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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 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Unique methionine-aromatic interactions govern the calmodulin redox sensor

Highlights: • Calmodulin’s open and closed states are stabilized by unique, redox sensitive methionine-aromatic interactions. • Methionine-aromatic interactions govern key conformational transitions in calmodulin through coupling with EF hand motion. • Methionine oxidation likely tunes target specificity by altering the strength of key methionine-aromatic interactions. Calmodulin contains multiple redox sensitive methionines whose oxidation alters the regulation of numerous targets. Molecular dynamics simulations were used to define the molecular principles that govern how calmodulin is structurally poised to detect and respond to methionine oxidation. We found that calmodulin's open and closed states were preferentially stabilized by unique, redox sensitive, methionine-aromatic interactions. Key methionine-aromatic interactions were coupled to reorientation of EF hand helices. Methionine to glutamine substitutions designed to mimic methionine oxidation strongly altered conformational transitions by modulating the strength of methionine-aromatic interactions. Together, these results suggest a broadly applicable redox sensing mechanism though which methionine oxidation by cellular oxidants alters the strength of methionine-aromatic interactions critical for functional protein dynamics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Simultaneous inhibition of ATM, ATR, and DNA-PK causes synergistic lethality

Here, in this paper, we report that simultaneous inhibition of the three primary DNA damage recognition PI3 kinase-like kinases (PIKKs) —ATM, ATR, and DNA-PK— induces severe combinatorial synthetic lethality in mammalian cells. Utilizing Chinese hamster cell lines CHO and V79 and their respective PIKK mutants, we evaluated effects of inhibiting these three kinases on cell viability, DNA damage response, and chromosomal integrity. Our results demonstrate that while single or dual kinase inhibition increased cytotoxicity, inhibition of all three PIKKs results in significantly higher synergistic lethality, chromosomal aberrations, and DNA double-strand break (DSB) induction as calculated by their synergy scores. These findings suggest that the overlapping redundancy of ATM, ATR, and DNA-PK functions is critical for cell survival, and their combined inhibition greatly disrupts DNA damage signaling and repair processes, leading to cell death. This study provides insights into the potential of multi-targeted DDR kinase inhibition as an effective anticancer strategy, necessitating further research to elucidate underlying mechanisms and therapeutic applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Ion-selective conformational stabilization of a disordered repeats-in-toxin protein domain

Ion-binding intrinsically disordered proteins (IDPs) recruit and bind to specific metal ions to perform critical biological functions. In proteins where ion binding and structural transitions are coupled, interactions with off-target toxic metals can dramatically disrupt protein structure and function, exemplified by lead and mercury poisoning. Understanding the complex mechanisms underlying how IDPs exclude or allow binding to different ionic species is crucial for addressing the origins of metal toxicity in biological systems. Here, we elucidate mechanisms of ion selectivity in an IDP that adopts a structure upon Ca 2+ binding. We probed ion-induced conformational changes of a repeats-in-toxin (RTX) protein domain in the presence of different ion ligands—Mg 2+ , Ca 2+ , Sr 2+ , and Ba 2+ —with chemical similarities but drastically different ionic radii. RTX adopts ion-selective conformations measured by x-ray crystallography, small-angle x-ray scattering, and circular dichroism. High-resolution x-ray structures reveal that Sr 2+ induces a nearly identical RTX structure as natively binding Ca 2+ , enabled by the intrinsic flexibility and disorder of the protein. Small-angle x-ray scattering and circular dichroism indicate that smaller Mg 2+ does not induce a significant conformational change in RTX, whereas larger Ba 2+ induces a partially folded structure. These results highlight the importance of geometric constraints imposed by protein structure in determining metal ion selectivity, yielding insights into how off-target ion binding may result in protein misfolding and malfunction.

