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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 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Molecular remodeling in Populus PdKOR RNAi roots profiled using LC-MS/MS proteomics

Plant endo-β-1,4-glucanases belonging to the Glycoside Hydrolase Family 9 have functional roles in cell wall biosynthesis and remodeling via endohydrolysis of (1→4)-β-D-glucosidic linkages. Modification of cell wall chemistry via RNAi-mediated downregulation of Populus deltoides KOR1 (PdKOR), a endo-β-1,4-glucanase gene, in Populus deltoides has been shown to have functional consequences for the composition of secondary metabolome and the ability of modified roots to interact with beneficial microbes. The molecular remodeling that underlies the observed differences at metabolic, physiological, and morphological levels in roots is not well understood. Here we used a LC-MS/MS-based proteome profiling approach to survey the molecular remodeling in root tissues of PdKOR and control plants. A total of 14316 peptides were identified and these mapped to 7139 P. deltoides proteins. Based on 90% sequence identity, the measured protein accessions represent 1187 functional protein groups. Analysis of GO categories and specific individual proteins showed differential expression of proteins relevant to plant-microbe interactions, cell wall chemistry, and metabolism. The new proteome dataset serves as a useful resource for deriving new hypotheses and empirical testing pertaining to functional roles of proteins and pathways in differential priming of plant roots to interactions with microbes.

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

Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation

Effective gene regulation by the tetrahydrofolate riboswitch depends not only on ligand affinity but also on the kinetics of ligand association, which involves two cooperative binding sites. Here, we have determined a 1.9-Å resolution crystal structure of the ligand-free THF riboswitch aptamer. The pseudoknot binding site ‘unwinds’ in the absence of ligand, whereby the adjacent helical domains (P1, P2, and P3) become disjointed, resulting in rotation and misalignment of the gene-regulatory P1 helix with respect to P3. In contrast, the second binding site at the three-way junction, which is the first to fold, is structurally conserved between apo and holo forms. This suggests a kinetic role for this site, in which binding of the first ligand molecule to the stably folded three-way junction promotes formation of the regulatory pseudoknot site and subsequent binding of the second molecule. As such, these findings provide a molecular basis for both conformational switching and kinetic control.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dynamic heterogeneity and nanophase separation in rubber-toughened amine-cured highly cross-linked polymer networks

Solid state nuclear magnetic resonance (NMR) spectroscopy and small-to wide-angle X-ray scattering (SWAXS) methods were used to characterize the heterogeneous dynamics and polymer domain structure in rubber modified thermoset materials containing the diglycidyl ether of bisphenol A (DGEBA) epoxy resin and a mixture of Jeffamine reactive rubber and 4,4-diaminodicyclohexylmethane (PACM) amine curing agent. The polymer chain dynamics and morphologies as a function of the PACM/Jeffamine ratio were determined. Using dipolar-filtered NMR experiments, the resulting networks are shown to be composed of mobile and rigid regions that are separated on nanometer length scales, along with a dynamically immobilized interface region. Proton NMR spin diffusion experiments measured the dimensions of the mobile phase to range between 9 and 66 nm and varied with the relative PACM concentration. Solid state 13 C magic angle spinning NMR experiments show that the highly mobile phase is composed entirely of the dynamically flexible polyether chains of the Jeffamine rubber, the immobilized interface region is a mixture of DGEBA, PACM, and the Jeffamine rubber, with the PACM cross-linked to DGEBA predominantly residing in the rigid phase. The SWAXS results showed compositional nanophase separation spanning the 11–77 nm range. These measurements of the nanoscale compositional and dynamic heterogeneity provide molecular level insight into the very broad and controllable glass transition temperature distributions observed for these highly cross-linked polymer networks.

