Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “functionalization”

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 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structural basis of impaired disaggregase function in the oxidation-sensitive SKD3 mutant causing 3-methylglutaconic aciduria

Abstract Mitochondria are critical to cellular and organismal health. To prevent damage, mitochondria have evolved protein quality control machines to survey and maintain the mitochondrial proteome. SKD3, also known as CLPB, is a ring-forming, ATP-fueled protein disaggregase essential for preserving mitochondrial integrity and structure. SKD3 deficiency causes 3-methylglutaconic aciduria type VII (MGCA7) and early death in infants, while mutations in the ATPase domain impair protein disaggregation with the observed loss-of-function correlating with disease severity. How mutations in the non-catalytic N-domain cause disease is unknown. Here, we show that the disease-associated N-domain mutation, Y272C, forms an intramolecular disulfide bond with Cys267 and severely impairs SKD3 Y272C function under oxidizing conditions and in living cells. While Cys267 and Tyr272 are found in all SKD3 isoforms, isoform-1 features an additional α-helix that may compete with substrate-binding as suggested by crystal structure analyses and in silico modeling, underscoring the importance of the N-domain to SKD3 function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

RNA language models predict mutations that improve RNA function

Structured RNA lies at the heart of many central biological processes, from gene expression to catalysis. RNA structure prediction is not yet possible due to a lack of high-quality reference data associated with organismal phenotypes that could inform RNA function. We present GARNET (Gtdb Acquired RNa with Environmental Temperatures), a new database for RNA structural and functional analysis anchored to the Genome Taxonomy Database (GTDB). GARNET links RNA sequences to experimental and predicted optimal growth temperatures of GTDB reference organisms. Using GARNET, we develop sequence- and structure-aware RNA generative models, with overlapping triplet tokenization providing optimal encoding for a GPT-like model. Leveraging hyperthermophilic RNAs in GARNET and these RNA generative models, we identify mutations in ribosomal RNA that confer increased thermostability to the Escherichia coli ribosome. The GTDB-derived data and deep learning models presented here provide a foundation for understanding the connections between RNA sequence, structure, and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Advanced multi-modal mass spectrometry imaging reveals functional differences of placental villous compartments at microscale resolution

The placenta is a complex and heterogeneous organ that links the mother and fetus, playing a crucial role in nourishing and protecting the fetus throughout pregnancy. Integrative spatial multi-omics approaches can provide a systems-level understanding of molecular changes underlying the mechanisms leading to the histological variations of the placenta during healthy pregnancy and pregnancy complications. Herein, we advance our metabolome-informed proteome imaging (MIPI) workflow to include lipidomic imaging, while also expanding the molecular coverage of metabolomic imaging by incorporating on-tissue chemical derivatization (OTCD). The improved MIPI workflow advances biomedical investigations by leveraging state-of-the-art molecular imaging technologies. Lipidome imaging identifies molecular differences between two morphologically distinct compartments of a placental villous functional unit, syncytiotrophoblast (STB) and villous core. Next, our advanced metabolome imaging maps villous functional units with enriched metabolomic activities related to steroid and lipid metabolism, outlining distinct molecular distributions across morphologically different villous compartments. Complementary proteome imaging on these villous functional units reveals a plethora of fatty acid- and steroid-related enzymes uniquely distributed in STB and villous core compartments. Integration across our advanced MIPI imaging modalities enables the reconstruction of active biological pathways of molecular synthesis and maternal-fetal signaling across morphologically distinct placental villous compartments with micrometer-scale resolution.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Structure of human MUTYH and functional profiling of cancer-associated variants reveal an allosteric network between its [4Fe-4S] cluster cofactor and active site required for DNA repair

Abstract MUTYH is a clinically important DNA glycosylase that thwarts mutations by initiating base-excision repair at 8-oxoguanine (OG):A lesions. The roles for its [4Fe-4S] cofactor in DNA repair remain enigmatic. Functional profiling of cancer-associated variants near the [4Fe-4S] cofactor reveals that most variations abrogate both retention of the cofactor and enzyme activity. Surprisingly, R241Q and N238S retained the metal cluster and bound substrate DNA tightly, but were completely inactive. We determine the crystal structure of human MUTYH bound to a transition state mimic and this shows that Arg241 and Asn238 build an H-bond network connecting the [4Fe-4S] cluster to the catalytic Asp236 that mediates base excision. The structure of the bacterial MutY variant R149Q, along with molecular dynamics simulations of the human enzyme, support a model in which the cofactor functions to position and activate the catalytic Asp. These results suggest that allosteric cross-talk between the DNA binding [4Fe-4S] cofactor and the base excision site of MUTYH regulate its DNA repair function.

