catalytic characteristics of these electrodes have remained largely unexplored. Because the C≡O stretching frequency of atop-bound CO (CO atop ) depends on the coordination of the underlying metal atom, the IR spectrum of this reaction intermediate on the copper electrode could, in principle, provide structural information about the catalytic surface during electrolysis. However, other effects, such as dynamic dipole coupling, easily obscure the dependence of the frequency on the surface morphology. Further, in the limit of low CO atop coverage, where coupling effects are small, the C≡O stretching frequencies of CO atop on Cu(111) and Cu(100) facets are virtually identical. Therefore, on the basis of the C≡O stretching frequency, it is not straightforward to distinguish between these two ubiquitous surface facets, which exhibit vastly different CO reduction activities. Herein, we show that key features of the atomic-level surface morphology of rough copper electrodes can be inferred from the potential dependence of the line shape of the C≡O stretching band of CO atop . Specifically, we compared two types of rough copper thin-film electrodes that are routinely employed in the context of surface-enhanced infrared absorption spectroscopy (SEIRAS). We found that copper films that are electrochemically deposited on Si-supported Au films (CuAu–Si) are poor catalysts for the reduction of CO to ethylene in comparison to copper films (Cu–Si) that are electrolessly deposited onto Si crystals. As quantified by differential electrochemical mass spectrometry (DEMS), the onset potential for ethylene is ~200 ± 65 mV more cathodic for CuAu–Si than that for Cu–Si. To reveal the origin of the disparate catalytic properties of Cu–Si and CuAu–Si, we probed the surfaces of the electrodes with cyclic voltammetry (CV) and SEIRAS. The CV characterization suggests that the (111) surface facet predominates on CuAu–Si, whereas the (100) facet is more common on Cu–Si. SEIRAS reveals that the line shape of the C≡O stretching of CO atop is composed of two bands that are attributable to CO atop on terrace and defect sites. The different surface structures manifest themselves in the form of starkly different potential dependences of the line shape of the C≡O stretching mode of CO atop on the two types of electrodes. With a simple Boltzmann model that considers the different adsorption energies of CO atop on terrace and defect sites, and the resulting CO atop populations on terrace and defect sites, we deduced that the observed electrode-specific potential dependence of the line shape is consistent with the presence of different predominant terrace sites on the two types of films. This strategy for assessing the atomic-level morphology is not restricted to SEIRAS but could also be applied to the C≡O stretching bands recorded with surface-enhanced Raman spectroscopy (SERS), which is suitable for probing a wide range of rough copper electrodes. Therefore, with this work, we establish the potential dependence of the C≡O stretching band of CO atop as a probe of the atomic-level surface structure of rough metal electrodes under electrochemical conditions. When it is coupled with complementary techniques, this methodology provides essential structural information for further improvement in the reaction selectivity of rough metal electrodes.

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

Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning

Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.

Lipo-chitooligosaccharides↗
DOE OSTI2020

Zymogen and activated protein C have similar structural architecture

Activated protein C is a trypsin-like protease with anticoagulant and cytoprotective properties that is generated by thrombin from the zymogen precursor protein C in a reaction greatly accelerated by the cofactor thrombomodulin. The molecular details of this activation remain elusive due to the lack of structural information. We now fill this gap by providing information on the overall structural organization of these proteins using single molecule Förster resonance energy transfer and small angle X-ray scattering. Under physiological conditions, both zymogen and protease adopt a conformation with all domains vertically aligned along an axis 76 Å long and maximal particle size of 120 Å. This conformation is stabilized by binding of Ca 2+ to the Gla domain and is affected minimally by interaction with thrombin. Hence, the zymogen protein C likely interacts with the thrombin-thrombomodulin complex through a rigid body association that produces a protease with essentially the same structural architecture. This scenario stands in contrast to an analogous reaction in the coagulation cascade where conversion of the zymogen prothrombin to the protease meizothrombin by the prothrombinase complex is linked to a large conformational transition of the entire protein. The presence of rigid EGF domains in protein C as opposed to kringles in prothrombin likely accounts for the different conformational plasticity of the two zymogens. The new structural features reported here for protein C have general relevance to vitamin K-dependent clotting factors containing EGF domains, such as factors VII, IX, and X.

