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Results for “Substrate specificity”

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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Cytochrome P450–catalyzed biosynthesis of furanoditerpenoids in the bioenergy crop switchgrass ( Panicum virgatum L.)

Specialized diterpenoid metabolites are important mediators of plant-environment interactions in monocot crops. To understand metabolite functions in plant environmental adaptation that ultimately can enable crop improvement strategies, a deeper knowledge of the underlying species-specific biosynthetic pathways is required. Furthermore, we report the genomics-enabled discovery of five cytochrome P450 monooxygenases (CYP71Z25-CYP71Z29) that form previously unknown furanoditerpenoids in the monocot bioenergy crop Panicum virgatum (switchgrass). Combinatorial pathway reconstruction showed that CYP71Z25-CYP71Z29 catalyze furan ring addition directly to primary diterpene alcohol intermediates derived from distinct class II diterpene synthase products. Transcriptional co-expression patterns and the presence of select diterpenoids in switchgrass roots support the occurrence of P450-derived furanoditerpenoids in planta. Integrating molecular dynamics, structural analysis and targeted mutagenesis identified active site determinants that contribute to the distinct catalytic specificities underlying the broad substrate promiscuity of CYP71Z25-CYP71Z29 for native and non-native diterpenoids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Design & Assembly of Atomically-Precise Quantum Materials & Devices (Final Report)

Atomic-layer honeycomb materials (Xene, where “X” may stand for a number of different elements) are a promising platform for new quantum states. When X is a heavier element such as tin (Sn) or bismuth (Bi), the edges of the honeycomb may conduct electron charge or spin without resistance - an effect that could persist up to room temperature in some cases. The type of edge states, and their robustness at room temperature, depend sensitively on (a) the substrate material that the Xene is sitting on; (b) out-of-plane buckling of the honeycomb structure; (c) the pattern of atoms or molecules sitting atop the honeycomb. This sensitivity suggests that Xene edge states could be tuned and rearranged to construct nanoscale electronic or spintronic devices. We report on theoretical progress in modeling the assembly and structure of Xenes, and their underlying substrates and overlaying atoms. Specifically, we model the stability of Sn atoms forming a single atomic layer (“stanene”), the stability and phase transitions

36 MATERIALS SCIENCE↗
DOE OSTI2021

Competition within low-density bacterial populations as an unexpected factor regulating carbon decomposition in bulk soil

Bacterial decomposition of organic matter in soils is generally believed to be mainly controlled by the access bacteria have to organic substrate. The influence of bacterial traits on this control has, however, received little attention. Using the substrate-dependent Monod growth model, we develop a bioreactive transport model to screen the interactive impacts of spatial dispersion and bacterial traits on mineralization. Bacterial traits primarily involved in the bacterial response to the substrate concentration, such as the maximum specific uptake rate and efficiency, the adaptation time of the uptake rate and the initial population density, are considered. We compare the model results with two sets of previously performed cm-scale soil-core experiments in which the mineralization of the pesticide 2,4-D was measured under well-controlled initial distributions and transport conditions. Bacterial dispersion away from the initial substrate location induced a significant increase in 2,4-D mineralization. Additionally, it reveals an increase of specific uptake rates at lower bacterial densities, more than compensating the decrease of specific uptake rates caused by substrate dilution. This regulation of bacterial activities by density, caused by the local depletion of substrate by competing bacteria, becomes dominant for bacteria with an efficient uptake of substrate at low substrate concentrations (a common feature of oligotrophs). Such oligotrophs, commonly found in soils, compete with each other for substrate even at remarkably low population densities. The ratio-dependent Contois growth model, which includes a density regulation in the expression of the uptake efficiency, is more accurate and convenient to calibrate than the substrate-dependent Monod model, at least under these conditions. In view of their strong interactions, bioreactive and transport processes cannot be handled independently but should be integrated, in particular when reactive processes of interest are carried out by oligotrophs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Epitaxial Thin Film Growth on Recycled SrTiO 3 Substrates Toward Sustainable Processing of Complex Oxides