Science & Technology - Other Topics↗
DOE OSTI2025

Climate-driven succession in marine microbiome biodiversity and biogeochemical function

Abstract Seasonal and El Niño-Southern Oscillation (ENSO) warming result in similar ocean changes as predicted with climate change. Climate-driven environmental cycles have strong impacts on microbiome diversity, but impacts on microbiome function are poorly understood. Here we quantify changes in microbial genomic diversity and functioning over 11 years covering seasonal and ENSO cycles at a coastal site in the southern California Current. We observe seasonal oscillations between large-genome lineages during cold, nutrient rich conditions in winter and spring versus small-genome lineages, including Prochlorococcus and Pelagibacter , in summer and fall. Parallel interannual changes separate communities depending on ENSO condition. Biodiversity shifts translate into clear oscillations in microbiome functional potential. Ocean warming induced an ecosystem with less iron but more macronutrient stress genes, depressed organic carbon degradation potential and biomass, and elevated carbon-to-nutrient biomass ratios. The consistent microbial response observed across time-scales points towards large climate-driven changes in marine ecosystems and biogeochemical cycles.

Larkin, Alyse A. (ORCID:0000000344660791)↗
DOE OSTI2020

Predicting synthesizable multi-functional edge reconstructions in two-dimensional transition metal dichalcogenides

Abstract Two-dimensional (2D) transition metal dichalcogenides (TMDCs) have attracted tremendous interest as functional materials due to their exceptionally diverse and tunable properties, especially in their edges. In addition to the conventional armchair and zigzag edges common to hexagonal 2D materials, more complex edge reconstructions can be realized through careful control over the synthesis conditions. However, the whole family of synthesizable, reconstructed edges remains poorly studied. Here, we develop a computational approach integrating ensemble-generation, force-relaxation, and electronic-structure calculations to systematically and efficiently discover additional reconstructed edges and screen their functional properties. Using MoS 2 as a model system, we screened hundreds of edge-reconstruction to discover over 160 reconstructed edges to be more stable than the conventional ones. More excitingly, we discovered nine new synthesizable reconstructred edges with record thermodynamic stability, in addition to successfully reproducing three recently synthesized edges. We also find our predicted reconstructed edges to have multi-functional properties—they show near optimal hydrogen evolution activity over the conventional edges, ideal for catalyzing hydrogen-evolution reaction (HER) and also exhibit half-metallicity with a broad variation in magnetic moments, making them uniquely suitable for nanospintronic applications. Our work reveals the existence of a wide family of synthesizable, reconstructed edges in 2D TMDCs and opens a new materials-by-design paradigm of ‘intrinsic’ edge engineering multifunctionality in 2D materials.

Hu, Guoxiang (ORCID:0000000329428564)↗
DOE OSTI2022

Sensitivity of the electronic and magnetic structures of cuprate superconductors to density functional approximations

Abstract We discuss the crystal, electronic, and magnetic structures of La 2− x Sr x CuO 4 (LSCO) for x = 0.0 and x = 0.25 employing 13 density functional approximations, representing the local, semi-local, and hybrid exchange-correlation approximations within the Perdew–Schmidt hierarchy. The meta-generalized gradient approximation (meta-GGA) class of functionals is found to perform well in capturing the key properties of LSCO, a prototypical high-temperature cuprate superconductor. In contrast, the localspin-density approximation, GGA, and the hybrid density functional fail to capture the metal-insulator transition under doping.

36 MATERIALS SCIENCE↗
DOE OSTI2023

High-throughput calculations of charged point defect properties with semi-local density functional theory—performance benchmarks for materials screening applications

Abstract Calculations of point defect energetics with Density Functional Theory (DFT) can provide valuable insight into several optoelectronic, thermodynamic, and kinetic properties. These calculations commonly use methods ranging from semi-local functionals with a-posteriori corrections to more computationally intensive hybrid functional approaches. For applications of DFT-based high-throughput computation for data-driven materials discovery, point defect properties are of interest, yet are currently excluded from available materials databases. This work presents a benchmark analysis of automated, semi-local point defect calculations with a-posteriori corrections, compared to 245 “gold standard” hybrid calculations previously published. We consider three different a-posteriori correction sets implemented in an automated workflow, and evaluate the qualitative and quantitative differences among four different categories of defect information: thermodynamic transition levels, formation energies, Fermi levels, and dopability limits. We highlight qualitative information that can be extracted from high-throughput calculations based on semi-local DFT methods, while also demonstrating the limits of quantitative accuracy.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils

Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden’s thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current activity. This revealed an active mobilome that shapes natural genetic diversity via differential impacts on major phyla and affects a wide range of functions, including metabolic genes involved in carbon flux and nutrient cycling. These findings and this analytic framework suggest avenues towards a better understanding of MGE diversity, activity, mobility and impacts across ecosystems.

