Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “structure function”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,189 records · Page 66
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Ecosystem leaf area, gross primary production, and evapotranspiration responses to wildfire in the Columbia River basin

Wildfires impact vegetation mortality and productivity and are increasing in intensity, frequency, and spatial area in the western United States. The rates of vegetation recovery after fires play a major role in the reestablishment of biomass and ecosystem functioning (e.g., structure, resilience, and productivity), but such recovery rates are poorly understood. Here we use remotely sensed data products from the Moderate Resolution Imaging Spectroradiometer (MODIS) to quantify the resistance and resilience of leaf area index (LAI), gross primary production (GPP), and evapotranspiration (ET) to 138 wildfires of various burn severity across the Columbia River basin (CRB) of the Pacific Northwest in 2015. Increasing burn severity caused lower resistance and resilience for all three variables. Resistance and resilience are highest in grasslands, intermediate in savanna, and lowest in needleleaf evergreen forests, consistent with the adaptation of these vegetation types to fire. LAI has consistently lower resistance and resilience than GPP and ET, which is consistent with physical and physiological mechanisms that compensate for reduced LAI. Resilience is influenced by precipitation, vapor pressure deficit (VPD), and burn severity across all three vegetation types; however, burn severity plays a more minor role in grasslands. Increasing wildfire severity will reduce the resistance and resilience and lengthen the recovery time of vegetation structure and fluxes with climate change, with significant consequences for the provision of ecosystem functioning and implications for model predictions.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2014

Time Course of Atrophic Remodeling: Effects of Exercise on Cardiac Morpology and Function

Early and consistent evaluation of cardiac morphology and function throughout an atrophic stimulus is critically important for the design and optimization of interventions. Exercise training is one intervention that has been shown to confer favorable improvements in LV mass and function during unloading. However, the format and intensity of exercise required to induce optimal cardiac improvements has not been investigated. PURPOSE: This randomized, controlled trial was designed to 1) comprehensively characterize the time course of unloading-induced morpho-functional remodeling, and 2) examine the effects of high intensity exercise training on cardiac structural and functional parameters during unloading. METHODS: Twenty six subjects completed 70 days of head down tilt bed rest (HDBR): 17 were randomized to exercise training (ExBR) and 9 remained sedentary. Exercise consisted of integrated high intensity, continuous, and resistance exercise. We assessed cardiac morphology (left ventricular mass; LVM) and function (speckle-tracking assessment of longitudinal, radial, and circumferential strain and twist) before (BR-2), during (BR7,21,31,70), and following (BR+0, +3) HDBR. Cardiorespiratory fitness (VO2max) was evaluated before (BR- 3), during (BR4,25,46,68) and following (BR+0) HDBR. RESULTS: Sedentary HDBR resulted in a progressive decline in LVM, longitudinal, radial, and circumferential strain, and an increase in twist. ExBR mitigated decreases in LVM and function. Change in twist was significantly related to change in VO2max (R=0.68, p<0.01). CONCLUSIONS: Alterations in cardiac morphology and function begin early during unloading. High-intensity exercise attenuates atrophic morphological and functional remodeling.

Scott, J. M.↗
NASA NTRS2019

Local frustration around enzyme active sites

Conflicting biological goals often meet in the specification of protein sequences for structure and function. Overall, strong energetic conflicts are minimized in folded native states according to the principle of minimal frustration, so that a sequence can spontaneously fold, but local violations of this principle open up the possibility to encode the complex energy landscapes that are required for active biological functions. We survey the local energetic frustration patterns of all protein enzymes with known structures and experimentally annotated catalytic residues. In agreement with previous hypotheses, the catalytic sites themselves are often highly frustrated regardless of the protein oligomeric state, overall topology, and enzymatic class. At the same time a secondary shell of more weakly frustrated interactions surrounds the catalytic site itself. We evaluate the conservation of these energetic signatures in various family members of major enzyme classes, showing that local frustration is evolutionarily more conserved than the primary structure itself.

Maria I. Freiberger↗
DOE OSTI2023

SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals

The main protease of SARS-CoV-2 (M pro ) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in M pro may alter the structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOCs) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and the rate of cleavage of a viral peptide. Crystal structures of 11 M pro mutants provided structural insight into their altered functionality. Additionally, we show M pro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and a subsequent significant decrease in cytokine secretion, providing evidence for alterations in the escape of host-antiviral mechanisms. Accordingly, mutations associated with the Gamma VOC and highly virulent Delta VOC resulted in a significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting M pro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.

