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At least 451 records · Page 25

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NASA NTRS1993

Mutations in the putative calcium-binding domain of polyomavirus VP1 affect capsid assembly

Calcium ions appear to play a major role in maintaining the structural integrity of the polyomavirus and are likely involved in the processes of viral uncoating and assembly. Previous studies demonstrated that a VP1 fragment extending from Pro-232 to Asp-364 has calcium-binding capabilities. This fragment contains an amino acid stretch from Asp-266 to Glu-277 which is quite similar in sequence to the amino acids that make up the calcium-binding EF hand structures found in many proteins. To assess the contribution of this domain to polyomavirus structural integrity, the effects of mutations in this region were examined by transfecting mutated viral DNA into susceptible cells. Immunofluorescence studies indicated that although viral protein synthesis occurred normally, infective viral progeny were not produced in cells transfected with polyomavirus genomes encoding either a VP1 molecule lacking amino acids Thr-262 through Gly-276 or a VP1 molecule containing a mutation of Asp-266 to Ala. VP1 molecules containing the deletion mutation were unable to bind 45Ca in an in vitro assay. Upon expression in Escherichia coli and purification by immunoaffinity chromatography, wild-type VP1 was isolated as pentameric, capsomere-like structures which could be induced to form capsid-like structures upon addition of CaCl2, consistent with previous studies. However, although VP1 containing the point mutation was isolated as pentamers which were indistinguishable from wild-type VP1 pentamers, addition of CaCl2 did not result in their assembly into capsid-like structures. Immunogold labeling and electron microscopy studies of transfected mammalian cells provided in vivo evidence that a mutation in this region affects the process of viral assembly.

Non-NASA Center↗

DOE OSTI2022

Characterization of CO2 Binding on Alkaline Metal Oxide Sorbents and DFMs for Combined Capture and Conversion

As the world endures environmental crises associated with climate change and the rise of atmospheric CO2 concentrations from anthropogenic CO2 emission, carbon capture and utilization (CCU) technologies are increasingly necessary. Reactive carbon capture (RCC) technologies, in which capture and conversion of CO2 occur in a single reactor, are more energetically and economically attractive by avoiding the need to purify, compress, and transport the captured CO2. To this end, the development of dual function materials (DFM) that enable CO2 capture and conversion to useful C1 products, namely (1) methane, (2) CO, and (3) methanol, are attractive near-term targets for commercial CCU processes for renewable fuels and chemicals. DFM are composed of sorbents and catalysts co-dispersed on the same high surface area carrier. The sorbent component allows for selective capture of CO2 from a gas stream and the catalyst component subsequently performs the in-situ conversion of the adsorbed CO2 upon introduction of a reactive gas (typically H2). The survey of DFM formulations reveals a variety of sorbent+catalyst combinations of interest. There is, however, a lack of depth in fundamental understanding of how the CO2 binds to these materials and how the subsequent reaction mechanisms are affected, which are critical features for the development of next-generation materials with improved performance. To this end, we will describe in this work the CO2 binding characteristics of established and/or new DFM and their sorbent-only counterparts. The surface CO2 binding mechanism and capture capacity will be probed using techniques such as in-situ DRIFTS, operando TGA, and CO2 chemisorption.

alkaline oxides↗

DOE OSTI2022

Post-synthetically modified metal-organic frameworks for selective binding of heavy metal ions in water

A composition of matter for selective binding of at least one heavy metal comprising at least one porous metal-organic framework (MOF) with unsaturated coordination sites, at least one organic ligand functionalized with at least one functional group tailored to bind to the at least one MOF, and at least one separate functional group tailored to bind to the at least one heavy metal.