Gudinas, Alana P. [Stanford Univ., CA (United Stat↗
DOE OSTI2023

Deep learning-enhanced design for functionally graded auxetic lattices

Auxetic materials with counterintuitive negative Poisson’s ratio have been of significant interest due to potential applications across diverse engineering fields. Functionally grading such auxetics further enables customization of the structural response and harnesses the potential for multi-functional applications. However, a critical challenge in designing functionally graded lattices is to efficiently determine the spatial variation of the functional gradient and the corresponding geometric designs to achieve the desired response. In this paper, a highly efficient deep learning-based inverse design framework for functionally graded tetra-petal auxetics with spatially tailored properties is presented. This framework significantly improves the efficiency of tailoring functionally graded auxetics where many unit cells need to be tailor-designed. The graded tetra-petal auxetics obtained from the inverse design framework are additively manufactured and subjected to impact tests. The results show superior impact performance compared with uniform designs, demonstrating the effectiveness of the proposed inverse design framework, which can be inspirable to promote advanced structures/materials with enhanced impact resistance.

42 ENGINEERING↗
DOE OSTI2022

Lithological controls on soil geochemistry and clay mineralogy across Spodosols in the coastal temperate rainforest of southeast Alaska

The interaction of similar soil forming factors with different parent materials determines soil chemical weathering, influencing soil processes and properties. In the coastal temperate rainforests of southeast Alaska, Spodosols is the dominant soil order in well-drained parent materials regardless of the lithology. Yet, the role of lithology on chemical weathering, base cation depletion, and mineral transformation during pedogenesis remains elusive. Here, we established a lithosequence comprised of soils derived from tonalite, phyllite, slate, and metavolcanic rocks to test the hypothesis that despite the soils in southeast Alaska presenting similar taxonomy and morphology, the influence of lithology in chemical weathering intensity and mineralogy can be detected. We evaluated physicochemical properties, clay mineralogy, Fe-Al oxides, chemical weathering, and elemental mass balance on eleven Spodosols sampled along the lithosequence. We also propose a new weathering index, the Weathering Index for Spodosols (WISP), suitable to evaluate the weathering degree of soils with Al mobility and base-rich parent materials. This index fills a gap in traditional weathering indices that uses Al as an immobile element and/or does not evaluate the leaching of main base cations. We found the pedons across the lithosequence expressed similar physicochemical properties, with predominantly thick profiles, presenting andic properties, relatively thick spodic horizons, and thin E horizons. Podzolization imposed similar mineral transformation trends, mainly dissolution of chlorite, mica alteration to interstratified mica-vermiculite, and formation of smectite in E horizons. Kaolinite was detected in the soils from all lithologies, but only in trace amounts in phyllite soils. Fe oxides depth distribution was similar but with a higher concentration in the slate (44.5 ± 4.2 g/kg), followed by metavolcanic (31.6 ± 4.0 g/kg), phyllite (27.9 ± 3.8 g/kg), and tonalite soils (19.9 ± 5.7 g/kg) and predominantly as organometallic complexes (extracted by Na-pyrophosphate). The stronger weathering of chlorite and mica in the E horizons was reflected in larger losses of Mg and K, while Ca and Na were more depleted in the spodic horizons, suggesting plagioclase weathering. Slate soils were the most depleted in base cations, followed by phyllite, tonalite, and metavolcanic soils. The more depleted status of slate soils was supported by the higher WISP values (WISP = 62), followed by phyllite (WISP = 55), tonalite (WISP = 53), and metavolcanic soils (WISP = 45). Our results demonstrated that lithology controlled elemental depletion intensities, Fe oxide concentrations, and partially the clay fraction mineralogy in addition to podzolization acting as a dominant pedogenic process across all sites. These findings advance our understanding of the role of lithology on soil mineralogy/geochemistry that impacts critical soil functions, such as the soil carbon cycle, elemental fluxes, organo-mineral interactions, and solid-solution reactions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Comprehensive structural characterization of charged polymers involved in moisture-driven direct air capture

