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At least 1,207 records · Page 67
All sourcesNASA NTRSDOE OSTI
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↗
NASA NTRS1975

Stellar evolution at high mass with semiconvective mixing according to the Ledoux criterion

The effects of semiconvective mixing are investigated in evolutionary sequences of models for stars of 10, 15, and 30 solar masses with four different initial chemical compositions. The models are constructed using the Ledoux criterion for both the definition of convective instability and the state of convective neutrality assumed to be attained in regions with a gradient of mean molecular weight. It is shown that semiconvection is nonexistent at 10 solar masses, of minor importance at 15 solar masses, but covers most of the intermediate zone at 30 solar masses, developing into full convection if the initial hydrogen and metals abundances are high. The effects of low initial hydrogen and metals abundances are examined, and the critical importance is demonstrated of the depths of the semiconvective zone and the outer convective envelope in promoting a blue loop and determining the maximum effective temperature on the loop. The extent of the thermally stable stages of the blue-loop phase is determined.

Stothers, R.↗
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↗
NASA NTRS1994

The sequence, and its evolutionary implications, of a Thermococcus celer protein associated with transcription

Through random search, a gene from Thermococcus celer has been identified and sequenced that appears to encode a transcription-associated protein (110 amino acid residues). The sequence has clear homology to approximately the last half of an open reading frame reported previously for Sulfolobus acidocaldarius [Langer, D. & Zillig, W. (1993) Nucleic Acids Res. 21, 2251]. The protein translations of these two archaeal genes in turn are homologs of a small subunit found in eukaryotic RNA polymerase I (A12.2) and the counterpart of this from RNA polymerase II (B12.6). Homology is also seen with the eukaryotic transcription factor TFIIS, but it involves only the terminal 45 amino acids of the archaeal proteins. Evolutionary implications of these homologies are discussed.

Non-NASA Center↗
NASA NTRS2006

Computer Modeling of Protocellular Functions: Peptide Insertion in Membranes

Lipid vesicles became the precursors to protocells by acquiring the capabilities needed to survive and reproduce. These include transport of ions, nutrients and waste products across cell walls and capture of energy and its conversion into a chemically usable form. In modem organisms these functions are carried out by membrane-bound proteins (about 30% of the genome codes for this kind of proteins). A number of properties of alpha-helical peptides suggest that their associations are excellent candidates for protobiological precursors of proteins. In particular, some simple a-helical peptides can aggregate spontaneously and form functional channels. This process can be described conceptually by a three-step thermodynamic cycle: 1 - folding of helices at the water-membrane interface, 2 - helix insertion into the lipid bilayer and 3 - specific interactions of these helices that result in functional tertiary structures. Although a crucial step, helix insertion has not been adequately studied because of the insolubility and aggregation of hydrophobic peptides. In this work, we use computer simulation methods (Molecular Dynamics) to characterize the energetics of helix insertion and we discuss its importance in an evolutionary context. Specifically, helices could self-assemble only if their interactions were sufficiently strong to compensate the unfavorable Free Energy of insertion of individual helices into membranes, providing a selection mechanism for protobiological evolution.

Rodriquez-Gomez, D.↗
NASA NTRS2010

Developing Biological ISRU: Implications for Life Support and Space Exploration

Main findings: 1) supplementing very dilute media for cultivation of CB with analogs of lunar or Martian regolith effectively supported the proliferation of CB; 2) O2 evolution by siderophilic cyanobacteria cultivated in diluted media but supplemented with iron-rich rocks was higher than O2 evolution by same strain in undiluted medium; 3) preliminary data suggest that organic acids produced by CB are involved in iron-rich mineral dissolution; 4) the CB studied can accumulate iron on and in their cells; 4) sequencing of the cyanobacterium JSC-1 genome revealed that this strain possesses molecular features which make it applicable for the cultivation in special photoreactors on Moon and Mars. Conclusion: As a result of pilot studies, we propose, to develop a concept for semi-closed integrated system that uses CB to extract useful elements to revitalize air and produce valuable biomolecules. Such a system could be the foundation of a self-sustaining extraterrestrial outpost (Hendrickx, De Wever et al., 2005; Handford, 2006). A potential advantage of a cyanobacterial photoreactor placed between LSS and ISRU loops is the possibility of supplying these systems with extracted elements and compounds from the regolith. In addition, waste regolith may be transformed into additional products such as methane, biomass, and organic and inorganic soil enrichment for the cultivation of higher plants.

Brown, I. I.↗
NASA NTRSDate not supplied

Low-Temperature Formation of Carbonaceous Grains from PAHs

Astronomical observations have detected interstellar carbon in the form of polycyclic aromatic hydrocarbons(PAHs) as well as carbonaceous dust, confirming its presence in both gaseous and solid phases. The goal of this study is to experimentally investigate low-temperature chemical pathways between these two phases in order to better understand the evolution of cosmic carbon. Cosmic dust analogs are produced in the supersonic expansion of an argon jet seeded with aromatic molecules: benzene, naphthalene, anthracene, phenanthrene, and pyrene. These are prototype aromatic molecules of compact and non compact structure, and are used to evaluate the effect of precursor structure on the molecular complexity of the resulting grains. The seeded jet is exposed to an electrical discharge and the carbonaceous grains are collected and probed ex situ via laser desorption mass spectrometry. Mass spectra reveal a rich molecular diversity within the grains, including fragments of the parent molecule but also growth into larger complex organic molecules (COMs). In all experiments, the largest number of products is found in the m/z range 200-250, and C16H10 (attributed to pyrene and/or its isomers) is found to be a dominant product, pointing at the formation of this stable PAH as a preferential route in the growth to larger PAHs. Comparison to mass spectra from the Murchison meteorite reveals a similar dominance of compounds related toC16H10 at m/z = 202. Evidence of the methyl addition-cyclization mechanism in the anthracene experiment is reported. PAH structure is found to impact the dust production yield, as seen by the greater yield for the anthracene compared to the phenanthrene experiment. PAH growth at low temperatures via barrierless routes involving the addition of alkyl- and phenyl-type radicals is suggested as a viable pathway to COMs. These results suggest that PAH growth and dust formation from PAHs are feasible at low temperatures in photon-dominated regions and circumstellar envelopes.

L Gavilan↗
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↗
DOE OSTI2023

Engineering Crassulacean Acid Metabolism in C 3 and C 4 Plants

Carbon dioxide (CO 2 ) 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 CO 2 reduction. Additionally, plants performing CAM (crassulacean acid metabolism) photosynthesis have a much higher water use efficiency than those performing C 3 or C 4 photosynthesis. Therefore, there is a great potential for engineering CAM in C 3 or C 4 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 C 3 /C 4 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 C 3 and C 4 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.

59 BASIC BIOLOGICAL SCIENCES↗