Britt, David↗

DOE OSTI2023

Anion binding agent lithium salts for battery electrolytes

A method for synthesizing a purified lithium (Li)+ anion binding agent (ABA-F)− salt and the corresponding Li+(ABA-F)− are disclosed. The method includes dissolving a boron-based acid in a polar solvent to form a solution. The solution is refluxed to form an anion binding agent. A stoichiometric amount of a small fluorinated salt, such as LiF, is added to the anion binding agent to form a mixture. The mixture is subsequently crystallized to obtain a substantially pure Li+(ABA-F)− salt. Example purified Li+(ABA-F)− salts include Ox-Li+(ABA-F), m-Li+(ABA-F), and BF3—Li+(ABA-F)−. These purified Li+(ABA-F)− salts provide the benefits of increased battery thermal safety without loss of electrochemical performance.

Orendorff, Christopher↗

DOE OSTI2024

A guayule C-repeat binding factor is highly activated in guayule under freezing temperature and enhances freezing tolerance when expressed in Arabidopsis thaliana

Natural Rubber (NR)-producing guayule (Parthenium argentatum Gray) has been developed as a new crop to diversify NR production. Guayule NR is mainly synthesized in its stem and is upregulated by cold temperatures. A guayule C-repeat binding factor 4 (PaCBF4) was highly expressed in cold-treated stem tissue, coinciding with active rubber biosynthesis and accumulation. Sequence alignments of PaCBF4 with other CBFs indicated that PaCBF4 contains DNA-binding domains responsible for regulating cold-regulated (COR) gene expression. Spatial gene expression profiling of PaCBF4 revealed that stems had the highest expression level among different organs examined. We further confirmed the function of PaCBF4 as regulator of cold-signaling processes by expressing it in the model plant Arabidopsis under a constitutive ubiquitin promoter from potato. Further, the resulting transgenic Arabidopsis lines expressing PaCBF4 turned on expression of a set of Arabidopsis COR genes under both room (24ºC) and cold (4ºC) temperatures, in contrast to the wild-type Arabidopsis that expressed these COR genes solely upon cold treatment. Furthermore, the transgenic plants displayed enhanced freezing tolerance at -5ºC, exhibiting a survival rate of 88–98% compared with 0% survival rate of wild-type plants. Our results suggest that PaCBF4 is a functional member of the guayule CBF gene family and plays a significant role in cold and freeze tolerance. Interestingly, overexpressing PaCBF4 in Arabidopsis did not affect the normal phenotype of the plant during vegetative and inflorescence growth, but the gene led to more undeveloped siliques after flowering.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Reexamining the relation between the binding energy of finite nuclei and the equation of state of infinite nuclear matter

The energy density is calculated in coordinate space for 12 C, 40 Ca, 48 Ca, and 208 Pb using a dispersive optical model constrained by all relevant data including the corresponding energy of the ground state. The energy density of 8 Be is also calculated using the Green’s function Monte-Carlo method employing the Argonne/Urbana two and three-body interactions. The nuclear interior minimally contributes to the total binding energy due to the 4πr 2 phase space factor. Thus, the volume contribution to the energy in the interior is not well constrained. The dispersive-optical-model energy densities are in good agreement with ab initio self-consistent Green’s function calculations of infinite nuclear matter restricted to treat only short-range and tensor correlations. These results call into question the degree to which the equation of state for nuclear matter is constrained by the empirical mass formula. In particular, the results in this work indicate that saturated nuclear matter does not require the canonical value of 16 MeV binding per particle but only about 13-14 MeV when the interior of 208 Pb is considered.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Influence of the symmetry energy on the nuclear binding energies and the neutron drip line position

