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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
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↗
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↗
DOE OSTI2023

Targeting the Spike Receptor Binding Domain Class V Cryptic Epitope by an Antibody with Pan-Sarbecovirus Activity

Novel therapeutic monoclonal antibodies (MAbs) must accommodate comprehensive breadth of activity against diverse sarbecoviruses and high neutralization potency to overcome emerging variants. Here, in this study, we report the crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain (RBD) in complex with MAb WRAIR-2063, a moderate-potency neutralizing antibody with exceptional sarbecovirus breadth, that targets the highly conserved cryptic class V epitope. This epitope overlaps substantially with the spike protein N-terminal domain (NTD) -interacting region and is exposed only when the spike is in the open conformation, with one or more RBDs accessible. WRAIR-2063 binds the RBD of SARS-CoV-2 WA-1, all variants of concern (VoCs), and clade 1 to 4 sarbecoviruses with high affinity, demonstrating the conservation of this epitope and potential resiliency against variation. We compare structural features of additional class V antibodies with their reported neutralization capacity to further explore the utility of the class V epitope as a pan-sarbecovirus vaccine and therapeutic target.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Archaeal protein containing domain of unknown function 2193 undergoes oligomeric reconfiguration upon iron–sulfur cluster binding

Methanogenic archaea are particularly rich in iron–sulfur proteins, yet their roles remain largely enigmatic. Here, we characterized aMethanococcus voltae(Mvo) protein from the domain of unknown function (DUF) 2193 family, a group of proteins present primarily in archaea and characterized by a conserved cysteine‐rich C‐terminal motif.MvoDUF2193 was heterologously expressed and characterized by a range of spectroscopic and analytical methods. The results demonstrate thatMvoDUF2193 binds a single [4Fe–4S] cluster per subunit and that cluster occupancy regulates the transition from an apo tetramer to a [4Fe–4S] monomeric form. We hypothesize thatMvoDUF2193 serves a regulatory role in the cell, mediated by [Fe–S] cluster binding and changes in oligomeric state.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Discovery of Complex Binding and Reaction Mechanisms from Ternary Gases in Rare Earth Metal–Organic Frameworks

Understanding the selectivity of metal–organic frameworks (MOFs) to complex acid gas streams will enable their use in industrial applications. In this study, ab initio molecular dynamic simulations (AIMD) were used to simulate ternary gas mixtures (H 2 O-NO 2 -SO 2 ) in rare earth 2,5-dihydroxyterephthalic acid (RE-DOBDC) MOFs. Stronger H 2 O gas-metal binding arose from thermal vibrations in the MOF sterically hindering access of SO 2 and NO 2 molecules to the metal sites. Gas-gas and gas-linker interactions within the MOF framework resulted in the formation of multiple secondary gas species including HONO, HNO 2 , NOSO, and HNO 3 ⁻. Four gas adsorption sites were identified along with a new de-protonation reaction mechanism not observable through experiment. This study not only provides valuable information on competitive gas binding energies in the MOF, but it also provides important chemical insights into transient chemical reactions and mechanisms.

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

Thorium Bis‐Salophen Trimers as Anion Detectors and Binding Agents

Bis‐salophen ligands are the condensation product of a tetramine and a salicylaldehyde derivative. They feature two binding sites, both of which are tetradentate with mixed O/N donor atoms. Reaction with the ligand precursor and thorium nitrate tetrahydrate forms a 3:3 metal‐to‐ligand trimer with a ΔΔΔ‐chirality confirmed by X‐ray crystallography of a racemic single crystal. The structure has a pore in the center of the triangular structure measuring 6.22 Å at its narrowest point. This compound is air‐ and water‐stable as well as soluble in organic solvents. Here, this compound was screened with a series of tetrabutyl ammonium halide salts, and tetrabutylammonium (TBA) chloride showed the strongest binding to the complex. After the addition of 2 equivalents of TBACl, the complex and salt precipitate out of solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

SEC ‐ SAXS / MC Ensemble Structural Studies of the Microtubule Binding Protein Cdt1 Show Monomeric, Folded‐Over Conformations