Biological and medical sciences↗
DOE OSTI2022

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis -regulatory elements

Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

De novo design of buttressed loops for sculpting protein functions

In natural proteins, structured loops have central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein functional sites has been very difficult to achieve by de novo protein design. Here we describe a solution to this problem that designs tandem repeat proteins with structured loops (9–14 residues) buttressed by extensive hydrogen bonding interactions. Experimental characterization shows that the designs are monodisperse, highly soluble, folded and thermally stable. Crystal structures are in close agreement with the design models, with the loops structured and buttressed as designed. We demonstrate the functionality afforded by loop buttressing by designing and characterizing binders for extended peptides in which the loops form one side of an extended binding pocket. The ability to design multiple structured loops should contribute generally to efforts to design new protein functions.

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

Cost function for low-dimensional manifold topology assessment

Abstract In reduced-order modeling, complex systems that exhibit high state-space dimensionality are described and evolved using a small number of parameters. These parameters can be obtained in a data-driven way, where a high-dimensional dataset is projected onto a lower-dimensional basis. A complex system is then restricted to states on a low-dimensional manifold where it can be efficiently modeled. While this approach brings computational benefits, obtaining a good quality of the manifold topology becomes a crucial aspect when models, such as nonlinear regression, are built on top of the manifold. Here, we present a quantitative metric for characterizing manifold topologies. Our metric pays attention to non-uniqueness and spatial gradients in physical quantities of interest, and can be applied to manifolds of arbitrary dimensionality. Using the metric as a cost function in optimization algorithms, we show that optimized low-dimensional projections can be found. We delineate a few applications of the cost function to datasets representing argon plasma, reacting flows and atmospheric pollutant dispersion. We demonstrate how the cost function can assess various dimensionality reduction and manifold learning techniques as well as data preprocessing strategies in their capacity to yield quality low-dimensional projections. We show that improved manifold topologies can facilitate building nonlinear regression models.

42 ENGINEERING↗
DOE OSTI2023

Identifying the secondary electron cutoff in ultraviolet photoemission spectra for work function measurements of non-ideal surfaces

Abstract Absolute values of work functions can be determined in ultraviolet photoemission spectroscopy (UPS) by measuring the minimum kinetic energy of secondary electrons generated by a known photon energy. However, some samples can produce spectra that are difficult to interpret due to additional intensity below the true secondary electron cutoff. Disordered absorbates on elemental metals add small intensity below the onset for the transition metal surfaces studied, which can be attributed to energy losses after photoelectrons are generated. In contrast, spectra from WO 3−x films can produce multiple onsets with comparable intensity which do not fit this model. False onsets (in the context of work function measurements) can be minimized by optimizing experimental detection parameters including limiting analyzer acceptance angles and pass energy. True work functions can be identified by examining the onsets as the sample bias is varied.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Sequence-structure-function characterization of the emerging tetracycline destructase family of antibiotic resistance enzymes

Tetracycline destructases (TDases) are flavin monooxygenases which can confer resistance to all generations of tetracycline antibiotics. The recent increase in the number and diversity of reported TDase sequences enables a deep investigation of the TDase sequence-structure-function landscape. Here, we evaluate the sequence determinants of TDase function through two complementary approaches: (1) constructing profile hidden Markov models to predict new TDases, and (2) using multiple sequence alignments to identify conserved positions important to protein function. Using the HMM-based approach we screened 50 high-scoring candidate sequences in Escherichia coli, leading to the discovery of 13 new TDases. The X-ray crystal structures of two new enzymes from Legionella species were determined, and the ability of anhydrotetracycline to inhibit their tetracycline-inactivating activity was confirmed. Using the MSA-based approach we identified 31 amino acid positions 100% conserved across all known TDase sequences. The roles of these positions were analyzed by alanine-scanning mutagenesis in two TDases, to study the impact on cell and in vitro activity, structure, and stability. These results expand the diversity of TDase sequences and provide valuable insights into the roles of important residues in TDases, and flavin monooxygenases more broadly.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Polyester functional graphenic materials as a mechanically enhanced scaffold for tissue regeneration