This study provides a comprehensive structural characterization of commercially available alkaline anion-exchange polymers (Fumasep FAA-3 and IRA 900) used in moisture-driven direct air capture (DAC) of carbon dioxide. Using X-ray diffraction, SAXS/WAXS, atomic force microscopy, FIB-SEM, and transmission electron microscopy, the authors identify nanoscale clustering, porosity, swelling behavior, and humidity-dependent structural changes that influence CO₂ adsorption and release. These findings establish structure–function relationships critical for designing more durable and energy-efficient DAC polymer materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Full core LOCA safety analysis for a PWR containing high burnup fuel

For economic reasons, the US nuclear industry is renewing efforts to build a technical basis to extend peak rod average burnup limits above the current regulatory burnup limit of 62 GWd/MTU. The primary driver of these efforts is to economically increase pressurized water reactor (PWR) cycle lengths to 24 months, reduce the number of fresh fuel assemblies, increase time online, thereby reducing number of outages and their associated cost, higher fuel utilization, and possibly reduce core design constraints. In order for US nuclear utilities to leverage these economic efficiencies, the US Nuclear Regulatory Commission (NRC) will likely require nuclear power plants (NPPs) to analyze a number of potential operational occurrences and their potential consequences with each new core design prior to resuming normal operation. Potential operational occurrences can be divided into three primary regimes: (1) normal operation, (2) anticipated operation occurrences (AOOs), and (3) design basis accidents (DBAs). Normal plant operation is an operating regime in which the plant operates within specified operational limits until the end of the cycle, whereas AOOs are events that result in the NPP deviating outside the normal operating regime. A key attribute of an AOO is that the occurrence should be expected. However, by definition, the occurrence of an AOO does not result in significant impact to critical safety functions. The last potential operational occurrence is a DBA. From the fuel performance point-of-view, DBAs can be subdivided into two bounding categories: (1) loss of coolant accidents (LOCAs), and (2) reactivity insertion accidents (RIAs). Unlike AOOs, DBAs may result in fuel rod failure. The NRC imposes fundamental acceptance criteria to minimize radiological consequences to the public and onsite staff. Furthermore, safety criteria are typically linked to the fulfillment of other acceptance criteria related to reactor safety equipment designed to mitigate DBAs.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2016

Effects of a human recombinant alkaline phosphatase on renal hemodynamics, oxygenation and inflammation in two models of acute kidney injury

Two small clinical trials indicated that administration of bovine intestinal alkaline phosphatase (AP) improves renal function in critically ill patients with sepsis-associated acute kidney injury (AKI), for which the mechanism of action is not completely understood. Here, we investigated the effects of a newly developed human recombinant AP (recAP) on renal oxygenation and hemodynamics and prevention of kidney damage and inflammation in two in vivo AKI models. To induce AKI, male Wistar rats (n = 18) were subjected to renal ischemia (30 min) and reperfusion (I/R), or sham-operated. In a second model, rats (n = 18) received a 30 min infusion of lipopolysaccharide (LPS; 2.5 mg/kg), or saline, and fluid resuscitation. In both models, recAP (1000 U/kg) was administered intravenously (15 min before reperfusion, or 90 min after LPS). Following recAP treatment, I/R-induced changes in renal blood flow, renal vascular resistance and oxygen delivery at early, and cortical microvascular oxygen tension at late reperfusion were no longer significantly affected. RecAP did not influence I/R-induced effects on mean arterial pressure. During endotoxemia, recAP treatment did not modulate the LPS-induced changes in systemic hemodynamics and renal oxygenation. In both models, recAP did exert a clear renal protective anti-inflammatory effect, demonstrated by attenuated immunostaining of inflammatory, tubular injury and pro-apoptosis markers. Whether this renal protective effect is sufficient to improve outcome of patients suffering from sepsis-associated AKI is being investigated in a large clinical trial. - Highlights: • Human recombinant alkaline phosphatase (recAP) is a potential new therapy for sepsis-associated acute kidney injury (AKI). • RecAP can modulate renal oxygenation and hemodynamics immediately following I/R-induced AKI. • RecAP did not modulate endotoxemia-induced changes in systemic hemodynamics and renal oxygenation. • RecAP did exert a clear renal protective anti-inflammatory effect in both models.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

