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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Dynamic Interfacial Architectures: Cruciferin‐Stabilized Oil/Water Interfaces for Sustainable Emulsions

Stabilizing oil-water interfaces in emulsions by plant-based proteins provides sustainable and tunable ways for designing emulsions with specific properties, for food, healthcare, and pharmaceuticals. Cruciferin, a protein from rapeseed, has great potential as green emulsifier, but details about its structure and mobility at oil-water interfaces are largely unknown. Here, these properties are studied with small angle neutron and x-ray scattering, and neutron spin echo spectroscopy, analyzed by atomistic modelling of scattering curves and coarse-grained modelling, to gain insight into interface coverage, and molecular conformation and mobility at the interface. Cruciferin assumes trimeric conformations at the interface, as in solution, but with its protrusions from the central core of the subunits (“arms”) more compressed. Interfacial mobility is only marginally lower than in solution, indicating the arms still transiently extend and preserve a network, for the first time revealing the mechanism how cruciferin forms highly elastic 2d gel-like oil-water interfaces, as observed in macroscopic rheology. The high interfacial mobility may help in self-repairing non-stabilized interfacial fractions, reducing coalescence. These findings provide a deeper molecular level understanding of proteins at oil-water interfaces, which can stimulate development of new plant-based emulsion products, and contribute to the global protein transition.

cruciferin↗
DOE OSTI2022

Comment on “Microhydration of Biomolecules: Revealing the Native Structures by Cold Ion IR Spectroscopy”

This paper presents a re-examination of the conclusions of a study reported in The Journal of Physical Chemistry Letters (Saparbaev et al., 2021, 12, 907) that compared the structure of microsolvated ions formed by electrospray ionization to those formed in the gas-phase via a previously published cryogenic ion trap approach. We conducted additional experiments that clearly show that most of the observed differences in the IR spectra can be accounted for by considering the different spectroscopic action schemes used to obtain them. In particular, the presence of the D 2 -tag induces shifts in some of the N-H and O-H peaks which need to be carefully considered before comparing spectra. Furthermore, once these spectral effects are taken into account, we show that both clustering approaches yields similar clusters structures for the small GlyH + (H 2 O)n species. Using unimolecular reaction rate theory, we also show that for the small complexes considered here, only the gas-phase equilibrium distribution of conformers should be expected in both experimental approaches. In addition, the barrier heights necessary to kinetically trap high-energy conformers at 298K is explored using a series of model polyalanine chains.

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

Critical role of structural order in bipolar redox-active molecules for organic redox flow batteries

Bipolar redox-active molecules (BRMs) have been suggested as a means to address crossover related issues in all-organic redox flow batteries (RFBs). In such species, electron donors (anolytes) and electron acceptors (catholytes) are linked by a chain, and the same chemical composition is used in both anode and cathode compartments to reduce chemical gradients and unbalanced ion transport. The resultant RFBs resemble the aqueous vanadium RFBs, but offer greater design flexibility and potentially more favorable electrochemical and physicochemical properties. Yet the complex trade-offs in these properties have been a complication. Here we developed a fundamental rubric to uncover the likely origins in the performance metrics of these BRMs that are salient for their use in RFBs. Methylene linked phenothiazine and phthalimide moieties were employed as model BRMs and variations in their properties and molecular conformations were evaluated by systematically varying the methylene linker. Our results revealed that even minimalistic changes in the linker length resulted in dramatic oscillations in the solubility and stability. Using crystallography, quantum chemistry, and molecular dynamics, we clarify that the seemingly fluctuating behavior is due to (1) the inter- and intra-molecular charge transfer between the donor and acceptor through bond or/and through space; (2) the formation of distinctive packing/clustering motifs. Both interactions are strongly dependent on the molecular conformation. As these structural factors modify the electronic structure of both electroactive functional groups and do not change monotonically, the structure–property response in BRMs is often complex. Finally, accordingly, these behaviors need to be taken into account in developing BRMs and knowledge of these structural factors will allow the more rational design of BRMs for grid-scale energy storage.