Complex oxide thin films cover a range of physical properties and multifunctionalities that are critical for logic, memory, and optical devices. Typically, the high‐quality epitaxial growth of these complex oxide thin films requires single crystalline oxide substrates such as SrTiO 3 (STO), MgO, LaAlO 3 , a‐Al 2 O 3, and many others. Recent successes in transferring these complex oxides as free‐standing films not only offer great opportunities in integrating complex oxides on other devices, but also present enormous opportunities in recycling the deposited substrates after transfer for cost‐effective and sustainable processing of complex oxide thin films. In this work, the surface modification effects introduced on the recycled STO are investigated, and their impacts on the microstructure and properties of subsequently grown epitaxial oxide thin films are assessed and compared with those grown on the pristine substrates. Detailed analyses using high‐resolution scanning transmission electron microscopy and geometric phase analysis demonstrate distinct strain states on the surfaces of the recycled STO versus the pristine substrates, suggesting a pre‐strain state in the recycled STO substrates due to the previous deposition layer. These findings offer opportunities in growing highly mismatched oxide films on the recycled STO substrates with enhanced physical properties. Specifically, yttrium iron garnet (Y 3 Fe 5 O 12 ) films grown on recycled STO present different ferromagnetic responses compared to that on the pristine substrates, underscoring the effects of surface modification. The study demonstrates the feasibility of reuse and redeposition using recycled substrates. Via careful handling and preparation, high‐quality epitaxial thin films can be grown on recycled substrates with comparable or even better structural and physical properties toward sustainable process of complex oxide devices.

pre-strained STO surfaces↗
DOE OSTI2024

Structural basis for C-degron selectivity across KLHDCX family E3 ubiquitin ligases

Abstract Specificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend on E3 ligases binding to peptide-like sequences - termed N- or C-degrons - at the termini of substrates. However, our knowledge of structural features distinguishing closely related C-degron substrate-E3 pairings is limited. Here, by systematically comparing ubiquitylation activities towards a suite of common model substrates, and defining interactions by biochemistry, crystallography, and cryo-EM, we reveal principles of C-degron recognition across the KLHDCX family of Cullin-RING ligases (CRLs). First, a motif common across these E3 ligases anchors a substrate’s C-terminus. However, distinct locations of this C-terminus anchor motif in different blades of the KLHDC2, KLHDC3, and KLHDC10 β-propellers establishes distinct relative positioning and molecular environments for substrate C-termini. Second, our structural data show KLHDC3 has a pre-formed pocket establishing preference for an Arg or Gln preceding a C-terminal Gly, whereas conformational malleability contributes to KLHDC10’s recognition of varying features adjacent to substrate C-termini. Finally, additional non-consensus interactions, mediated by C-degron binding grooves and/or by distal propeller surfaces and substrate globular domains, can substantially impact substrate binding and ubiquitylatability. Overall, the data reveal combinatorial mechanisms determining specificity and plasticity of substrate recognition by KLDCX-family C-degron E3 ligases.

Science & Technology - Other Topics↗
DOE OSTI2020

Pore-scale view of microbial turnover: combining 14 C imaging, μCT, and zymography after adding soluble carbon to soil pores of specific sizes