The journey of integrins and partners in a complex interactions landscape studied by super-resolution microscopy and single protein tracking

Cells adjust their adhesive and cytoskeletal organizations according to changes in the biochemical and physical nature of their surroundings. In return, by adhering and generating forces on the extracellular matrix (ECM) cells organize their microenvironment. Integrin-dependent focal adhesions (FAs) are the converging zones integrating biochemical and biomechanical signals arising from the ECM and the actin cytoskeleton. Thus, integrin-mediated adhesion and mechanotransduction, the conversion of mechanical forces into biochemical signals, are involved in critical cellular functions such as migration, proliferation and differentiation, and their deregulation contributes to pathologies including cancer. A challenging problem is to decipher how stochastic protein movements and interactions lead to formation of dynamic architecture such as integrin-dependent adhesive structures. In this review, we will describe recent advances made possible by super-resolution microscopies and single molecule tracking approaches that provided new understanding on the organization and the dynamics of integrins and intracellular regulators at the nanoscale in living cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

MicroRNA-133b inhibits hepatocellular carcinoma cell progression by targeting Sirt1

MicroRNAs (miRNAs) are a class of small non-coding RNAs that function as critical gene regulators by targeting mRNAs for translational repression or degradation. In this study, we showed that the expression level of miR-133b was decreased, while Sirt1 mRNA expression levels were increased in hepatocellular carcinoma (HCC) and cell lines, and we identified Sirt1 as a novel direct target of miR-133b. The over-expression of miR-133b suppressed Sirt1 expression. In addition, miR-133b over-expression resulted in attenuating HCC cell proliferation and invasion together with apoptosis increase in vitro. HepG2 cell transplantation revealed that up-regulation of miR-133b could inhibit HCC tumor genesis in vivo. Forced expression of Sirt1 partly rescued the effect of miR-133b in vitro. Furthermore, our study showed that miR-133b over-expression or Sirt1 down-regulation elevated E-cadherin expression, and repressed glypican-3 (GPC3) and the anti-apoptotic proteins (Bcl-2, Bcl-xL, and Mcl-1) expression. The inhibition of GPC3 expression repressed Bcl-2, Bcl-xL, and Mcl-1 expression, and elevated E-cadherin expression. Moreover, the Sirt1 up-regulation resulted in increases in HCC cell proliferation and invasion together with decreases apoptosis, and increases in the cytosolic accumulation and nuclear translocation of the transcription factor β-catenin in vitro. But the effect of Sirt1 up-regulation was partly reversed by GPC3 down-regulation in vitro. Taken together, these findings provide insight into the role and mechanism of miR-133b in regulating HCC cell proliferation, invasion and apoptosis via the miR-133b/Sirt1/GPC3/Wnt β-catenin axis, and miR-133b may serve as a potential therapeutic target in HCC in the future. - Highlights: • Sirt1 is a direct target of miR-133b in HCC. • miR-133b over-expression suppresses HCC progression in vitro and in vivo. • Sirt1 restoration reverses the effect of miR-133b over-expression on HCC cells. • GPC3 down-regulation reverses the effect of Sirt1 up-regulation on HCC cells. • Sirt1 activates Wnt β-catenin signaling by GPC3 in vitro.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides

