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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 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Molecular mechanism of Rubisco activase: Dynamic assembly and Rubisco remodeling

Ribulose-1,5-bisphosphate (RuBP) carboxylase-oxygenase (Rubisco) enzyme is the limiting step of photosynthetic carbon fixation, and its activation is regulated by its co-evolved chaperone, Rubisco activase (Rca). Rca removes the intrinsic sugar phosphate inhibitors occupying the Rubisco active site, allowing RuBP to split into two 3-phosphoglycerate (3PGA) molecules. This review summarizes the evolution, structure, and function of Rca and describes the recent findings regarding the mechanistic model of Rubisco activation by Rca. New knowledge in these areas can significantly enhance crop engineering techniques used to improve crop productivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Size-dependent errors in real-time electron density propagation

Real-time (RT) electron density propagation with time-dependent density functional theory (TDDFT) or Hartree–Fock (TDHF) is one of the most popular methods to model the charge transfer in molecules and materials. However, both RT-TDHF and RT-TDDFT within the adiabatic approximation are known to produce inaccurate evolution of the electron density away from the ground state in model systems, leading to large errors in charge transfer and erroneous shifting of peaks in absorption spectra. Given the poor performance of these methods with small model systems and the widespread use of the methods with larger molecular and material systems, here we bridge the gap in our understanding of these methods and examine the size-dependence of errors in RT density propagation. We analyze the performance of RT density propagation for systems of increasing size during the application of a continuous resonant field to induce Rabi-like oscillations, during charge-transfer dynamics, and for peak shifting in simulated absorption spectra. We find that the errors in the electron dynamics are indeed size dependent for these phenomena, with the largest system producing the results most aligned with those expected from linear response theory. The results suggest that although the RT-TDHF and RT-TDDFT methods may produce severe errors for model systems, the errors in charge transfer and resonantly driven electron dynamics may be much less significant for more realistic, large-scale molecules and materials.

Chemistry↗
DOE OSTI2023

Universal and interpretable classification of atomistic structural transitions via unsupervised graph learning

Materials processing often occurs under extreme dynamic conditions leading to a multitude of unique structural environments. These structural environments generally occur at high temperatures and/or high pressures, often under non-equilibrium conditions, which results in drastic changes in the material's structure over time. Computational techniques, such as molecular dynamics simulations, can probe the atomic regime under these extreme conditions. However, characterizing the resulting diverse atomistic structures as a material undergoes extreme changes in its structure has proved challenging due to the inherently non-linear relationship between structures as large-scale changes occur. Here, we introduce SODAS++, a universal graph neural network framework, that can accurately and intuitively quantify the atomistic structural evolution corresponding to the transition between any two arbitrary phases. We showcase SODAS++ for both solid–solid and solid–liquid transitions for systems of increasing geometric and chemical complexity, such as colloidal systems, elemental Al, rutile and amorphous TiO 2 , and the non-stoichiometric ternary alloy Ag 26 Au 5 Cu 19 . Finally, we show that SODAS++ can accurately quantify all transitions in a physically interpretable manner, showcasing the power of unsupervised graph neural network encodings for capturing the complex and non-linear pathway, a material's structure takes as it evolves.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Effect of Stress on Irradiation Responses of Highly Oriented Pyrolytic Graphite

The effect of stress on irradiation responses of highly oriented pyrolytic graphite (HOPG) was studied by combing molecular dynamics (MD) simulation, proton irradiation, and Raman characterization. MD simulations of carbon knock-on at energies < 60 eV were used to obtain average threshold displacement energies (E¯d) as a function of strain ranging from 0 to 10%. Simulations at a higher irradiation energy of 2–5 keV were used to study the effect of strain on damage cascade evolution. With increasing tensile strain, E¯d was reduced from 35 eV at 0% strain to 31 eV at 10% strain. The strain-reduced E¯d led to a higher damage peak and more surviving defects (up to 1 ps). Furthermore, high strains induced local cleavage around the cavities, as one additional mechanism of damage enhancement. Experimentally, HOPG film was folded, and the folded region with the maximum tensile stress was irradiated by a 2 MeV proton beam. Raman characterization showed significantly enhanced D to G modes in comparison to the stress-free irradiation. Based on the strain dependence of E¯d and the Kinchin–Pease model, a formula for displacement estimation under different tensile strains is proposed. The stress effects need to be considered in graphite applications in a reactor’s harsh environment where both neutron damage and stress are present.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Distinct Gas-Particle Partitioning and Viscosity Characteristics of Secondary Organic Aerosols Derived from α-Pinene versus Ocimene