Traditional metal implants such as titanium, cobalt, and chromium have found wide utility in medicine; however, these come with a risk of toxicity. To overcome metal-related toxicity and enable degradability, polyesters including polycaprolactone (PCL), polylactic acid (PLA), and polyglycolic acid (PGA) show promise for the replacement of various biomedical applications of metals due to their accepted biocompatibility and FDA approval. However, polyesters are less stiff than their metallic counterparts, limiting their application to non-load bearing injury sites, such as fixation hardware for fingers. To improve mechanical properties, graphene oxide (GO)-polyester composites are a promising class of biodegradable scaffolds. Initial reports of these composites are encouraging, but mechanical properties still fall short. Traditional composites rely on non-covalent association between GO and the polyesters, which often leads to failure at the interface and weakens the overall strength of the material. Herein, we present a strategy for attachment of these FDA-approved polyesters onto a derivative of GO using a robust covalent bond. By covalently functionalizing the graphenic backbone with polyesters and without metal catalysts, we create functional graphenic materials (FGMs) to not only simultaneously retain biodegradability and compatibility, but also mechanically strengthen PCL, PLA, and PGA; we observed an average increase in the Young's modulus of over 140% compared to the graphenic backbone. These polyester-functionalized FGMs are a promising platform technology for tissue implants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Development of sterically hindered siloxide-functionalized polyoxotungstates for the complexation of 5d-metals

In this study, we extend the family of organosilyl-functionalized trivacant Keggin polyoxotungstates, [PW 9 O 34 (RSiOH) 3 ] 3− (R = n Pr, i Pr, t Bu), through the introduction of bulky aryl and aliphatic silanol substituents, namely phenyl, cyclohexyl and biphenyl. This work was performed in order to study the impact of these large functional groups on the accessibility of the well-defined tridentate coordination site. Coordination of hafnium to these type II hybrid polyoxotungstates was conducted in order to study the ability of the bulkier ligand pockets to support larger cations in comparison to those previously reported (e.g. Ti 4+ , V 3+ , V 5+ , Ge 4+ ). Increased steric hindrance around the coordination site from the biphenyl groups resulted in much longer reaction times for the complexation reaction compared to the other functional groups used, but the impact of our design toward stabilizing reactive species proved limited, as all complexes easily undergo hydrolysis of the Hf-O t Bu bond in the presence of water. As a result, electrochemical investigations of the ligands and hafnium complexes reveal that the redox events centered on the polyoxotungstate core can be tuned by varying the substituents on the silyl fragment, and exhibit a cathodic shift after coordination of the redox inactive tetravalent cation.

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

Ab initio calculation of X-ray and related core-level spectroscopies: Green's function approaches

X-Ray and related spectroscopies are powerful probes of atomic, vibrational, and electronic structure. In order to unlock the full potential of such experimental techniques, accurate and efficient theoretical and computational approaches are essential. Here we review the status of a variety of first-principles and nearly first principles techniques for X-ray spectroscopies such as X-ray absorption, X-ray emission, and X-ray photoemission, with a focus on Green's function based methods. In particular, we describe the current state of multiple scattering Green's function techniques available in the FEFF10 code and cumulant Green's function techniques for including the effects of many-body electronic excitations. Furthermore, illustrative examples are shown for a variety of materials and compared with other theoretical and experimental results.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Insights into dual-functional modification for water stability enhancement of mesoporous zirconium metal–organic frameworks

The stability of metal–organic frameworks (MOFs) in water affects their ability to function as chemical catalysts, their capacity as adsorbents for separations in water vapor presence, and their usefulness as recyclable water harvesters. Here, we have examined water stability of four node-modified variants of the mesoporous MOF, NU-1000, namely formate-, Acac-, TFacac-, and Facac-NU-1000, comparing these with node-accessible NU-1000. These NU-1000 variants present ligands grafted to NU-1000's hexa-Zr(IV)-oxy nodes by displacing terminal aqua and hydroxo ligands. Facac-NU-1000, containing the most hydrophobic ligands, showed the greatest water stability, being able to undergo at least 20 water adsorption/desorption cycles without loss of water uptake capacity. Computational studies revealed dual salutary functions of installed Facac ligands: (1) enhancement of framework mechanical stability due to electrostatic interactions; and (2) transformation and shielding of the otherwise highly hydrophilic nodes from H-bonding interactions with free water, presumably leading to weaker channel-stressing capillary forces during water evacuation – consistent with trends in free energies of dehydration across the NU-1000 variants. Water harvesting and hydrolysis of chemical warfare agent simulants were examined to gauge the functional consequences of modification and mechanical stabilization of NU-1000 by Facac ligands. The studies revealed a harvesting capacity of ~1.1 L of water vapor per gram of Facac-NU-1000 per sorption cycle. They also revealed retention of catalytic MOF activity following 20 water uptake and release cycles. This study provides insights into the basis for node-ligand-engendered stabilization of wide-channel MOFs against collapse during water removal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