36 MATERIALS SCIENCE↗
DOE OSTI2025

DancePartner: Python Package to Mine Multiomics Relationship Networks from Literature and Databases

A goal of multi-omics experiments is to understand how mechanistic molecular biology is altered between conditions, typically a control group and experimental groups. Oftentimes this involves studying changes in biomolecule relationships (e.g. interactions, metabolic relationships) of several types of biomolecules (e.g. proteins, lipids, metabolites). Though several databases contain relationships between biomolecules, understudied species may have little to no relationship information in databases and thus must be mined from literature. There are several challenges to literature mining, including automated full-text extraction, duplicate biomolecule term collapsing, and implementing complex machine learning tools. To make relationship extraction more accessible to the community, a python package called DancePartner was developed to allow for the extraction of relationships from literature and databases, with functions to map biomolecule synonyms to standardized identifiers and visualize and characterize the resulting multi-omics network. Here, in this study, an example dataset involving Caenorhabditis elegans is presented, where relationships are mined from 1443 publications using DancePartner. These relationships are combined with relationships from KEGG, WikiPathways, UniProt, and LipidMaps, and visualized.

BERT↗
DOE OSTI2026

Shining a Light on Some Fundamental Research Opportunities in Semiconductor Photoelectrochemistry

Decades of research in semiconductor photoelectrochemistry have yielded a deep understanding of charge transfer, energetics, and stability at solid−liquid interfaces. Theoretical frameworks developed by Gerischer and contemporaries, together with extensive experimental validation, have clarified the key principles affecting the interfacial kinetics and energetics of semiconductor photoelectrodes. Nevertheless, significant opportunities remain for advances in fundamental understanding of semiconductor photoelectrochemistry. Exciting opportunities include exploiting advances in theory, synthesis, and instrumentation to determine the chemical identity and reactivity of surface states; exerting control of band-edge energetics through molecular-level surface modification processes; and systematically improving emerging photoelectrode protection strategies to enable long-term photoelectrode operation under both oxidative and reductive conditions. Advanced morphologies, such as nanowire and microwire arrays, present new pathways to combine efficient light absorption with effective charge collection and catalyst integration. Unique light−matter interactions during photoelectrochemical deposition of p-type semiconductors readily allow preparation at scale of complex 3D morphologies that are difficult, if not impossible, to access by other methods. Continued exploration of these avenues will expand the fundamental understanding of semiconductor−liquid interfaces and could additionally advance the realization of efficient, stable, and scalable systems for solar fuel generation and other emerging photoelectrochemical applications.

Bean, Paul J. L. [California Institute of Technolo↗
DOE OSTI2026

pH-Driven Restructuring of Hydration Layers and Cation Adsorption at the Alumina–Water Interface

Oxide−water interfaces underpin ion separations, catalysis, and electrochemical energy technologies, where the electrical double layer (EDL) controls adsorption, transport, and reactivity. However, the molecular-scale links between pHdependent surface protonation, hydration-layer structure, and counterion adsorption remain poorly defined. Here, we combine in situ crystal truncation rod (CTR) and resonant anomalous X-ray reflectivity (RAXR) with streaming potential measurements and ab initio molecular dynamics (AIMD) simulations to resolve the chemical and structural evolution of the EDL at the single-crystal alumina (012)−water interface in 10 mM Rb + over pH 3−12. CTR measurements reveal two distinct adsorbed water layers at ∼2.2 and ∼3.5 Å above the surface. Each water layer shifts toward the substrate at transition pHs near 6.5 and 10.6, respectively, reflecting changes in primary hydration layer structure in response to the deprotonation of bridging and terminal aluminol groups. RAXR shows a 10-fold increase in Rb + coverage and a decrease in mean adsorption height from ∼3.5 to ∼2.7 Å with increasing pH, indicating enhanced counterion binding accompanied by Stern layer contraction. Streaming potential measurements demonstrate that the zeta potential, i.e., the potential at the hydrodynamic shear plane, is positive at pH 3 and becomes negative at pH ≥ 3.5. The negative charge magnitude increases with increasing pH, consistent with progressive surface deprotonation at higher pH. AIMD identifies inner- and outer-sphere Rb+ complexes whose adsorption heights and coordination geometries depend sensitively on the protonation state of surface oxygens, providing atomistic support for the experimentally inferred trends. These measurements establish two discrete, site-specific pH transitions in hydration-layer structure that track aluminol (de)protonation and quantitatively link them to a pH-driven contraction of the Stern layer (increasing Rb + coverage and decreasing adsorption height). This provides a direct structural basis for connecting surface acid−base chemistry to ion binding distances at an oxide−water interface.