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

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration

Abstract Motivation Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools. Results This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics. Availability and implementation ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.

Lai, Jhih-Siang (ORCID:0000000156775890)↗
DOE OSTI2023

Sandia Mechanics Challenge 2023 Information Packet: Structure with a Threaded Fastener Joint

The Sandia Mechanics Challenge (SMC) provides the solid-mechanics community a forum for assessing its ability to predict mechanical behavior in structures and materials through a blind, round-robin format. Computationalists are asked to predict the behavior of an unfamiliar geometry given experimental calibration data, their predictions are compared to experimental measurements of the SMC scenario, and then the participants assess and compare their approaches, documenting their findings. The SMC broadens the scope of Sandia-hosted benchmarking problems that previously focused on ductile failure through the Sandia Fracture Challenges, enabling an enduring, community-wide self-assessment of predictive capabilities for a variety of mechanics topics. The SMC is part of the Structural Reliability Partnership, which offers other benchmarking challenges hosted by several participating institutions.

42 ENGINEERING↗
DOE OSTI2025

Cryo-EM Visualization of Intermolecular π-Electron Interactions within π-Conjugated Peptidic Supramolecular Polymers

The self-assembly of “π-peptides” – molecules with π-electron cores substituted with two or more oligopeptide chains – brings organic electronic function into biologically relevant nanomaterials. π-Peptides assemble into fibrillar nanomaterials as driven by enthalpic peptide-based hydrogen bonding networks and pi-core-based quadrupolar interactions. A large body of spectroscopic, morphological and computational studies informs on the nature of the self-assembly process and the resulting nanostructures, but detailed structural information has remained elusive. Here, inspired by the recent use of cryogenic electron microscopy (cryo-EM) to provide high-resolution structures for synthetic peptide nanomaterials, we present here the use of cryo-EM to offer ca. 3 Å resolution of π-peptide nanomaterial assemblies, visualizing for the first time the nature of the intermolecular π-core electronic interactions responsible for energy transport through these supramolecular materials.

Group theory↗
DOE OSTI2021

Scanning Electrochemical and Photoelectrochemical Microscopy on Finder Grids: Toward Correlative Multitechnique Imaging of Surfaces

Scanning electrochemical microscopy (SECM) is a powerful technique for mapping surface reactivity and investigating heterogeneous processes on the nanoscale. Despite significant advances in high-resolution SECM and photo-SECM imaging, they cannot provide atomic scale structural information about surfaces. By correlating the SECM images with atomic scale structural and bonding information obtained by transmission electron microscopy (TEM) techniques with one-to-one correspondence, one can elucidate the nature of the active sites and understand the origins of heterogeneous surface reactivity. Here, to enable multitechnique imaging of the same nanoscale portion of the electrode surface, we develop a methodology for using a TEM finder grid as a conductive support in SECM and photo-SECM experiments. In this paper, we present the results of our first nanoscale SECM and photo-SECM experiments on carbon TEM grids, including imaging of semiconductor nanorods.

14 SOLAR ENERGY↗
DOE OSTI2025

De Novo Design of High‐Affinity Miniprotein Binders Targeting Francisella Tularensis Virulence Factor

Abstract Francisella tularensis poses considerable public health risk due to its high infectivity and potential for bioterrorism. Francisella‐like lipoprotein (Flpp3), a key virulence factor unique to Francisella, plays critical roles in infection and immune evasion, making it a promising target for therapeutic development. However, the lack of well‐defined binding pockets and structural information on native interactions has hindered structure‐guided ligand discovery against Flpp3. Here, we used a combination of physics‐based and deep‐learning methods to design high‐affinity miniprotein binders targeting two distinct sites on Flpp3. We identified four binders for site I with binding affinities ranging between 24–110 nM. For the second site, an initial binder showed a dissociation constant ( K D ) of 81 nM, and subsequent site saturation mutagenesis yielded variants with sub‐nanomolar affinities. Circular dichroism confirmed the topology of designed miniproteins. The X‐ray crystal structure of Flpp3 in complex with a site I binder is nearly identical to the design model (Cα root‐mean‐square deviation (RMSD): 0.9 Å). These designed miniproteins provide research tools to explore the roles of Flpp3 in tularemia and should enable the development of new therapeutic candidates.