The location of microorganisms and substrates within soil pore networks plays a crucial role for organic carbon (C) processing, its microbial utilization and turnover, and has direct consequences for C and nutrient cycling. An optimal approach to quantify responses to new C inputs from microorganisms residing in specific pores is the addition of new C to pores of target sizes in undisturbed soil cores. We used the matric potential approach to add 14 C labeled glucose to small (< 40 μm, root free) or large (60-180 μm, potentially inhabited by roots) pores of undisturbed soil cores. Localization of glucose-derived C via 14 C imaging was related to pore size distributions and connectivity, characterized via X-ray computed micro-tomography (μCT), and to β-glucosidase activity, characterized via zymography. After two-week incubations, 1.3 times more glucose was mineralized ( 14 CO 2 ) when it was added to the large pores, however more 14 C remained in microbial biomass when glucose was added to the small pores. Consequently, while utilizing the same amounts of easily available C, the microorganisms localized in the large pores had faster turnover compared to microorganisms in small pores. Stronger associations between β-glucosidase activity and glucose-derived C were observed when glucose was added to the large pores. We conclude that 1) the matric potential approach allows placing, albeit not exactly, soluble substrates into pores of target diameter range, and 2) microorganisms localized in large pores respond to new C inputs with faster turnover, greater growth, and more intensive enzyme production compared to those inhabiting the small pores.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Salt supplementation-induced metabolic reprogramming in Streptomyces coelicolor

Members of the genus Streptomyces are major producers of a wide variety of secondary metabolites that serve as bioactive compounds. Many secondary metabolites are produced in response to environmental signals such as biotic and abiotic stresses. In this study, we identified salt supplementation as one of the stimuli activating secondary metabolism in the model Streptomyces species, Streptomyces coelicolor. Comparative metabolomics revealed overproduction of several known secondary metabolites, most notably undecylprodigiosin and coelimycin P1, in addition to their biosynthetic intermediates and derivatives, as well as many unknown metabolites. Transcriptomic analysis revealed activation of diverse biological processes including cation uptake, compatible solute production, and the phosphate limitation stress response through conserved and species-specific mechanisms, presumably to overcome the increased salinity. This response leads to activation of a variety of regulatory and metabolic pathways required for production of secondary metabolites including activation of conserved metabolic pathways for energy and substrate supply and species-specific secondary metabolite biosynthetic gene clusters. Furthermore, several promoter sequences contributing to upregulation of secondary metabolism induced by salt supplementation were identified. Overall, our data show how S. coelicolor copes with the increased salinity and tailors the cellular metabolism toward secondary metabolism in a conserved and species-specific manner.

Otani, Hiroshi [USDOE Joint Genome Institute (JGI)↗
DOE OSTI2022

Microbial maintenance energy quantified and modeled with microcalorimetry

Refining the energetic costs of cellular maintenance is essential for predicting microbial growth and survival in the environment. In this work, we evaluate a simple batch culture method to quantify energy partitioning between growth and maintenance using microcalorimetry and thermodynamic modeling. The constants derived from the batch culture system were comparable to those that have been reported from meta-analyses of data derived from chemostat studies. The model accurately predicted temperature-dependent biomass yield and the upper temperature limit of growth for Desulfovibrio alaskensis G20, suggesting the method may have broad application. An Arrhenius temperature dependence for the specific energy consumption rate, inferred from substrate consumption and heat evolution, was observed over the entire viable temperature range. By combining this relationship for specific energy consumption rates and observed specific growth rates, the model describes an increase in nongrowth associated maintenance at higher temperatures and the corresponding decrease in energy available for growth. This analytical and thermodynamic formulation suggests that simply monitoring heat evolution in batch culture could be a useful complement to the recognized limitations of estimating maintenance using extrapolation to zero growth in chemostats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Defective internal allosteric network imparts dysfunctional ATP/substrate-binding cooperativity in oncogenic chimera of protein kinase A