Adsorption↗
DOE OSTI2023

A crucial role for dynamic expression of components encoding the negative arm of the circadian clock

In the Neurospora circadian system, the White Collar Complex (WCC) drives expression of the principal circadian negative arm component frequency ( frq ). FRQ interacts with FRH (FRQ-interacting RNA helicase) and CKI, forming a stable complex that represses its own expression by inhibiting WCC. In this study, a genetic screen identified a gene, designated as brd-8 , that encodes a conserved auxiliary subunit of the NuA4 histone acetylation complex. Loss of brd-8 reduces H4 acetylation and RNA polymerase (Pol) II occupancy at frq and other known circadian genes, and leads to a long circadian period, delayed phase, and defective overt circadian output at some temperatures. In addition to strongly associating with the NuA4 histone acetyltransferase complex, BRD-8 is also found complexed with the transcription elongation regulator BYE-1. Expression of brd-8, bye-1, histone h2a.z , and several NuA4 subunits is controlled by the circadian clock, indicating that the molecular clock both regulates the basic chromatin status and is regulated by changes in chromatin. Taken together, our data identify auxiliary elements of the fungal NuA4 complex having homology to mammalian components, which along with conventional NuA4 subunits, are required for timely and dynamic frq expression and thereby a normal and persistent circadian rhythm.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Liquid-induced topological transformations of cellular microstructures

The fundamental topology of cellular structures—the location, number and connectivity of nodes and compartments—can profoundly affect their acoustic, electrical5, chemical, mechanical and optical properties, as well as heat, fluid and particle transport. Approaches that harness swelling, electromagnetic actuation and mechanical instabilities in cellular materials have enabled a variety of interesting wall deformations and compartment shape alterations, but the resulting structures generally preserve the defining connectivity features of the initial topology. Achieving topological transformation presents a distinct challenge for existing strategies: it requires complex reorganization, repacking, and coordinated bending, stretching and folding, particularly around each node, where elastic resistance is highest owing to connectivity. Here we introduce a two-tiered dynamic strategy that achieves systematic reversible transformations of the fundamental topology of cellular microstructures, which can be applied to a wide range of materials and geometries. Our approach requires only exposing the structure to a selected liquid that is able to first infiltrate and plasticize the material at the molecular scale, and then, upon evaporation, form a network of localized capillary forces at the architectural scale that ‘zip’ the edges of the softened lattice into a new topological structure, which subsequently restiffens and remains kinetically trapped. Reversibility is induced by applying a mixture of liquids that act separately at the molecular and architectural scales (thus offering modular temporal control over the softening–evaporation–stiffening sequence) to restore the original topology or provide access to intermediate modes. Guided by a generalized theoretical model that connects cellular geometries, material stiffness and capillary forces, we demonstrate programmed reversible topological transformations of various lattice geometries and responsive materials that undergo fast global or localized deformations. In conclusion, we then harness dynamic topologies to develop active surfaces with information encryption, selective particle trapping and bubble release, as well as tunable mechanical, chemical and acoustic properties.