25 ENERGY STORAGE↗
DOE OSTI2023

Structure of metallochaperone in complex with the cobalamin-binding domain of its target mutase provides insight into cofactor delivery

G-protein metallochaperone MeaB in bacteria [methylmalonic aciduria type A (MMAA) in humans] is responsible for facilitating the delivery of adenosylcobalamin (AdoCbl) to methylmalonyl-CoA mutase (MCM), the only AdoCbl-dependent enzyme in humans. Genetic defects in the switch III region of MMAA lead to the genetic disorder methylmalonic aciduria in which the body is unable to process certain lipids. Here, we present a crystal structure of Methylobacterium extorquens MeaB bound to a nonhydrolyzable guanosine triphosphate (GTP) analog guanosine-5'-[(β,γ)-methyleno]triphosphate (GMPPCP) with the Cbl-binding domain of its target mutase enzyme (MeMCM cbl ). This structure provides an explanation for the stimulation of the GTP hydrolyase activity of MeaB afforded by target protein binding. We find that upon MCM cbl association, one protomer of the MeaB dimer rotates ~180°, such that the inactive state of MeaB is converted to an active state in which the nucleotide substrate is now surrounded by catalytic residues. Importantly, it is the switch III region that undergoes the largest change, rearranging to make direct contacts with the terminal phosphate of GMPPCP. These structural data additionally provide insights into the molecular basis by which this metallochaperone contributes to AdoCbl delivery without directly binding the cofactor. Our data suggest a model in which GTP-bound MeaB stabilizes a conformation of MCM that is open for AdoCbl insertion, and GTP hydrolysis, as signaled by switch III residues, allows MCM to close and trap its cofactor. Substitutions of switch III residues destabilize the active state of MeaB through loss of protein:nucleotide and protein:protein interactions at the dimer interface, thus uncoupling GTP hydrolysis from AdoCbl delivery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

NN-OpInf

SAND2026-18878O The NN-OpInf tool is a PyTorch-based approach to operator inference that uses composable, structure-preserving neural networks to represent nonlinear operators. Operator inference is a machine learning method for inferring low-dimensional systems from data and polynomial models for system dynamics. However, many systems do not conform to polynomial structures, which NN-OpInf addresses by parameterizing operators with neural networks. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

SciDAC↗
DOE OSTI2021

Sierra/SolidMechanics 5.0 Capabilities in Development

This user’s guide documents capabilities in Sierra/SolidMechanics which remain “in-development” and thus are not tested and hardened to the standards of capabilities listed in Sierra/SM 5.0 User’s Guide. Capabilities documented herein are available in Sierra/SM for experimental use only until their official release. These capabilities include, but are not limited to, novel discretization approaches such as peridynamics and the conforming reproducing kernel (CRK) method, numerical fracture and failure modeling aids such as the extended finite element method (XFEM) and $\textit{J}$-integral, explicit time step control techniques, dynamic mesh rebalancing, as well as a variety of new material models and finite element formulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Sierra/SolidMechanics 5.2 Capabilities in Development

This user’s guide documents capabilities in Sierra/SolidMechanics which remain “in-development” and thus are not tested and hardened to the standards of capabilities listed in Sierra/SM 5.2 User’s Guide. Capabilities documented herein are available in Sierra/SM for experimental use only until their official release. These capabilities include, but are not limited to, novel discretization approaches such as the conforming reproducing kernel (CRK) method, numerical fracture and failure modeling aids such as the extended finite element method (XFEM) and J-integral, explicit time step control techniques, dynamic mesh rebalancing, as well as a variety of new material models and finite element formulations.

42 ENGINEERING↗
DOE OSTI2022

Sierra/SolidMechanics 5.4 Capabilities in Development

This user’s guide documents capabilities in Sierra/SolidMechanics which remain “in-development” and thus are not tested and hardened to the standards of capabilities listed in Sierra/SM 5.4 User’s Guide. Capabilities documented herein are available in Sierra/SM for experimental use only until their official release. These capabilities include, but are not limited to, novel discretization approaches such as the conforming reproducing kernel (CRK) method, numerical fracture and failure modeling aids such as the extended finite element method (XFEM) and J-integral, explicit time step control techniques, dynamic mesh rebalancing, as well as a variety of new material models and finite element formulations.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Sierra/SolidMechanics 5.6 Capabilities in Development

This user's guide documents capabilities in Sierra/SolidMechanics which remain "in-development" and thus are not tested and hardened to the standards of capabilities listed in Sierra/SM 5.6 User's Guide. Capabilities documented herein are available in Sierra/SM for experimental use only until their official release. These capabilities include, but are not limited to, novel discretization approaches such as the conforming reproducing kernel (CRK) method, numerical fracture and failure modeling aids such as the extended finite element method (XFEM) and J-integral, explicit time step control techniques, dynamic mesh rebalancing, as well as a variety of new material models and finite element formulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Sierra/SolidMechanics 5.8 In-Development Manual

This user’s guide documents capabilities in Sierra/SolidMechanics which remain “in-development” and thus are not tested and hardened to the standards of capabilities listed in Sierra/SM 5.8 User’s Guide. Capabilities documented herein are available in Sierra/SM for experimental use only until their official release. These capabilities include, but are not limited to, novel discretization approaches such as the conforming reproducing kernel (CRK) method, numerical fracture and failure modeling aids such as the extended finite element method (XFEM) and J-integral, explicit time step control techniques, dynamic mesh rebalancing, as well as a variety of new material models and finite element formulations.