An aberrant fusion of the DNAJB1 and PRKACA genes generates a chimeric protein kinase (PKA-C DNAJB1 ) in which the J-domain of the heat shock protein 40 is fused to the catalytic α subunit of cAMP-dependent protein kinase A (PKA-C). Deceivingly, this chimeric construct appears to be fully functional, as it phosphorylates canonical substrates, forms holoenzymes, responds to cAMP activation, and recognizes the endogenous inhibitor PKI. Nonetheless, PKA-C DNAJB1 has been recognized as the primary driver of fibrolamellar hepatocellular carcinoma and is implicated in other neoplasms for which the molecular mechanisms remain elusive. Here we determined the chimera’s allosteric response to nucleotide and pseudo-substrate binding. We found that the fusion of the dynamic J-domain to PKA-C disrupts the internal allosteric network, causing dramatic attenuation of the nucleotide/PKI binding cooperativity. Our findings suggest that the reduced allosteric cooperativity exhibited by PKA-C DNAJB1 alters specific recognitions and interactions between substrates and regulatory partners contributing to dysregulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Vertically Aligned Carbon Nanotubes Grown on Copper Foil as Electrodes for Electrochemical Double Layer Capacitors

This study reports a binder-free, catalyst-free method for fabricating vertically aligned carbon nanotubes (VACNTs) directly on copper (Cu) foil using plasma-enhanced chemical vapor deposition (PECVD) for electrochemical double-layer capacitor (EDLC) applications. This approach eliminates the need for catalyst layers, polymeric binders, or substrate pre-treatments, simplifying electrode design and enhancing electrical integration. The resulting VACNTs form a dense, uniform, and porous array with strong adhesion to the Cu substrate, minimizing contact resistance and improving conductivity. Electrochemical analysis shows gravimetric specific capacitance (C grav ) and areal specific capacitance (C areal ) of 8 F g −1 and 3.5 mF cm −2 at a scan rate of 5 mV/s, with low equivalent series resistance (3.70 Ω) and charge transfer resistance (0.48 Ω), enabling efficient electron transport and rapid ion diffusion. The electrode demonstrates excellent rate capability and retains 92% of its initial specific capacitance after 3000 charge–discharge cycles, indicating strong cycling stability. These results demonstrate the potential of directly grown VACNT-based electrodes for high-performance EDLCs, particularly in applications requiring rapid charge–discharge cycles and sustained energy delivery.

25 ENERGY STORAGE↗
DOE OSTI2024

Role of Solvent in the Oriented Growth of Conductive Ni‐CAT‐1 Metal‐Organic Framework at Solid–Liquid Interfaces

Abstract A controlled growth of two‐dimensional (2D) π‐conjugated metal‐organic frameworks (MOFs) on solid substrates can open exciting opportunities for the application of 2D MOFs as optoelectronic devices. Some factors like solvent composition and type of substrates are known to influence the properties of solution‐processed 2D MOF crystals; however, a mechanistic understanding of how interactions between solvent, substrate, and precursors affect heterogeneous nucleation has been limited. Here, it is reported that the structure of Ni‐catecholate (Ni‐CAT‐1) MOFs at a solid–liquid interface is controlled by solvent–substrate and solvent–MOF precursor interactions. Specifically, the structure of the MOF film can be controlled by varying the affinity of the solvent to the substrate. As a fraction of N , N ‐dimethylformamide (DMF) in a binary solvent mixture of water and DMF increases, the arrangement of Ni‐CAT‐1 crystals varies from vertically aligned nanorods to the graphite substrate to less ordered nanorods with the lower initial nucleation number density of Ni‐CAT‐1 crystals on the surface.

2D materials↗
DOE OSTI2025

Surface-Tailoring and Morphology Control as Strategies for Sustainable Development in Transport Sector

Surface wetting plays an important role in the corrosion protection processes of aerospace applications. Here, we demonstrate the use of ultrafast femtosecond (fs) laser processing techniques to tailor the wetting properties of aluminum (Al) substrates by creating diverse surface morphologies. Specifically, two distinct laser scanning methods—dot-hatching and cross-hatching—were employed to fabricate microstructures on the substrates. By varying the incident laser parameters, we confirmed that the resulting surface morphologies exhibit different wetting behaviors, spanning from hydrophilicity to hydrophobicity. Furthermore, time-resolved spreading tests validate that dynamic wetting behaviors can also be modified. This fs laser processing approach provides a straightforward, one-step fabrication method for effectively modifying the wetting properties of Al alloys.