A clear connection can be established between properties of nuclear matter and finite-nuclei observables, such as the correlation between the slope of the symmetry energy and the dipole polarizability, or between compressibility and the isoscalar monopole giant resonance excitation energy. Establishing a connection between realistic atomic nuclei and an idealized infinite nuclear matter leads to a better understanding of underlying physical mechanisms that govern nuclear dynamics. In this work, we aim to study the dependence of the binding energies and related quantities (e.g., location of drip lines, the total number of bound even-even nuclei) on the symmetry energy S 2 (ρ). The properties of finite nuclei are calculated by employing the relativistic Hartree-Bogoliubov model, assuming even-even axial and reflection symmetric nuclei. Calculations are performed by employing two families of relativistic energy density functionals, based on different effective Lagrangians, constrained to a specific symmetry energy at the saturation density J within the interval of 30–36 MeV. Nuclear binding energies and related quantities of bound nuclei are calculated between 8 ≤ Z ≤ 104 from the two-proton to the two-neutron drip line. As the neutron drip line is approached, the interactions with stiffer J tend to predict more bound nuclei, resulting in a systematic shift of the two-neutron drip line towards more neutron-rich nuclei. Consequentially, a correlation between the number of bound nuclei N nucl and S 2 (ρ) is established for a set of functionals constrained using the similar optimization procedures. Furthermore the direction of the relationship between the number of bound nuclei and the symmetry energy highly depends on the density under consideration.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Distilling the Essential Elements of Nuclear Binding via Neural-Network Quantum States

To distill the essential elements of nuclear binding, we seek the simplest Hamiltonian capable of modeling atomic nuclei with percent-level accuracy. A critical aspect of this endeavor consists of accurately solving the quantum many-body problem without incurring an exponential computing cost with the number of nucleons. Furthermore, we address this challenge by leveraging a variational Monte Carlo method based on a highly expressive neural-network quantum state ansatz. In addition to computing binding energies and charge radii of nuclei with up to 𝐴 = 20 nucleons, by evaluating their magnetic moments, we demonstrate that neural-network quantum states are able to correctly capture the self-emerging nuclear shell structure. To this end, we introduce a novel computational protocol based on adding an external magnetic field to the nuclear Hamiltonian, which allows the neural network to learn the preferred polarization of the nucleus within the given magnetic field.

Binding energy & masses↗

NASA NTRS2002

Genes encoding calmodulin-binding proteins in the Arabidopsis genome

Analysis of the recently completed Arabidopsis genome sequence indicates that approximately 31% of the predicted genes could not be assigned to functional categories, as they do not show any sequence similarity with proteins of known function from other organisms. Calmodulin (CaM), a ubiquitous and multifunctional Ca(2+) sensor, interacts with a wide variety of cellular proteins and modulates their activity/function in regulating diverse cellular processes. However, the primary amino acid sequence of the CaM-binding domain in different CaM-binding proteins (CBPs) is not conserved. One way to identify most of the CBPs in the Arabidopsis genome is by protein-protein interaction-based screening of expression libraries with CaM. Here, using a mixture of radiolabeled CaM isoforms from Arabidopsis, we screened several expression libraries prepared from flower meristem, seedlings, or tissues treated with hormones, an elicitor, or a pathogen. Sequence analysis of 77 positive clones that interact with CaM in a Ca(2+)-dependent manner revealed 20 CBPs, including 14 previously unknown CBPs. In addition, by searching the Arabidopsis genome sequence with the newly identified and known plant or animal CBPs, we identified a total of 27 CBPs. Among these, 16 CBPs are represented by families with 2-20 members in each family. Gene expression analysis revealed that CBPs and CBP paralogs are expressed differentially. Our data suggest that Arabidopsis has a large number of CBPs including several plant-specific ones. Although CaM is highly conserved between plants and animals, only a few CBPs are common to both plants and animals. Analysis of Arabidopsis CBPs revealed the presence of a variety of interesting domains. Our analyses identified several hypothetical proteins in the Arabidopsis genome as CaM targets, suggesting their involvement in Ca(2+)-mediated signaling networks.