Secondary organic aerosols (SOA) have complex, multicomponent composition that controls particle viscosity and gas-particle partitioning, key factors to their atmospheric evolution. This study investigates the chemical composition, volatility and viscosity of SOA formed by ozonolysis of cyclic α-pinene (PSOA) and acyclic ocimene (OSOA) monoterpenes. Using Temperature-Programmed Desorption combined with Direct Analysis in Real-Time ionization and High-Resolution Mass Spectrometry, we determined the molecular composition and saturation mass concentration of individual SOA constituents. These data enabled gas-particle partitioning and viscosity estimates under varied atmospheric conditions. PSOA, composed of higher molecular weight and less oxidized species, shows higher condensability and viscosity under high total organic mass (tOM) loadings. Here, in contrast, OSOA, consisting of more oxidized, lower molecular weight species, exhibits greater sensitivity to tOM, with viscosity increasing significantly upon dilution. Poke-flow experiments support this trend, indicating that OSOA undergoes more dynamic compositional and phase changes during atmospheric aging. These observations reveal distinct dynamic trends in the atmospheric transformations and reactivity of SOA from cyclic and acyclic monoterpenes, with the latter showing greater compositional changes during aging that alter viscosity and diffusion. This highlights the importance of incorporating such dynamic transformations into atmospheric models to improve predictions of SOA atmospheric loadings, lifetimes, and impacts.

cyclic and acyclic monoterpenes↗
DOE OSTI2023

Engineering Crassulacean Acid Metabolism in C3 and C4 Plants

Carbon dioxide (CO2) is a major greenhouse gas contributing to changing climatic conditions, which is a grand challenge affecting the security of food, energy, and environment. Photosynthesis plays the central role in plant-based CO2 reduction. Plants performing CAM (crassulacean acid metabolism) photosynthesis have a much higher water use efficiency than those performing C3 or C4 photosynthesis. Therefore, there is a great potential for engineering CAM in C3 or C4 crops to enhance food/biomass production and carbon sequestration on arid, semiarid, abandoned, or marginal lands. Recent progresses in CAM plant genomics and evolution research, along with new advances in plant biotechnology, have provided a solid foundation for bioengineering to convert C3/C4 plants into CAM plants. Here, we first discuss the potential strategies for CAM engineering based on our current understanding of CAM evolution. Then we describe the technical approaches for engineering CAM in C3 and C4 plants, with a focus on an iterative four-step pipeline: (1) designing gene modules, (2) building the gene modules and transforming them into target plants, (3) testing the engineered plants through an integration of molecular biology, biochemistry, metabolism, and physiological approaches, and (4) learning to inform the next round of CAM engineering. Finally, we discuss the challenges and future opportunities for fully realizing the potential of CAM engineering.

Yang, Xiaohan↗
DOE OSTI2025

Shear Response of Ionizable Polymer Melts at the Crossover from Ionomers to Polyelectrolytes