de Almeida Prado, Luis Antonio Sanchez↗
DOE OSTI2022

The N3/TiO 2 interfacial structure is dependent on the pH conditions during sensitization

The electronic structure of the N3/TiO 2 interface can directly influence the performance of a dye sensitized solar cell (DSSC). Therefore, it is crucial to understand the parameters that control the dye’s orientation on the semiconductor’s surface. A typical step in DSSC fabrication is to submerge the nanoparticulate semiconductor film in a solution containing the dye, the sensitizing solution. The pH of the N3 sensitizing solution determines the distribution of the N3 protonation states that exist in solution. Altering the pH of the sensitizing solution changes the N3 protonation states that exist in solution and, subsequently, the N3 protonation states that anchor to the TiO 2 substrate. We utilize the surface specific technique of heterodyne detected vibrational sum frequency generation spectroscopy to determine the binding geometry of N3 on a TiO 2 surface as a function of the sensitizing solution pH conditions. It is determined that significant reorientation of the dye occurs in pH ≤ 2.0 conditions due to the lack of N3-dye carboxylate anchoring groups participating in adsorption to the TiO 2 substrate. Consequently, the change in molecular geometry is met with a change in the interfacial electronic structure that can hinder electron transfer in DSSC architectures.

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

Self‐Assembly and Oriented Growth of Conductive Ni‐CAT‐1 Metal‐Organic Framework at Solid–Liquid Interfaces

Abstract Two‐dimensional (2D) conductive metal‐organic frameworks (MOF) represent a unique class of electrode materials with high capacity and power density. Understanding molecular mechanisms and pathways for heterogeneous nucleation of 2D π‐conjugated MOFs is highly desirable for controlling the structure and properties of conductive MOFs on solid substrates. Herein, a systematic study of nucleation and growth of 2D π‐conjugated Ni‐catecholate (Ni‐CAT‐1) MOFs on highly oriented pyrolytic graphite (HOPG) and copper substrates is reported. It is discovered that the nucleation density and growth kinetics of the MOF film can be controlled by varying substrate interactions with the organic linker. Specifically, π–π interactions between the linker and the HOPG dictate lower nucleation density, whereas π–metal interactions between the linker and the copper substrate dictate faster nucleation and higher nucleation densities. These studies reveal the key mechanism for Ni‐CAT‐1 nucleation on different surfaces and provide insights into interfacial control over the growth of other 2D π‐conjugated MOF films on solid substrates to inform synthesis of functional materials.

2D materials↗
DOE OSTI2023

Growth of carbon nanotube forests on flexible metal substrates: Advances, challenges, and applications

Owing to their remarkable properties and ordered architecture, vertically aligned CNT forests (VACNT) hold promises for countless applications ranging from energy storage to multifunctional fiber production. Over the last three decades, studies of carbon nanotube (CNT) growth have provided invaluable insight into the CNT nucleation and growth mechanism and enabled critical advancements in nanotechnology. Nevertheless, the ability to fully harness the exceptional VACNT properties in commercial devices is bottlenecked by compatibility of current CNT synthesis processes with large-scale manufacturing. Metal foil substrates present an economic alternative to traditional insulating substrates, like silicon or quartz, and are compatible with both roll-to-roll and automated, large-scale, batch processes. Compared to CNT growth on Si substrates, metal foils present additional challenges, such as increased roughness and reactivity at high temperatures. Nonetheless, many successful VACNT growths on conducting metal foils have been reported, which demonstrate the feasibility of metal substrate use for large-volume production of high-quality CNTs. Here, in this review, we discuss advancements in the field of VACNT growth on metal foil and specifically examine different choices for metal substrates, barrier and catalyst layers, deposition and growth methods, resulting CNT characteristics, and highlight a number of applications that benefit from CNT growth on metal substrates and transition to large-scale manufacturing.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Site-specific surface reactivity on SnO 2 : Evaluating selective atomic layer deposition processes