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

Electronic structure of chromium trihalides beyond density functional theory

In this work, we explore the electronic band structure of freestanding monolayers of chromium trihalides Cr X 3 , X = Cl, Br, I, within an advanced ab initio theoretical approach based on the use of Green's function functionals. We compare the local density approximation with the quasiparticle self-consistent GW (QS GW ) approximation and its self-consistent extension ( QS G W ^ ) by solving the particle-hole ladder Bethe-Salpeter equations to improve the effective interaction W . We show that, at all levels of theory, the valence band consistently changes shape in the sequence Cl → Br → I , and the valence band maximum shifts from the M point to the Γ point. By analyzing the dynamic and momentum-dependent self-energy, we show that QS G W ^ adds to the localization of the systems in comparison with QS GW , thereby leading to a narrower band and reduced amount of halogens in the valence band manifold. Further analysis shows that X = Cl is most strongly correlated, and X = I is least correlated (most bandlike) as the hybridization between Cr d and X p enhances in the direction Cl → Br → I . For CrBr 3 and CrI 3 , we observe remarkable differences between the QS GW and QS G W ^ valence band structures, while their eigenfunctions are very similar. We show that weak perturbations, like moderate strain, weak changes to the d - p hybridization, and adding small U , can flip the valence band structures between these two solutions in these materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1978

Fault-tolerant software for aircraft control systems

Concepts for software to implement real time aircraft control systems on a centralized digital computer were discussed. A fault tolerant software structure employing functionally redundant routines with concurrent error detection was proposed for critical control functions involving safety of flight and landing. A degraded recovery block concept was devised to allow collocation of critical and noncritical software modules within the same control structure. The additional computer resources required to implement the proposed software structure for a representative set of aircraft control functions were discussed. It was estimated that approximately 30 percent more memory space is required to implement the total set of control functions. A reliability model for the fault tolerant software was described and parametric estimates of failure rate were made.

Source record↗
DOE OSTI2020

The Antioxidant Enzyme Methionine Sulfoxide Reductase A (MsrA) Interacts with Jab1/CSN5 and Regulates Its Function

Methionine sulfoxide (MetO) is an oxidative posttranslational modification that primarily occurs under oxidative stress conditions, leading to alteration of protein structure and function. This modification is regulated by MetO reduction through the evolutionarily conserved methionine sulfoxide reductase (Msr) system. The Msr type A enzyme (MsrA) plays an important role as a cellular antioxidant and promotes cell survival. The ubiquitin- (Ub) like neddylation pathway, which is controlled by the c-Jun activation domain-binding protein-1 (Jab1), also affects cell survival. Jab1 negatively regulates expression of the cell cycle inhibitor cyclin-dependent kinase inhibitor 1B (P27) through binding and targeting P27 for ubiquitination and degradation. Here we report the finding that MsrA interacts with Jab1 and enhances Jab1's deneddylase activity (removal of Nedd8). In turn, an increase is observed in the level of deneddylated Cullin-1 (Cul-1, a component of E3 Ub ligase complexes). Furthermore, the action of MsrA increases the binding affinity of Jab1 to P27, while MsrA ablation causes a dramatic increase in P27 expression. Thus, an interaction between MsrA and Jab1 is proposed to have a positive effect on the function of Jab1 and to serve as a means to regulate cellular resistance to oxidative stress and to enhance cell survival.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal structures of OrfX1, OrfX2 and the OrfX1–OrfX3 complex from the orfX gene cluster of botulinum neurotoxin E1

Botulinum neurotoxins (BoNTs) are among the most lethal toxins known to humans, comprising seven established serotypes termed BoNT/A–G encoded in two types of gene clusters (ha and orfX) in BoNT-producing clostridia. The ha cluster encodes four non-toxic neurotoxin-associated proteins (NAPs) that assemble with BoNTs to protect and enhance their oral toxicity. However, the structure and function of the orfX-type NAPs remain largely unknown. Here, we report the crystal structures for OrfX1, OrfX2, and an OrfX1–OrfX3 complex, which are encoded in the orfX cluster of a BoNT/E1-producing Clostridium botulinum strain associated with human foodborne botulism. These structures lay the foundation for future studies on the potential roles of OrfX proteins in oral intoxication and pathogenesis of BoNTs.

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

Controlling the symmetry of cadmium arsenide films by epitaxial strain

Epitaxial strains offer unique opportunities to obtain topological states in thin films and heterostructures that do not exist in their bulk counterparts. Here, we investigate the point group symmetries of coherently strained films of cadmium arsenide (Cd 3 As 2 ), a prototype three-dimensional Dirac semimetal, by convergent beam electron diffraction. We report a loss of the fourfold rotational axis and adoption of the orthorhombic mmm point group in (112)-oriented films under biaxial compressive stress. (001)-oriented Cd 3 As 2 films that are under a small biaxial tensile stress retain the fourfold rotational symmetry that protects the bulk nodes but adopt the non-centrosymmetric 4mm point group symmetry. This, in turn, suggests that (001) films adopt a different crystal structure in biaxial tension, one that differs in the arrangement of the ordered Cd vacancies that are an inherent feature of the crystal structure of Cd 3 As 2 and that are key to its nodal electronic structure. Density functional theory calculations confirm the experimental findings of the stability of the non-centrosymmetric structure under biaxial tension, whereas the centrosymmetric structure is stable under biaxial compression. The results show that bulk Cd 3 As 2 is already close to structural instability and showcase the extraordinary tunability of the topological states of Cd 3 As 2 .