Nonlinear shear response of polymers is affected by inherent barriers for diffusive motion, including entanglements and topology. In ionizable polymers, ionic clusters further constrain the intrinsic dynamics of the polymers, significantly enhancing their viscosity. Here, using fully atomistic molecular dynamics simulations, the nonlinear shear response of ionizable polymers is presented, across the transition from the ionomer regime where distinctive clusters dominate the structure to the polyelectrolyte regime where clusters percolate, in polystyrene randomly sulfonated with fractions of SO 3 − groups of f = 0.20 and 0.35, in pristine and tetrahydrofuran (THF) swollen polyelectrolyte melts. For f = 0.20, the ionic clusters first fracture into smaller clusters followed by splitting into individual ionic groups and eventually reform. At higher f, the clusters morph in shape but do not break under high shear. At very high shear rates, all of the chains stretch and recoil rapidly. As the shear rate is reduced, some chains stretch and recoil, while others remain largely unaffected by the shear. Macroscopically, for all systems, the shear viscosity displays initially an elastic response, followed by nonlinear shear stress overshoot and, eventually, a steady state. The evolution of viscosity with time and shear reflects that of the ionizable domains.

cluster chemistry↗
DOE OSTI2020

In-situ/operando X-ray absorption spectroscopic investigation of the electrode/electrolyte interface on the molecular scale

A method for performing X-ray absorption spectroscopy (XAS) in the soft X-ray region was developed to investigate the surface-sensitive electron signal of electrode/electrolyte interfaces in common multivalent based organic solvents under in situ/operando conditions. Our approach enables us to probe the molecular-scale structure of electrode interfaces by measuring total electron yield and is suitable for redox systems exhibiting low intrinsic electrochemical current. In-situ F K-edge XAS measurements in a 0.5 M Magnesium bis(trifluoromethanesulfonimide)/2-Methyltetrahydrofuran (Mg(TFSI) 2 /2-MeTHF) electrolyte were carried out to determine the evolution of interfacial species during the electrochemical charging/discharging process. Time-dependent density-functional theory (TD-DFT) simulation indicate that the F K-edge evolution is the result of interfacial chemical environment change driven by electrochemical potential. In addition, we performed the “operando XAS” which runs the CV and collects spectra simultaneously. Furthermore, by using this method, the non-equilibrium state of condensed matter interfaces and interfacial dynamical transient process can be revealed.

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

Commodity Thermoplastic Elastomer-Enabled Templated Synthesis of Large-Pore Ordered Mesoporous Materials

Fabrication of ordered mesoporous materials (OMMs) has predominantly relied on templating-based methods. However, these methods are constrained by several limitations, especially the limited pore sizes attainable with commercially available surfactants used as structure-directing agents. To unlock the full potential of the OMMs, it is essential to develop synthetic strategies that facilitate the production of large-pore OMMs using scalable processes and cost-effective precursors. This work demonstrates the use of thermoplastic elastomer (TPE)-derived carbon replicas for synthesizing ordered mesoporous silica (OMS) and metal oxides (OMMOs) via precursor infiltration and template removal. The nanostructural evolution of the resulting inorganic materials was systematically investigated. Specifically, using tetraethyl orthosilicate (TEOS) as a silica precursor, this method can produce an OMS with relatively large pores. To establish the generalizability of this process, the fabrication approach was extended to other commercially available TPEs with varied chemical compositions and molecular weights while consistently resulting in ordered structures. Additionally, this synthetic strategy can be successfully applied to the production of OMMOs, including tin and titanium oxide matrix chemistries, yielding pore sizes of 16.0 and 19.2 nm, respectively. By developing a general method and using low-cost precursors, this work presents a scalable approach for fabricating large-pore OMMs with tunable pore textures and matrix chemistries.

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

Structural Insights into the Mechanism of a Polyketide Synthase Thiocysteine Lyase Domain