NASA Discipline Plant Biology↗

NASA NTRS1997

Intracellular distributions and putative functions of calcium-binding proteins in the bullfrog vestibular otolith organs

Hair cells in the bullfrog vestibular otolith organs were immunolabeled by monoclonal and polyclonal antisera against calbindin (CaB), calmodulin (CaM), calretinin (CaR), and parvalbumin (PA). S-100, previously shown to immunolabel striolar hair cells in fish vestibular organs, only weakly immunolabeled hair cells in the bullfrog vestibular otolith organs. Immunolabeling was not detected in supporting cells. With the exception of CaR, myelinated axons and unmyelinated nerve terminals were immunolabeled by all of the above antisera. Immunolabeling was seen in all saccular hair cells, although hair cells at the macular margins were immunolabeled more intensely for CaB, CaM, and PA than more centrally located hair cells. As the macula margins are known to be a growth zone, this labeling pattern suggests that marginal hair cells up-regulate their calcium-binding proteins during hair cell development. In the utriculus, immunolabeling for CaM and PA was generally restricted to striolar hair cells. CaR immunolabeling was restricted to the stereociliary array. Immunolabeling for other calcium-binding proteins was generally seen in both the cell body and hair bundles of hair cells, although this labeling was often localized to the stereociliary array and the apical portion of the cell body. CaM and PA immunolabeling in the stereociliary array in saccular and utricular striolar cells suggests a functional role for these proteins in mechanoelectric transduction and adaptation.

NASA Discipline Number 40-10↗

DOE OSTI2023

Implementation of extrinsic cohesive zone model (ECZM) in 2D finite-discrete element method (FDEM) using node binding scheme

The combined finite-discrete element method (FDEM) has been widely used for rock fracturing simulations. Conventionally, FDEM is realized using the intrinsic cohesive zone model (ICZM); however, it has the drawback of artificial compliance and high computational expense. As a complement, the extrinsic cohesive zone model (ECZM) is seen to be realized in FDEM recently, whereas the node splitting scheme utilized is cumbersome. Here, within the framework of ICZM-based FDEM, we propose a node binding scheme to efficiently bind the pre-discretized finite elements and thus guarantee the continuum behavior of materials in the elastic stage. The yield surfaces, controlled by ECZM, are dynamically embedded by invoking the pre-inserted cohesive elements. The effectiveness and efficiency of the proposed approach are validated and tested by performing a suite of numerical experiments. Compared with ICZM-based FDEM, the proposed approach can correctly capture material deformation and reduce the computation cost. In contrast to the existing ECZM-based FDEM, the proposed approach can overcome the frequent and complex element topology updating. Finally, this work provides a novel perspective that fully inherits the advantages of both ICZM and ECZM, but circumvents their shortcomings, which guarantees a more efficient and effective simulation of brittle material evolution from continuum to discontinuum.

58 GEOSCIENCES↗

DOE OSTI2026

Exploring the binding properties and activities of ancestral expansins

Bacterial expansins are non-lytic proteins capable of loosening cellulose networks, offering promising applications in agriculture, biotechnology, and material science. Their ability to disrupt noncovalent interactions in biopolymer matrices such as cellulose and chitin positions them as valuable tools for upgrading abundant natural materials. However, their industrial use remains limited due to their relatively low wall-loosening activity compared to plant expansins. To address this limitation, we applied Ancestral Sequence Resurrection (ASR) to reconstruct and characterize ancient variants of the Bacillus subtilis expansin BsEXLX1. ASR is a powerful evolutionary tool that enables the inference and synthesis of ancestral proteins, allowing researchers to explore functional traits that may have been lost over time. This approach not only provides insights into protein evolution but also facilitates the design of proteins with enhanced properties, such as improved substrate affinity or structural stability. In this study, we combined biochemical and biophysical assays to evaluate the activity and binding behavior of ancestral expansins. Our results reveal that ancestral variants exhibit increased cellulose affinity, reduced binding to acidic polysaccharides, and greater salt resistance. Furthermore, these traits enhance their wall-loosening activity and demonstrate the utility of ASR in engineering surface-active proteins for industrial applications, particularly in biomass processing and cellulose modification.