Protein phosphorylation is a critical post-translational modification (PTM). Despite recent technological advances in reversed-phase liquid chromatography (RPLC)-mass spectrometry (MS)-based proteomics, comprehensive phosphoproteomic coverage in complex biological systems remains challenging, especially for hydrophilic phosphopeptides with enriched regions of serines, threonines, and tyrosines that often orchestrate critical biological functions. It is known that G protein coupled receptors (GPCRs) are regulators of cellular signaling events and rely on phosphorylation of serines and threonines within the GPCR C-terminus for appropriate signaling. However, the low abundance of GPCRs, combined with the hydrophilicity of C-terminal phosphopeptides, has prevented robust RPLC-MS analysis of potentially crucial regions. To address this issue, we developed a simple, easily implemented method to introduce a commonly used tandem mass tag (TMT) to increase peptide hydrophobicity, effectively enhancing RPLC-MS analysis of hydrophilic peptides. This method was applied to study the peptide QPSSSR, a tryptic peptide located on the C-terminus of the GPCR CXCR3 not been reported, and validated by comparative RPLC-MS analyses of both a hydrophilic QPSSSR peptide library as well as common phosphopeptides before and after TMT labeling. We further confirmed the utility of this method by quantifying QPSSSR phosphorylation abundances in HEK 293 cells under different treatement conditions predicted to alter QPSSSR phosphorylation. We anticipate that this simple TMT-labeling method can be broadly used not only for decoding GPCR phosphoproteomes, but also for effective RPLC-MS analysis of other highly hydrophilic analytes.

Tsai, Chia-Feng↗
DOE OSTI2023

Ultrafast Optical Nanoscopy of Carrier Dynamics in Silicon Nanowires

Carrier distribution and dynamics in semiconductor materials often govern their physical properties that are critical to functionalities and performance in industrial applications. The continued miniaturization of electronic and photonic devices calls for tools to probe carrier behavior in semiconductors simultaneously at the picosecond time and nanometer length scales. Here, in this paper, we report pump–probe optical nanoscopy in the visible-near-infrared spectral region to characterize the carrier dynamics in silicon nanostructures. By coupling experiments with the point-dipole model, we resolve the size-dependent photoexcited carrier lifetime in individual silicon nanowires. We further demonstrate local carrier decay time mapping in silicon nanostructures with a sub-50 nm spatial resolution. Our study enables the nanoimaging of ultrafast carrier kinetics, which will find promising applications in the future design of a broad range of electronic, photonic, and optoelectronic devices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

In-Situ Atomic-Scale Revelation of Amorphous Metallic Iron Formation during Hydrogen-Driven Reduction of Iron Oxides

The transition to hydrogen as a green reductant in metal production is critical for decarbonizing the metallurgical industry, yet atomic-scale mechanisms governing reduction pathways and phase evolution remain unresolved. Using in-situ environmental transmission electron microscopy, we identify a hidden pathway that reveals dynamic formation of amorphous metallic iron (Fe) during the hydrogen-driven reduction of ferrous oxides of Fe 3 O 4 and FeO. Real-time imaging uncovers three coexisting transformation routes: (i) Fe 3 O 4 → FeO, (ii) Fe 3 O 4 → amorphous Fe, and (iii) FeO → amorphous Fe. The resulting amorphous Fe exhibits fluid-like mobility, enabling its rapid aggregation and crystallization into core-shell nanostructures, with a crystalline core enveloped by an amorphous shell. Complementary ab initio molecular dynamics simulations trace the amorphous Fe formation to interfacial strain at the metal/oxide interfaces, where large lattice mismatches destabilize the metal lattice during initial metallization. This interplay between thermodynamics and kinetics governs phase evolution: thermodynamics favors a self-limiting amorphous Fe overlayer, while rapid oxide reduction kinetics drives amorphous overgrowth. Our findings demonstrate that amorphous intermediates bypass rate-limiting crystalline steps, providing mechanistic insights to optimize H 2 -based processes for sustainable steelmaking. In conclusion, these insights bridge the gap between macroscopic process engineering and atomic-scale dynamics, with broader implications for catalysis and nanostructured material synthesis, where oxide reduction pathways critically shape functional phases and microstructures.