36 MATERIALS SCIENCE↗
DOE OSTI2022

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Abstract Motivation Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for. Results Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. Availability and implementation Our code and examples are available at: https://github.com/spetti/SMURF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Nanoscale modulation of flat bands via controllable charge density wave defects in 4⁢𝐻⁡𝑏−Ta⁢S 2

Electron correlation is a main driver of exotic quantum phases and their interplay. The 4H b-TaS 2 system, possessing an intrinsic heterostructure of 1T- and 1H -TaS 2 monolayers, offers a unique opportunity to control electron correlation by distorting the atomic lattice or tuning interlayer coupling. Here, we investigated intrinsically deformed charge-density waves (CDWs) in the 1T layer of 4H b-TaS 2 to elucidate and control their effects on flat bands using scanning tunneling microscopy and spectroscopy (STM/S) combined with first-principles calculations. We identified two types of CDW defects: Type 1 has structural distortion and locally suppressed flat bands, while Type 2 features an increased flat band filling factor of intact CDW structure. Density functional theory calculations indicate that a sulfur vacancy in the 1T layer distorts the CDW structure and gives rise to a Type 1, whereas a sulfur vacancy in the 1H layer reduces the interlayer charge transfer and leads to a Type 2. Furthermore, we demonstrated creating and erasing individual CDW defects via STM manipulation. Here, our findings provide a pathway to not only tune flat bands but also selectively manipulate the interaction between CDW, the atomic lattice, and interlayer coupling in strongly correlated systems with atomic precision.

Charge density waves↗
NASA NTRS1991

Materials and light thermal structures research for advanced space exploration

The Light Thermal Structures Center at the University of Virginia sponsors educational and research programs focused on the development of reliable, lightweight structures to function in hostile thermal environments. Technology advances in materials and design methodology for light thermal structures will contribute to improved space vehicle design concepts with attendant weight savings. This paper highlights current research activities in three areas relevant to space exploration: low density, high temperature aluminum alloys, composite materials, and structures with thermal gradients. Advances in the development of new aluminum-lithium alloys and mechanically alloyed aluminum alloys are described. Material properties and design features of advanced composites are highlighted. Research studies in thermal structures with temperature gradients include inelastic panel buckling and thermally induced unstable oscillations. Current and future research is focused on the integration of new materials with applications to structural components with thermal gradients.

Thornton, Earl A.↗
NASA NTRS1993

Research in image management and access

Presently, the problem of over-all library system design has been compounded by the accretion of both function and structure to a basic framework of requirements. While more device power has led to increased functionality, opportunities for reducing system complexity at the user interface level have not always been pursued with equal zeal. The purpose of this book is therefore to set forth and examine these opportunities, within the general framework of human factors research in man-machine interfaces. Human factors may be viewed as a series of trade-off decisions among four polarized objectives: machine resources and user specifications; functionality and user requirements. In the past, a limiting factor was the availability of systems. However, in the last two years, over one hundred libraries supported by many different software configurations have been added to the Internet. This document includes a statistical analysis of human responses to five Internet library systems by key features, development of the ideal online catalog system, and ideal online catalog systems for libraries and information centers.

Vondran, Raymond F.↗
DOE OSTI2021

Probing the subcellular nanostructure of engineered human cardiomyocytes in 3D tissue

Abstract The structural and functional maturation of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) is essential for pharmaceutical testing, disease modeling, and ultimately therapeutic use. Multicellular 3D-tissue platforms have improved the functional maturation of hiPSC-CMs, but probing cardiac contractile properties in a 3D environment remains challenging, especially at depth and in live tissues. Using small-angle X-ray scattering (SAXS) imaging, we show that hiPSC-CMs matured and examined in a 3D environment exhibit a periodic spatial arrangement of the myofilament lattice, which has not been previously detected in hiPSC-CMs. The contractile force is found to correlate with both the scattering intensity ( R 2 = 0.44) and lattice spacing ( R 2 = 0.46). The scattering intensity also correlates with lattice spacing ( R 2 = 0.81), suggestive of lower noise in our structural measurement than in the functional measurement. Notably, we observed decreased myofilament ordering in tissues with a myofilament mutation known to lead to hypertrophic cardiomyopathy (HCM). Our results highlight the progress of human cardiac tissue engineering and enable unprecedented study of structural maturation in hiPSC-CMs.