42 ENGINEERING↗
DOE OSTI2024

Measurement of coherent vibrational dynamics with X-ray Transient Absorption Spectroscopy simultaneously at the Carbon K- and Chlorine L 2,3 - edges

X-ray Transient Absorption Spectroscopy (XTAS) is a powerful probe for ultrafast molecular dynamics. The evolution of XTAS signal is controlled by the shapes of potential energy surfaces of the associated core-excited states, which are difficult to directly measure. Here, we study the vibrational dynamics of Raman activated CCl 4 with XTAS targeting the C 1s and Cl 2p electrons. The totally symmetric stretching mode leads to concerted elongation or contraction in bond lengths, which in turn induce an experimentally measurable red or blue shift in the X-ray absorption energies associated with inner-shell electron excitations to the valence antibonding levels. The ratios between slopes of different core-excited potential energy surfaces (CEPESs) thereby extracted agree very well with Restricted Open-Shell Kohn-Sham calculations. The other, asymmetric, modes do not measurably contribute to the XTAS signal. The results highlight the ability of XTAS to reveal coherent nuclear dynamics involving < 0.01 Å atomic displacements and also provide direct measurement of forces on CEPESs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Ab initio molecular dynamics on quantum computers

Ab initio molecular dynamics (AIMD) is a valuable technique for studying molecules and materials at finite temperatures where the nuclei evolve on potential energy surfaces obtained from accurate electronic structure calculations. In this work, we present an approach to running AIMD simulations on noisy intermediate-scale quantum (NISQ)-era quantum computers. The electronic energies are calculated on a quantum computer using the variational quantum eigensolver (VQE) method. Algorithms for computation of analytical gradients entirely on a quantum computer require quantum fault-tolerant hardware, which is beyond NISQ-era. Therefore, we compute the energy gradients numerically using finite differences, the Hellmann-Feynman theorem, and a correlated sampling technique. This method only requires additional classical calculations of electron integrals for each degree of freedom without any additional computations on a quantum computer beyond the initial VQE run. As a proof of concept, AIMD simulations are demonstrated for the H-2 molecule on IBM quantum devices. In addition, we demonstrate the validity of the method for larger molecules using full configuration interaction wave functions. As quantum hardware and noise mitigation techniques continue to improve, the method can be utilized for studying larger molecular systems.

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

Dispersive optical systems for scalable Raman driving of hyperfine qubits

Hyperfine atomic states are among the most promising candidates for qubit encoding in quantum information processing. In atomic systems, hyperfine transitions are typically driven through a two-photon Raman process by a laser field which is amplitude modulated at the hyperfine qubit frequency. Here we introduce a method for generating amplitude modulation by phase modulating a laser and reflecting it from a highly dispersive optical element known as a chirped Bragg grating. This approach is passively stable, offers high efficiency, and is compatible with high-power laser sources, enabling large Rabi frequencies and improved quantum coherence. We benchmark this approach by globally driving an array of approximately 300 neutral 87 Rb atomic qubits trapped in optical tweezers and obtain Rabi frequencies of 2 MHz with photon-scattering error rates of less than 2×10 -4 per π pulse. This robust approach can be directly integrated with local addressing optics in both neutral atom and trapped ion systems to facilitate high-fidelity single-qubit operations for quantum information processing.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

The conserved AAA ATPase PCH-2 distributes its regulation of meiotic prophase events through multiple meiotic HORMADs in C. elegans

During meiotic prophase, the essential events of homolog pairing, synapsis, and recombination are coordinated with meiotic progression to promote fidelity and prevent aneuploidy. The conserved AAA+ ATPase PCH-2 coordinates these events to guarantee crossover assurance and accurate chromosome segregation. How PCH-2 accomplishes this coordination is poorly understood. Here, we provide evidence that PCH-2 decelerates pairing, synapsis and recombination in C. elegans by remodeling meiotic HORMADs. We propose that PCH-2 converts the closed versions of these proteins, which drive these meiotic prophase events, to unbuckled conformations, destabilizing interhomolog interactions and delaying meiotic progression. Further, we find that PCH-2 distributes this regulation among three essential meiotic HORMADs in C. elegans: PCH-2 acts through HTP-3 to regulate pairing and synapsis, HIM-3 to promote crossover assurance, and HTP-1 to control meiotic progression. In addition to identifying a molecular mechanism for how PCH-2 regulates interhomolog interactions, our results provide a possible explanation for the expansion of the meiotic HORMAD family as a conserved evolutionary feature of meiosis. Taken together, our work demonstrates that PCH-2’s remodeling of meiotic HORMADs has functional consequences for the rate and fidelity of homolog pairing, synapsis, recombination and meiotic progression, ensuring accurate meiotic chromosome segregation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

pH-Driven Restructuring of Hydration Layers and Cation Ad-sorption at the Alumina-Water Interface