Polyketide synthases (PKSs) are renowned for the structural diversity of the polyketide natural products they produce, but sulfur-containing functionalities are rarely installed by PKSs. We previously characterized thiocysteine lyase (SH) domains involved in the biosynthesis of the leinamycin (LNM) family of natural products, exemplified by LnmJ-SH and guangnanmycin (GnmT-SH). Here we report a detailed investigation into the PLP-dependent reaction catalyzed by the SH domains, guided by a 1.8 Å resolution crystal structure of GnmT-SH. A series of elaborate substrate mimics were synthesized to answer specific questions garnered from the crystal structure and from the biosynthetic logic of the LNM family of natural products. Here, through a combination of bioinformatics, molecular modeling, in vitro assays, and mutagenesis, we have developed a detailed model of acyl carrier protein (ACP)-tethered substrate-SH, and interdomain interactions, that contribute to the observed substrate specificity. Comparison of the GnmT-SH structure with archetypical PLP-dependent enzyme structures revealed how Nature, via evolution, has modified a common protein structural motif to accommodate an ACP-tethered substrate, which is significantly larger than any of those previously characterized. Overall, this study demonstrates how PLP-dependent chemistry can be incorporated into the context of PKS assembly lines and sets the stage for engineering PKSs to produce sulfur-containing polyketides.

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

Geometric transformation and three-dimensional hopping of Hopf solitons

Arising in many branches of physics, Hopf solitons are three-dimensional particle-like field distortions with nontrivial topology described by the Hopf map. Despite their recent discovery in colloids and liquid crystals, the requirement of applied fields or confinement for stability impedes their utility in technological applications. Here we demonstrate stable Hopf solitons in a liquid crystal material without these requirements as a result of enhanced stability by tuning anisotropy of parameters that describe energetic costs of different gradient components in the molecular alignment field. Nevertheless, electric fields allow for inter-transformation of Hopf solitons between different geometric embodiments, as well as for their three-dimensional hopping-like dynamics in response to electric pulses. Numerical modelling reproduces both the equilibrium structure and topology-preserving out-of-equilibrium evolution of the soliton during switching and motions. Our findings may enable myriads of solitonic condensed matter phases and active matter systems, as well as their technological applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection

Evaluation of immunogenic epitopes for universal vaccine development in the face of ongoing SARS-CoV-2 evolution remains a challenge. Herein, we investigate the genetic and structural conservation of an immunogenically relevant epitope (C662–C671) of spike (S) protein across SARS-CoV-2 variants to determine its potential utility as a broad-spectrum vaccine candidate against coronavirus diseases. Comparative sequence analysis, structural assessment, and molecular dynamics simulations of C662–C671 epitope were performed. Mathematical tools were employed to determine its mutational cost. We found that the amino acid sequence of C662–C671 epitope is entirely conserved across the observed major variants of SARS-CoV-2 in addition to SARS-CoV. Its conformation and accessibility are predicted to be conserved, even in the highly mutated Omicron variant. Costly mutational rate in the context of energy expenditure in genome replication and translation can explain this strict conservation. These observations may herald an approach to developing vaccine candidates for universal protection against emergent variants of coronavirus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Beryllium-driven structural evolution at the divertor surface

Erosion of the beryllium first wall material in tokamak reactors has been shown to result in transport and deposition on the tungsten divertor. Experimental studies of beryllium implantation in tungsten indicate that mixed W–Be intermetallic deposits can form, which have lower melting temperatures than tungsten and can trap tritium at higher rates. To better understand the formation and growth rate of these intermetallics, we performed cumulative molecular dynamics (MD) simulations of both high and low energy beryllium deposition in tungsten. In both cases, a W–Be mixed material layer (MML) emerged at the surface within several nanoseconds, either through energetic implantation or a thermally-activated exchange mechanism, respectively. While some ordering of the material into intermetallics occurred, fully ordered structures did not emerge from the deposition simulations. Targeted MD simulations of the MML to further study the rate of Be diffusion and intermetallic growth rates indicate that for both cases, the gradual re-structuring of the material into an ordered intermetallic layer is beyond accessible MD time scales(≤1 μs). However, the rapid formation of the MML within nanoseconds indicates that beryllium deposition can influence other plasma species interactions at the surface and begin to alter the tungsten material properties. Therefore, beryllium deposition on the divertor surface, even in small amounts, is likely to cause significant changes in plasma-surface interactions and will need to be considered in future studies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Exploring the Structure–Function Relationship in Iridium–Cobalt Oxide Catalyst for Oxygen Evolution Reaction across Different Electrolyte Media