36 MATERIALS SCIENCE↗
NASA NTRS1994

Inventing and improving ribozyme function: rational design versus iterative selection methods

Two major strategies for generating novel biological catalysts exist. One relies on our knowledge of biopolymer structure and function to aid in the 'rational design' of new enzymes. The other, often called 'irrational design', aims to generate new catalysts, in the absence of detailed physicochemical knowledge, by using selection methods to search a library of molecules for functional variants. Both strategies have been applied, with considerable success, to the remodeling of existing ribozymes and the development of ribozymes with novel catalytic function. The two strategies are by no means mutually exclusive, and are best applied in a complementary fashion to obtain ribozymes with the desired catalytic properties.

Review, Tutorial↗
DOE OSTI2023

Room temperature colossal superparamagnetic order in aminoferrocene–graphene molecular magnets

Intensive studies are published for graphene-based molecular magnets due to their remarkable electric, thermal, and mechanical properties. However, to date, most of all produced molecular magnets are ligand based and subject to challenges regarding the stability of the ligand(s). The lack of long-range coupling limits high operating temperature and leads to a short-range magnetic order. Herein, we introduce an aminoferrocene-based graphene system with room temperature superparamagnetic behavior in the long-range magnetic order that exhibits colossal magnetocrystalline anisotropy of 8 × 10 5 and 3 × 10 7 J/m 3 in aminoferrocene and graphene-based aminoferrocene, respectively. These values are comparable to and even two orders of magnitude larger than pure iron metal. Aminoferrocene [C 10 H 11 FeN] + is synthesized by an electrophilic substitution reaction. It was then reacted with graphene oxide that was prepared by the modified Hammers method. The phase structure and functionalization of surface groups were characterized and confirmed by XRD, FT-IR, and Raman spectroscopy. To model the behavior of the aminoferrocene between two sheets of hydroxylated graphene, we have used density functional theory by placing the aminoferrocene molecule between two highly ordered hydroxylated sheets and allowing the structure to relax. Here, the strong bowing of the isolated graphene sheets suggests that the charge transfer and resulting magnetization could be strongly influenced by pressure effects. In contrast to strategies based on ligands surface attachment, our present work that uses interlayer intercalated aminoferrocene opens routes for future molecular magnets as well as the design of qubit arrays and quantum systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Symmetry in Seeded Metal Nanocrystal Growth

Symmetry underpins the structure and function of the world around us and is also captured in modern nanomaterials, where changing the symmetry of a nanocrystal or the interparticle spacing and orientation of nanocrystal building blocks in a superlattice can give new function. However, the synthesis and assembly of nanocrystals have been limited largely to simple compositions and structures. It remains a grand challenge to achieve nanocrystals with compositional and structural complexity while maintaining the monodispersity required for their use. This Account will illustrate through recent examples that seeded methods enable the synthesis of compositionally and structurally complex multimetallic crystals with defined and predictable symmetries for applications in plasmonics and catalysis. This outcome arises because the barrier for heterogeneous nucleation (i.e., seeded) is lower than that of homogeneous nucleation, where seeds can serve as preferential sites for the growth of complex structures and crystal phases. Our analysis begins by considering metal overgrowth from single-crystalline seeds of different shapes and symmetries, where the kinetics of adatom addition to seeds relative to their diffusion across seeds accounts for the expressed nanocrystal shapes. These results are then compared to overgrowth from seeds with different internal structures (i.e., planar defects), where the relationships between nanocrystal size and volumetric strain energy and surface energy are discussed. A major finding from this analysis is that often the underlying symmetry of seeds can be predictably transferred to the final crystals during overgrowth processes. Consequences of this finding are the predictable syntheses of crystals with different hierarchies akin to snowcrystals as well as nanocrystals with complex compositions (e.g., quaternary nanoparticles). Yet, there are subtle aspects to seeded growth that pave a path toward examples where nanocrystal symmetry has been reduced compared to the original seeds in a controlled manner. As we found, both the concentrations of metal precursors and capping agents can impact whether symmetry is transferred or reduced during overgrowth. Examples from our laboratory will be placed in context to other reported strategies for symmetry breaking. As will be argued, understanding what conditions favor symmetry preservation versus symmetry reduction during seeded crystal growth is central to accessing next-generation crystal forms. The Account concludes by outlining synthetic challenges associated with forming nanoscale heterostructures with precise 3-D placement of different materials within a given nanocrystal as well as facet control within different material domain and interface engineering. Furthermore, we envision meeting these challenges through regioselective and chemoselective seeded syntheses for which a foundation is outlined herein.

36 MATERIALS SCIENCE↗