Oxide-water interfaces underpin ion separation, catalysis, and electrochemical energy technologies, where the electrical double layer (EDL) controls adsorption, transport, and reactivity. Yet, the molecular-scale link between pH-dependent surface protonation, hydration-layer structure, and counter-ion adsorption remains poorly defined. Here, we combine in situ crystal truncation rod (CTR) and resonant anomalous X-ray reflectivity (RAXR) with streaming potential measurements and ab initio molecular dynamics (AIMD) simulations to resolve the chemical and structural evolution of the EDL at the single-crystal alumina (012)-water interface in 10 mM Rb+ over pH 3-12. CTR measurements reveal two distinct adsorbed water layers at ~2.2 and ~3.5 Å above the surface that each shift toward the substrate at transition pHs near 6.5 and 10.6, respectively, directly reflecting changes in primary hydration layer structure in response to the deprotonation of bridging and terminal aluminol groups. RAXR shows a 10-fold increase in Rb+ coverage and a decrease in mean adsorption height from ~3.5 to ~2.7 Å with increasing pH, indicating enhanced counter-ion binding accompanied by Stern layer contraction. Streaming potential measurements demonstrate that the zeta potential, i.e., potential at the hydrodynamic shear plane, is positive at pH 3 and becomes negative at pH ≥3.5. This negative charge magnitude increases with increasing pH, consistent with progressive surface deprotonation at higher pH. AIMD identifies inner- and outer-sphere Rb+ complexes whose adsorption heights and coordination geometries depend sensitively on the protonation state of surface oxygens, providing atomistic support for the experimentally inferred trends. These measurements establish two discrete, site-specific pH transitions in hydration-layer structure that track aluminol (de)protonation and quantitatively link them to a pH-driven contraction of the Stern layer (increasing Rb+ coverage and decreasing adsorption height). This provides a direct structural basis for connecting surface acid-base chemistry to ion binding distances at an oxide-water interface.

Electrical double layer (EDL), Surface protonation↗
DOE OSTI2020

Fluorescence Enhancement in the Solid State by Isolating Perylene Fluorophores in Metal–Organic Frameworks

Polycyclic aromatic hydrocarbons such as perylene, pyrene, and their derivatives are highly emissive fluorophores in solution. Furthermore, the practical applications of these materials in the field of molecular electronic and light emitting devices are often hindered by self-quenching effects due to the formation of non-fluorescent aggregates in concentrated solutions or in the solid state. Herein, we demonstrate that aggregation caused quenching of perylenes can be minimalized by molecular incorporation into metalorganic frameworks (MOFs). This study utilized a stable Zr 6 cluster-based MOF, UiO-67, as a matrix. Linear linkers containing the photo-responsive moieties were designed and incorporated into the parent UiO-67 scaffold through the partially replacement of the non-fluorescent linkers of a similar length, forming mixed-linker MOFs. Here, the average distance between perylene moieties was tuned by changing the linker ratios, thus controlling the fluorescence intensity, emission wavelength, and quantum yield. Molecular modeling was further adopted to correlate the number of isolated perylene linkers within the framework to the ratio between the two linkers, therefore rationalizing the change in the observed fluorescent properties. Taking advantage of the tunable fluorescence, inherent porosity, and high chemical stability of this MOF platform, it was applied as a fluorescent sensor for oxygen detection in the gas phase, a model reaction, showing fast response and good recyclability.