36 MATERIALS SCIENCE↗
DOE OSTI2022

van der Waals Semiconductor Empowered Vertical Color Sensor

We report biomimetic artificial vision is receiving significant attention nowadays, particularly for the development of neuromorphic electronic devices, artificial intelligence, and microrobotics. Nevertheless, color recognition, the most critical vision function, is missed in the current research due to the difficulty of downscaling of the prevailing color sensing devices. Conventional color sensors typically adopt a lateral color sensing channel layout and consume a large amount of physical space, whereas compact designs suffer from an unsatisfactory color detection accuracy. In this work, we report a van der Waals semiconductor-empowered vertical color sensing structure with the emphasis on compact device profile and precise color recognition capability. More attractive, we endow color sensor hardware with the function of chromatic aberration correction, which can simplify the design of an optical lens system and, in turn, further downscales the artificial vision systems. Also, the dimension of a multiple pixel prototype device in our study confirms the scalability and practical potentials of our developed device architecture toward the above applications.

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

Improving the Quasi‐Biennial Oscillation via a Surrogate‐Accelerated Multi‐Objective Optimization

Accurate simulation of the quasi-biennial oscillation (QBO) is challenging due to uncertainties in representing convectively generated gravity waves. We develop an end-to-end uncertainty quantification workflow that calibrates these gravity wave processes in E3SM for a realistic QBO. Central to our approach is a domain knowledge-informed, compressed representation of high-dimensional spatio-temporal wind fields. By employing a parsimonious statistical model that learns the fundamental frequency from complex observations, we extract interpretable and physically meaningful quantities capturing key attributes. Building on this, we train a probabilistic surrogate model that approximates the fundamental characteristics of the QBO as functions of critical physics parameters governing gravity wave generation. Leveraging the Karhunen–Loève decomposition, our surrogate efficiently represents these characteristics as a set of orthogonal features, capturing cross-correlations among multiple physics quantities evaluated at different pressure levels and enabling rapid surrogate-based inference at a fraction of the computational cost of full-scale simulations. Finally, we analyze the inverse problem using a multi-objective approach. Our study reveals a tension between amplitude and period that constrains the QBO representation, precluding a single optimal solution. To navigate this, we quantify the bi-criteria trade-off and generate a set of Pareto optimal parameter values that balance the conflicting objectives. This integrated workflow improves the fidelity of QBO simulations and offers a versatile template for uncertainty quantification in complex geophysical models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Depinning transition of a domain wall in ferromagnetic films

Here, we report first principle numerical study of domain wall (DW) depinning in two-dimensional magnetic film, which is modeled by 2D random-field Ising system with the dipole-dipole interaction. We observe non-conventional activation-type motion of DW and reveal the fractal structure of DW near the depinning transition. We determine scaling functions describing critical dynamics near the transition and obtain universal exponents establishing connection between thermal softening of pinning potential and critical dynamics. In addition, we observe that tuning the strength of the dipole-dipole interaction switches DW dynamics between two different universality classes, corresponding to two distinct dynamic regimes characterized by non-Arrhenius and conventional Arrhenius-type DW motions.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Topology of tokamak plasma equilibria with toroidal current reversal

Some general principles about scalar functions with critical points are used to rigorously ascertain that magnetic equilibria with both toroidal current reversal and nested magnetic surfaces are atypical solutions and highly unstable to arbitrary perturbations of boundary conditions and other parameters. The cause for such is shown to lie in the condition of nested magnetic surfaces and not in the possibility of current reversal and consequent vanishing of the poloidal field inside the plasma. Rather than supporting the claim that instability against experimentally driven perturbations forbids configurations with toroidal current reversal, it is argued that these can be attained if an axisymmetric island system is allowed for in order to break the condition of nested magnetic surfaces. A number of results previously reported in the literature are discussed and reinterpreted under the proposed framework, providing some physical insight on the nature of equilibria with toroidal current reversal.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