42 ENGINEERING↗
DOE OSTI2022

Sierra/SolidMechanics 5.10 In-Development Manual

This user’s guide documents capabilities in Sierra/SolidMechanics which remain “in-development” and thus are not tested and hardened to the standards of capabilities listed in Sierra/SM 5.10 User’s Guide. Capabilities documented herein are available in Sierra/SM for experimental use only until their official release. These capabilities include, but are not limited to, novel discretization approaches such as the conforming reproducing kernel (CRK) method, numerical fracture and failure modeling aids such as the extended finite element method (XFEM) and J-integral, explicit time step control techniques, dynamic mesh rebalancing, as well as a variety of new material models and finite element formulations.

42 ENGINEERING↗
DOE OSTI2023

Sierra/SolidMechanics 5.16 Capabilities in Development Manual

This user’s guide documents capabilities in Sierra/SolidMechanics which remain “in-development” and thus are not tested and hardened to the standards of capabilities listed in Sierra/SM 5.16 User’s Guide. Capabilities documented herein are available in Sierra/SM for experimental use only until their official release. These capabilities include, but are not limited to, novel discretization approaches such as the conforming reproducing kernel (CRK) method, numerical fracture and failure modeling aids such as the extended finite element method (XFEM) and J-integral, explicit time step control techniques, dynamic mesh rebalancing, as well as a variety of new material models and finite element formulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Eigenstate entanglement scaling for critical interacting spin chains

With increasing subsystem size and energy, bipartite entanglement entropies of energy eigenstates cross over from the groundstate scaling to a volume law. In previous work, we pointed out that, when strong or weak eigenstate thermalization (ETH) applies, the entanglement entropies of all or, respectively, almost all eigenstates follow a single crossover function. The crossover functions are determined by the subsystem entropy of thermal states and assume universal scaling forms in quantum-critical regimes. This was demonstrated by field-theoretical arguments and the analysis of large systems of non-interacting fermions and bosons. Here, we substantiate such scaling properties for integrable and non-integrable interacting spin-1/2 chains at criticality using exact diagonalization. In particular, we analyze XXZ and transverse-field Ising models with and without next-nearest-neighbor interactions. Indeed, the crossover of thermal subsystem entropies can be described by a universal scaling function following from conformal field theory. Furthermore, we analyze the validity of ETH for entanglement in these models. Even for the relatively small system sizes that can be simulated, the distributions of eigenstate entanglement entropies are sharply peaked around the subsystem entropies of the corresponding thermal ensembles.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗
DOE OSTI2022

Ethanol-Induced Condensation and Decondensation in DNA-Linked Nanoparticles: A Nucleosome-like Model for the Condensed State

Inspired by the conventional use of ethanol to induce DNA precipitation, ethanol condensation has been applied as a routine method to dynamically tune “bond” lengths (i.e., the surface-to-surface distances between adjacent nanoparticles that are linked by DNA) and thermal stabilities of colloidal crystals involving DNA-linked nanoparticles. However, the underlying mechanism of how the DNA bond that links gold nanoparticles changes in this class of colloidal crystals in response to ethanol remains unclear. Here, we conducted a series of all-atom molecular dynamic (MD) simulations to explore the free energy landscape for DNA condensation and decondensation. Our simulations confirm that DNA condensation is energetically much more favorable under 80% ethanol conditions than in pure water, as a result of ethanol’s role in enhancing electrostatic interactions between oppositely charged species. Moreover, the condensed DNA adopts B-form in pure water and A-form in 80% ethanol, which indicates that the higher-order transition does not affect DNA’s conformational preferences. We further propose a nucleosome-like supercoiled model for the DNA condensed state, and we show that the DNA end-to-end distance derived from this model matches the experimentally measured DNA bond length of about 3 nm in the fully condensed state for DNA where the measured length is 16 nm in water. Altogether, this study provides an atomistic understanding of the mechanism underlying ethanol-induced condensation and water-induced decondensation, while our proposed nucleosome-like model allows the design of new strategies for interpreting experimental studies of DNA condensation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