Area selective atomic layer deposition (AS-ALD) is a bottom-up synthesis approach with potential for deposition with molecular level precision. Here, the site-specific hydration of metal oxide substrates, combined with surface H 2 O-selective ALD processes, provides a potentially powerful path to targeted synthesis. Density functional theory (DFT) calculations are used to predict the thermodynamics of ALD precursor reactivity and hydration for (001), (101), (110), and (100) rutile SnO 2 facets as a function of temperature. Trimethylaluminum (TMA) and dimethyl aluminum isopropoxide (DMAI) dimers are predicted to react with both dehydrated and hydrated SnO 2 (001), (101), and (110) facets at ALD-relevant temperatures, while the SnO 2 (100) facet is predicted to be uniquely unreactive with TMA and DMAI monomers as well as dehydrate near 177 °C making this facet more amenable to targeted ALD. In situ ellipsometric studies of Al 2 O 3 ALD on polycrystalline SnO 2 at 150 °C are consistent with the computational predictions of rapid and unselective nucleation, in stark contrast to inhibited and selective ALD on isostructural rutile TiO 2 .

Atomic Layer Deposition↗
DOE OSTI2021

Predictability as a probe of manifest and latent physics: The case of atomic scale structural, chemical, and polarization behaviors in multiferroic Sm-doped BiFeO 3

The predictability of a certain effect or phenomenon is often equated with the knowledge of relevant physical laws, typically understood as a functional or numerically derived relationship between the observations and known states of the system. Correspondingly, observations inconsistent with prior knowledge can be used to derive new knowledge on the nature of the system or indicate the presence of yet unknown mechanisms. In this work, we explore the applicability of Gaussian processes (GP) to establish predictability and uncertainty of local behaviors from multimodal observations, providing an alternative to this classical paradigm. Using atomic resolution scanning transmission electron microscopy (STEM) of multiferroic Sm-doped BiFeO 3 across a broad composition range, we directly visualize the atomic structure and structural, physical, and chemical order parameter fields for the material. GP regression is used to establish the predictability of the local polarization field from different groups of parameters, including the adjacent polarization values and several combinations of physical and chemical descriptors, including lattice parameters, column intensities, etc. We observe that certain elements of microstructure, including charged and uncharged domain walls and interfaces with the substrate, are best predicted with specific combinations of descriptors, and this predictability and associated uncertainties are consistent across the composition series. The associated generative physical mechanisms are discussed. It is also found that certain parameter combinations tend to predict the orthorhombic phase in the cases where rhombohedral phase is observed, suggesting a potential role of clamping and confinement phenomena in phase equilibrium in Sm-BiFeO 3 system close to morphotropic phase boundary. We argue that predictability and uncertainty in observational data offer a new pathway to probe the physics of condensed matter systems from multimodal local observations.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Craspase is a CRISPR RNA-guided, RNA-activated protease

The CRISPR-Cas type III-E RNA-targeting effector complex gRAMP/Cas7-11 is associated with a caspase-like protein (TPR-CHAT/Csx29) to form Craspase (CRISPR-guided caspase). Here, we use cryo–electron microscopy snapshots of Craspase to explain its target RNA cleavage and protease activation mechanisms. Target-guide pairing extending into the 5' region of the guide RNA displaces a gating loop in gRAMP, which triggers an extensive conformational relay that allosterically aligns the protease catalytic dyad and opens an amino acid side-chain–binding pocket. We further define Csx30 as the endogenous protein substrate that is site-specifically proteolyzed by RNA-activated Craspase. This protease activity is switched off by target RNA cleavage by gRAMP and is not activated by RNA targets containing a matching protospacer flanking sequence. We thus conclude that Craspase is a target RNA–activated protease with self-regulatory capacity.

Science & Technology - Other Topics↗