Renewable hydrogen generation from water electrolysis offers a viable path to decarbonization if the costs can be reduced. The iridium-based anode catalyst is one of the most expensive components in electrolyzers. We propose reducing iridium usage by substituting Ir with Co, a more affordable metal, in the mixed oxide phase to enhance the catalytic activity while minimizing Ir consumption. A modified surfactant-assisted Adams fusion synthesis technique was developed as a scalable method for producing IrCo oxide nanoparticles. The synthesized material outperforms the commercial baseline, iridium oxide with carbon (IrOx_C), in both acidic and alkaline media. Acid etching (IrCo_ae) further enhances activity by selectively removing Co to expose more active sites. IrCo_ae achieved a significantly lower overpotential at 10 mA/cm 2 compared to IrOx_C, with reductions of approximately 18% under acidic conditions and 14% under alkaline conditions. This work demonstrates that the proposed synthesis method enables efficient Ir utilization and can be adapted to enhance catalyst stability for renewable hydrogen production.

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

Toward Tunable Magnetic Dirac Semimetals: Mn Doping of Cd 3 As 2

Magnetic impurities provide a route toward increasing functionality in electronic materials, often enabling new device concepts and architectures. In the case of topological semimetals, dilute magnetic doping presents a particularly attractive approach for inducing a Dirac to Weyl phase change via time reversal symmetry breaking. However, efforts to realize changes in the electronic structure have been limited by challenges in incorporating magnetic impurities into crystals with sufficiently high electron mobilities to detect them via transport or spectroscopic techniques. Here, we demonstrate incorporation of Mn into Cd 3 ⁢As 2 Dirac semimetal thin films grown by molecular beam epitaxy (MBE). Using As-rich growth conditions and [001] oriented thin films, Mn compositions of >10% are achieved. Films contain uniform distributions of Mn with no evidence of secondary phases and exhibit electron mobilities greater than 10 000–30 000 cm 2 /Vs up to 5% Mn. An evolution in the magnetization behavior along with the emergence of a second quantum oscillation frequency at low Mn concentrations provide preliminary evidence of Mn-induced changes in the electronic structure that are consistent with a Weyl phase. This work demonstrates the potential of magnetically doping topological semimetal thin films and a pathway for synthesizing them.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Highly Structured Water Networks in Microhydrated Dodecaborate Clusters

Here, we report a combined photoelectron spectroscopy and theoretical investigation of a series of size-selected hydrated closo-dodecaborate clusters B 12 X 12 2– ·nH 2 O (X = H, F, or I; n = 1–6). Distinct structural arrangements of water clusters from monomer to hexamer can be achieved by using different B 12 X 12 2– bases, illustrating the evident solute specificity. Because B–H···H–O dihydrogen bonds are stronger than O···H–O hydrogen bonds in water, the added water molecules are arranged in a unified binding mode by forming highly structured water networks manipulated by B 12 H 12 2– . As a comparison, the hydrated B 12 F 12 2– clusters display similar water evolution for n values of 1 and 2 but different binding modes for larger clusters, while water networks in B 12 I 12 2– share similarities with the free water clusters. This finding provides a consistent picture of the structural diversity of hydrogen bonding networks in microhydrated dodecaborates and a molecular-level understanding of microsolvation dynamics in aqueous borate chemistry.

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

A review of displacement cascade simulations using molecular dynamics emphasizing interatomic potentials for TPBAR components

This review explores molecular dynamics simulations for studying radiation damage in Tritium Producing Burnable Absorber Rod (TPBAR) materials, emphasizing the role of interatomic potentials in displacement cascades. Recent machine learning potentials (MLPs), trained on quantum data, enhance prediction accuracy over traditional models like EAM. We highlight temperature, PKA energy, and composition effects on damage evolution in TPBAR components, recommending suitable potentials and discussing advancements for materials in extreme radiation environments.

36 MATERIALS SCIENCE↗