ABSTRACT Cdt1 is a mixed folded protein critical for DNA replication licensing and it also has a “moonlighting” role at the kinetochore via direct binding to microtubules and the Ndc80 complex. However, it is unknown how the structure and conformations of Cdt1 could allow it to participate in these multiple, unique sets of protein complexes. While robust methods exist to study entirely folded or unfolded proteins, structure–function studies of combined, mixed folded/disordered proteins remain challenging. In this work, we employ orthogonal biophysical and computational techniques to provide structural characterization of mitosis‐competent human Cdt1. Thermal stability analyses shows that both folded winged helix domains1 are unstable. CD and NMR show that the N‐terminal and linker regions are intrinsically disordered. DLS shows that Cdt1 is monomeric and polydisperse, while SEC‐MALS confirms that it is monomeric at high concentrations, but without any apparent inter‐molecular self‐association. SEC‐SAXS enabled computational modeling of the protein structures. Using the program SASSIE, we performed rigid body Monte Carlo simulations to generate a conformational ensemble of structures. We observe that neither fully extended nor extremely compact Cdt1 conformations are consistent with SAXS. The best‐fit models have the N‐terminal and linker disordered regions extended into the solution and the two folded domains close to each other in apparent “folded over” conformations. We hypothesize the best‐fit Cdt1 conformations could be consistent with a function as a scaffold protein that may be sterically blocked without binding partners. Our study also provides a template for combining experimental and computational techniques to study mixed‐folded proteins.

Cell Biology↗
DOE OSTI2023

Coordination Stoichiometry Effects on the Binding Hierarchy of Histamine and Imidazole–M 2+ Complexes

Histidine–M 2+ coordination bonds are a recognized bond motif in biogenic materials with high hardness and extensibility, which has led to growing interest in their use in soft materials for mechanical function. However, the effect of different metal ions on the stability of the coordination complex remains poorly understood, complicating their implementation in metal-coordinated polymer materials. Herein, rheology experiments and density functional theory calculations are used to characterize the stability of coordination complexes and establish the binding hierarchy of histamine and imidazole with Ni 2+ , Cu 2+ , and Zn 2+ . It is found that the binding hierarchy is driven by the specific affinity of the metal ions to different coordination states, which can be macroscopically tuned by changing the metal-to-ligand stoichiometry of the metal-coordinated network. These findings facilitate the rational selection of metal ions for optimizing the mechanical properties of metal-coordinated materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Molecular dynamics analysis of the binding of human interleukin-6 with interleukin-6 α-receptor

Human interleukin-6 (hIL-6) is a multifunctional cytokine that regulates immune and inflammatory responses in addition to metabolic and regenerative processes and cancer. hIL-6 binding to the IL-6 receptor (IL-6Rα) induces homodimerization and recruitment of the glycoprotein (gp130) to form a hexameric signaling complex. Anti-IL-6 and IL-6R antibodies are clinically approved inhibitors of IL-6 signaling pathway for treating rheumatoid arthritis and Castleman's disease, respectively. There is a potential to develop novel small molecule IL-6 antagonists derived from understanding the structural basis for IL-6/IL-6Rα interactions. In this work, we combine homology modeling with extensive molecular dynamics (MD) simulations to examine the association of hIL-6 with IL-6Rα. A comparison with MD of apo hIL-6 reveals that the binding of hIL-6 to IL-6Rα induces structural and dynamic rearrangements in the AB loop region of hIL-6, disrupting intraprotein contacts and increasing the flexibility of residues 48 to 58 of the AB loop. In contrast, due to the involvement of residues 59 to 78 in forming contacts with the receptor, these residues of the AB loop are observed to rigidify in the presence of the receptor. The binary complex is primarily stabilized by two pairs of salt bridges, Arg181 (hIL-6)- Glu182 (IL-6Rα) and Arg184 (hIL-6)- Glu183 (IL-6Rα) as well as hydrophobic and aromatic stacking interactions mediated essentially by Phe residues in both proteins. An interplay of electrostatic, hydrophobic, hydrogen bonding, and aromatic stacking interactions facilitates the formation of the hIL-6/IL-6Rα complex.

59 BASIC BIOLOGICAL SCIENCES↗