Gokce‐Alpkilic, Gizem [Molecular Engineering and S↗
DOE OSTI2023

Quantifying uncertainties due to optical potentials in one-neutron knockout reactions

One-neutron knockout reactions have been widely used to extract information about the single-particle structure of nuclei from the valley of stability to the drip lines. The interpretation of knockout data relies on reaction models, where the uncertainties are typically not accounted for. In this work, we quantify uncertainties of optical potentials used in these reaction models and propagate them, for the first time, to knockout observables using a Bayesian analysis. We study two reactions in the present paper, the first of which involves a loosely bound halo projectile, 11 Be, and the second a tightly bound projectile, 12 C. We first quantify the parametric uncertainties associated with phenomenological optical potentials. Complementing this approach, we also quantify the model uncertainties associated with the chiral forces that can be used to construct microscopic optical potentials. For the phenomenological study, we investigate the impact of the imaginary terms of the optical potential on the breakup and stripping components of the knockout cross sections as well as the impact of the angular range. For the 11 Be case, the theoretical uncertainty from the phenomenological method is on the order of the experimental uncertainty of the knockout observables; however, for the 12 C case, the theoretical uncertainty is significantly larger. Additionally, the widths of the uncertainty bands for the knockout observables obtained for the microscopic study and the phenomenological approach are of similar orders of magnitude. Based on this work we conclude that structure information inferred from the ratio of the knockout cross sections will carry a theoretical uncertainty of at least 20% for halo nuclei and at least 40% for tightly bound nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

MFNets: data efficient all-at-once learning of multifidelity surrogates as directed networks of information sources

We present an approach for constructing a surrogate from ensembles of information sources of varying cost and accuracy. The multifidelity surrogate encodes connections between information sources as a directed acyclic graph, and is trained via gradient-based minimization of a nonlinear least squares objective. While the vast majority of state-of-the-art assumes hierarchical connections between information sources, our approach works with flexibly structured information sources that may not admit a strict hierarchy. The formulation has two advantages: (1) increased data efficiency due to parsimonious multifidelity networks that can be tailored to the application; and (2) no constraints on the training data—we can combine noisy, non-nested evaluations of the information sources. Finally, numerical examples ranging from synthetic to physics-based computational mechanics simulations indicate the error in our approach can be orders-of-magnitude smaller, particularly in the low-data regime, than single-fidelity and hierarchical multifidelity approaches.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Informative and non-informative decomposition of turbulent flow fields

Not all the information in a turbulent field is relevant for understanding particular regions or variables in the flow. Here, we present a method for decomposing a source field into its informative Φ I (x, t) and residual Φ R (x, t) components relative to another target field. The method is referred to as informative and non-informative decomposition (IND). All the necessary information for physical understanding, reduced-order modelling and control of the target variable is contained in Φ I (x, t), whereas Φ R (x, t) offers no substantial utility in these contexts. The decomposition is formulated as an optimisation problem that seeks to maximise the time-lagged mutual information of the informative component with the target variable while minimising the mutual information with the residual component. The method is applied to extract the informative and residual components of the velocity field in a turbulent channel flow, using the wall shear stress as the target variable. We demonstrate the utility of IND in three scenarios: (i) physical insight into the effect of the velocity fluctuations on the wall shear stress; (ii) prediction of the wall shear stress using velocities far from the wall; and (iii) development of control strategies for drag reduction in a turbulent channel flow using opposition control. In case (i), IND reveals that the informative velocity related to wall shear stress consists of wall-attached high- and low-velocity streaks, collocated with regions of vertical motions and weak spanwise velocity. This informative structure is embedded within a larger-scale streak–roll structure of residual velocity, which bears no information about the wall shear stress. In case (ii), the best-performing model for predicting wall shear stress is a convolutional neural network that uses the informative component of the velocity as input, while the residual velocity component provides no predictive capabilities. Finally, in case (iii), we demonstrate that the informative component of the wall-normal velocity is closely linked to the observability of the target variable and holds the essential information needed to develop successful control strategies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning

The 2024 Nobel Prize in Chemistry was awarded in part for de novo protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and three-dimensional structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these AI/ML models operate on the long-standing hypothesis that the structure of a protein is determined by its amino acid sequence. More recently, AlphaFold2 has been adapted for the prediction of multiple protein conformations by subsampling multiple sequence alignments. Herein, we provide an overview of the deterministic relationship between sequence and structure, which was hypothesized over half a century ago with profound implications for the biological sciences ever since. We postulate that protein conformational dynamics are also determined, at least in part, by amino acid sequence and that this relationship may be leveraged for construction of AI/ML models dedicated to predicting protein conformational ensembles. Accordingly, we describe a conceptual model architecture, which may be trained on sequence data in combination with conformationally sensitive structural information, coming primarily from nuclear magnetic resonance (NMR) spectroscopy. Notwithstanding certain limitations in this context, NMR offers abundant structural heterogeneity conducive to conformational ensemble prediction. As NMR and other data continue to accumulate, sequence-informed prediction of protein structural dynamics with AI/ML has the potential to emerge as a transformative capability across the biological sciences.

Artificial intelligence↗
DOE OSTI2024

Solvation Structure of Methanol-in-Salt Electrolyte Revealed by Small-Angle X-ray Scattering and Simulations

The solvation structure of water-in-salt electrolytes was thoroughly studied, and two competing structures—anion solvated structure and anion network—were well-defined in recent publications. To further reveal the solvation structure in those highly concentrated electrolytes, particularly the influence of solvent, methanol was chosen as the solvent for this proposed study. In this work, small-angle X-ray scattering, small-angle neutron scattering, Fourier-transform infrared spectroscopy, and Raman spectroscopy were utilized to obtain the global and local structural information. With the concentration increment, the anion network formed by TFSI - became the dominant structure. Meanwhile, the hydrogen bonds among methanol were interrupted by the TFSI - anion and formed a new connection with them. Further, molecular dynamic simulations with two different force fields (GAFF and OPLS-AA) are tested, and GAFF agreed with synchrotron small-angle X-ray scattering/wide-angle X-ray scattering (SAXS/WAXS) results well and provided insightful information about molecular/ion scale solvation structure. This article not only deepens the understanding of the solvation structure in highly concentrated solutions, but more importantly, it provides additional strong evidence for utilizing SAXS/WAXS to validate molecular dynamics simulations.

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

Hydrothermal synthesis of chiral carbon dots

Abstract Nanocolloids that are cumulatively referred to as nanocarbons, attracted significant attention during the last decade because of facile synthesis methods, water solubility, tunable photoluminescence, easy surface modification, and high biocompatibility. Among the latest development in this reserach area are chiral nanocarbons exemplified by chiral carbon dots (CDots). They are expected to have applications in sensing, catalysis, imaging, and nanomedicine. However, the current methods of CDots synthesis show often contradictory chemical/optical properties and structural information that required a systematic study with careful structural evaluation. Here, we investigate and optimize chiroptical activity and photoluminescence of L‐ and D‐ CDots obtained by hydrothermal carbonization of L‐ and D‐ cysteine, respectively. Nuclear magnetic resonance spectroscopy demonstrates that they are formed via gradual dehydrogenation and condensation reactions of the starting amino acid leading to particles with a wide spectrum of functional groups including aromatic cycles. We found that the chiroptical activity of CDots has an inverse correlation with the synthesis duration and temperature, whereas the photoluminescence intensity has a direct one, which is associated with degree of carbonization. Also, our studies show that the hydrothermal synthesis of cysteine in the presence of boric acid leads to the formation of CDots rather than boron nitride nanoparticles as was previously proposed in several reports. These results can be used to design chiral carbon‐based nanoparticles with optimal chemical, chiroptical, and photoluminescent properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