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

Effect of Networking Density on the Patterning Performance of Molecular Layer Deposited Alucone Electron Beam/EUV Resists

One of the main barriers to continued device scaling in the era of extreme ultraviolet (EUV) lithography is the need for improved photoresist chemistries to address challenges such as poor EUV sensitivity, inadequate etch resistance, and pattern collapse. Metal-organic photoresists are a promising class of materials that can address many of these challenges, and among them, resists deposited via hybrid molecular layer deposition (MLD) have attracted interest for their unique advantages in thickness control, chemical homogeneity, and compatibility with vacuum processing. However, despite many successful demonstrations of patterning, little is known about how the molecular design of hybrid MLD resists affects their lithographic performance. In this work, we study the effect of the network structure, a common feature among all hybrid MLD resists, via a series of aluminum alkoxide ("alucone") negative tone resists with varying networking density. Their patterning mechanism is investigated via electron beam lithography (EBL)─a common proxy for EUV─and compared to their EUV-induced reactions studied via flood exposure and in situ characterization. In conclusion, we show that the resist with the least networking density demonstrates the best sensitivity and resolution, with the ability to resolve dense line/space gratings as small as 14 nm half pitch via EBL.

electron beam lithography↗
DOE OSTI2023

High-temperature chromium diffusion in austenitic stainless steel: Ab initio molecular dynamics simulations

Chromium self-diffusion through stainless steel (SS) matrix and along grain boundaries is an important mechanism controlling SS structural materials corrosion. For this work, Cr diffusion in austenitic SS was simulated using canonical ab initio molecular dynamics with realistic models of type-316 SS bulk, with and without Cr vacancies, and a low-energy Σ3 twin boundary typically observed at active corrosion sites. Cr self-diffusion coefficients at 750 and 850 °C calculated using Einstein’s diffusion equation are 4.2 × 10 –6 and 8.1 × 10 –6 Å 2 ps –1 in pristine bulk, 3.8 × 10 –3 and 5.5 × 10 –3 Å 2 ps –1 in bulk including Cr vacancies, and 9.5 × 10 –2 and 1.0 × 10 –1 Å 2 ps –1 at a Σ3[1 1 1]60° twin boundary.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Insights into Probing the Effect of Molecular Weight of Poly(carboxybetaine methacrylate) on the Performance of Forward Osmosis Desalination

Zwitterionic polymers have proven to be a promising nonfouling material that can be applied in the design of selective layers of thin film composite (TFC) membranes. Extending the permeability and usage of TFC membranes have attracted increasing interest in membrane-based desalination processes since water-flux reduction associated with biofouling nowadays persists as a common challenge. By virtue of its strong hydration, this polymer category is very useful to counteract biofouling in marine and biomedical systems, but the benefits from their application in membrane technology are still emerging. The efficacy of the nonfouling property as a function of the polymer’s molecular weight remains unknown. In pursuit of that vision, this study fosters new scientific insights via probing different molecular weights of poly(carboxybetain methacrylate) (PCBMA) coated on the surface as a selective layer for the prepared TFC membranes. The coated zwitterionic membranes (zM) exhibited excellent performance in preventing water flux decay in a bench-scale forward osmosis system. The prepared zM membranes revealed enhanced hydrophilic properties and retained their operational water flux when compared to the control. Our results suggest that using an intermediate-size molecular weight (PCBMA M n 50,000) will result in the best operational performance. The intermediate size resulted in the lowest flux decline rate (R t ) of 0.01 ± 0.001 (zM-50) when compared to the unmodified control membrane 0.56 ± 0.071 (M0) after using a model BSA foulant solution. Furthermore, all coated membranes exhibited similar trends in the observed reverse salt flux profiles, as well. In conclusion, the constructed zM membranes will serve as a model to develop further selective layers in the construction of TFC membranes.

36 MATERIALS SCIENCE↗