09 BIOMASS FUELS↗

DOE OSTI2024

Metal Independent Correlations for Site-specific Binding Energies of Relevant Catalytic Intermediates

Establishing energy correlations among different metals can accelerate the discovery of efficient and cost-effective catalysts for complex reactions. Using a recently introduced coordination-based model, we can predict site specific metal binding energies (∆EM) that can be used as a descriptor for chemical reactions. In this study, we have examined a range of metals including Ag, Au, Co, Cu, Ir, Ni, Os, Pd, Pt, Rh, and Ru and found linear correlations between predicted ∆EM and adsorption energies of CH and O (∆ECH and ∆EO) at various coordination environment for all the considered metals. Interestingly, all the metals correlate with one another under specific surface site coordination, indicating that different metals are interrelated in a particular coordination environment. Furthermore, we have tested and verified for PtPd and PtIr-based alloys that they follow a similar behavior. Moreover, we have expanded the metal space by taking some early transition metals along with few s-block metals and shown a cyclic behavior of the adsorbate binding energy (∆EA) versus ∆EM. Therefore, ∆ECH and ∆EO can be efficiently interpolated between metals, alloys and intermetallics based on information related to one metal only. This simplifies the process of screening new metal catalyst formulations and their reaction energies.

Density function theory↗

DOE OSTI2021

Nanoparticle-Mediated Assembly of Peptoid Nanosheets Functionalized with Solid-Binding Proteins: Designing Heterostructures for Hierarchy

The fabrication of ordered architectures that intimately integrate polymer, protein and inorganic components remains difficult. Two promising building blocks to tackle this challenge are peptoids, peptide mimics capable of self-assembly into well-defined structures, and solid-binding peptides, which offer a biological path to controlled inorganic assembly. Here, we report on the synthesis of 3.3 nm-thick, thiol-reactive peptoid nanosheets from equimolar mixtures of unmodified and maleimide-derivatized versions of the Nbpe 6 Nce 6 oligomer, optimize the location of engineered cysteine residues in silica-binding derivatives of superfolder green fluorescent protein for maleimide conjugation, and react the two components to form proteinpeptoid hybrids exhibiting partial or uniform protein coverage on both of their sides. Using 10 nm silica nanoparticles, we trigger the stacking of these 2D structures into a multi-layer material comprised of alternating peptoid, protein and organic layers. This simple and modular approach to hierarchical hybrid synthesis should prove useful in bioimaging and photocatalysis applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Density Functional Tight Binding Insights into Plasmonic Silver–Platinum Nanoparticles and Alloys for Enhanced Photocatalysis

Developing accurate and efficient Slater-Koster (SK) tight-binding parameter sets is essential for quantum plasmonic studies of alloyed metal nanoparticles, as conventional time dependent density functional theory (TD-DFT) calculations are computationally prohibitive for larger clusters. In this work, we develop and validate density functional tight binding (DFTB) parameter sets for both ground state (GS-SK) and excited state (ES-SK) calculations to study the structural, electronic, and optical properties of silver (Ag), platinum (Pt), and Ag–Pt nanoalloys. Our investigation of the ground state properties demonstrates that the GS-SK parameters enable DFTB to closely reproduce the electronic structures of platinum clusters with diverse sizes and geometries – showing qualitative agreement with DFT for density of states (DOS) profiles and energy levels. The ES-SK parameters accurately describe excited-state properties compared to TD-DFT reference calculations, including the broad, featureless absorption profiles of Pt that are dominated by interband transitions. Using the ES-SK parameters within a real-time TD-DFTB framework, we compute size-dependent optical absorption spectra of Ag, Pt and Ag-Pt nanocubes containing up to 1099 atoms (size ∼4.18 nm). A detailed study of Ag–Pt and Pt-Ag core–shell nanoparticles shows quenching of the Ag plasmon resonance even at monolayer coverage for Ag-Pt, but not for Pt-Ag. We also show how to define submonolayer Ag-core Pt-shell cubic structures that have similar optical properties to those generated experimentally for much larger particles, which offers potential for describing plasmon-enhanced photocatalysis. Collectively, the GS-SK and ES-SK parameter sets provide an accurate, computationally efficient approach for modeling the complex optical and electronic behavior of noble–transition metal nanostructures and their alloys.

SPR↗

DOE OSTI2026

Leveraging Hydration Forces for Size-Specific Nanoparticle Enrichment with a Redox-Responsive Silica-Binding Elastin-Like Polypeptide

Elastin-like polypeptides (ELPs) are low-complexity proteins that coacervate above a characteristic lower critical solution temperature (LCST). While the thermoresponsiveness of ELPs has been widely exploited in the biomedical and biomaterials fields, their ability to mediate nanoparticle assembly below their transition temperature remains largely unexplored. Here, we show that unmodified ELPs induce the reversible flocculation of silica nanoparticles (SiNPs) by forming backbone hydrogen bonds with surface silanols. Interparticle bridging is modulated by ELP length and concentration and by the presence of N- and C-terminal anchoring groups such as a cysteine residue and a Car9 silica-binding peptide. Using a redox-responsive fusion protein consisting of disulfide-bonded ELP domains terminated by Car9 segments, we stabilize 20 nm SiNPs under oxidizing conditions while triggering particle flocculation upon addition of reductant. We find that SiNP sedimentation under reducing conditions exhibits a sharp dependency on particle size that arises from the curvature-dependent structure of surface silanols. While the isolated silanols of SiNPs smaller than 30 nm are efficiently engaged by the ELP domains of Car9-anchored proteins, repulsion forces associated with the presence of a layer of molecular water together with increased electrostatic repulsion preclude efficient engagement of H-bonded silanols displayed on the surface of SiNPs larger than 60 nm. We harness these findings to selectively enrich SiNPs based on size and expand the concept to titania (TiO2) by demonstrating that rutile nanoparticles can be stabilized or sedimented with solid-binding ELPs by adjusting the solution pH to promote or discourage the formation of a hydration layer. These strategies should prove broadly useful for the separation of other oxides and their polymorphs and provide a tunable strategy for nanoparticle assembly and bioinspired colloidal design.

ELP↗

DOE OSTI2024

Towards predictive control of reversible nanoparticle assembly with solid-binding proteins

Although a broad range of ligand-functionalized nanoparticles and physico-chemical triggers have been exploited to create stimuli-responsive colloidal systems, little attention has been paid to the reversible assembly of unmodified nanoparticles with non-covalently bound proteins. Previously, we reported that a derivative of green fluorescent protein engineered with oppositely located silica-binding peptides mediates the repeated assembly and disassembly of 10-nm silica nanoparticles when pH is toggled between 7.5 and 8.5. We captured the subtle interplay between interparticle electrostatic repulsion and their protein-mediated short-range attraction with a multiscale model energetically benchmarked to collective system behavior captured by scattering experiments. Here, in this work, we show that both solution conditions (pH and ionic strength) and protein engineering (sequence and position of engineered silica-binding peptides) provide pathways for reversible control over growth and fragmentation, leading to clusters ranging in size from 25 nm protein-coated particles to micrometer-size aggregate. We further find that the higher electrolyte environment associated with successive cycles of base addition eventually eliminates reversibility. Our model accurately predicts these multiple length scales phenomena. The underpinning concepts provide design principles for the dynamic control of other protein- and particle-based nanocomposites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Accurate tight-binding model for twisted bilayer graphene describes topological flat bands without geometric relaxation

A major hurdle in understanding the phase diagram of twisted bilayer graphene is the roles of lattice relaxation and electronic structure on isolated band flattening near magic twist angles. Here in this work, the authors develop an accurate local environment tight-binding model fit to tight-binding parameters computed from ab initio density-functional theory calculations across many atomic configurations. With the accurate parametrization, it is found that the magic angle shifts to slightly lower angles than often quoted, from around 1.05° to around 0.99°, and that isolated flat bands appear for rigidly rotated graphene layers, with enhancement of the flat bands when the layers are allowed to distort. Study of the orbital localization supports the emergence of fragile topology in the isolated flat bands without the need for lattice relaxation.

36 MATERIALS SCIENCE↗