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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Genetic control of morphological transitions in a coacervating protein template

Nature routinely exploits liquid–liquid phase separation (LLPS) of proteins to control the assembly and mineralization of hybrid materials. Here, we show that fusion of the Car9 silica-binding peptide to an elastin-like polypeptide (ELP) yields temperature- and sequence-programmable soft matter templates for the synthesis of silicified architectures ranging in size from nanometers to micrometers. Specifically, we demonstrate unprecedented control over the diameter of silica nanoparticles (SiNP) in the 30–60 nm range with 4 nm precision, show that a single arginine residue (R4) in the Car9 sequence underpins the transition from micelles to proteinosomes, and find that substitutions in other basic residues modulate electrostatic repulsion and solvation to enable access to kinetically trapped species. These structures, which include interconnected micelles, small (∼200 nm) and large (>5 µm) vesicles, are readily visualized by SEM imaging following silicification. Molecular dynamics (MD) simulations and AlphaFold predictions reveal that mutations in positively charged residues alter interfacial packing, hydration, and conformational freedom of the silica-binding segments. Overall, our results establish sequence and thermal energy as synergistic levers for morphological control across length scales using solid-binding ELPs and establish mineralization as a powerful tool to visualize the structure of dynamic soft matter assemblies.

hierarchy↗
DOE OSTI2021

Femtosecond dynamics and coherence of ionic retro-Diels–Alder reactions

Ultrafast tunnel ionization enables femtosecond time-resolved dynamic measurements of the retro-Diels–Alder reactions of positively charged cyclohexene, norbornene, and dicyclopentadiene. Unlike the reaction times of 500–600 ps that are observed following UV excitation of neutral species, on the ionic potential energy surfaces, these reactions occur on a single picosecond timescale and, in some cases, exhibit vibrational coherence. In the case of norbornene, a 270 cm –1 vibrational mode is found to modulate the retro-Diels–Alder reaction.

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

Solid-state synthesis of UV-plasmonic Cr2N nanoparticles

Materials that exhibit plasmonic response in the UV region can be advantageous for many applications, such as biological photodegradation, photocatalysis, disinfection, and bioimaging. Transition metal nitrides have recently emerged as chemically and thermally stable alternatives to metal-based plasmonic materials. However, most free-standing nitride nanostructures explored so far have plasmonic responses in the visible and near-IR regions. Herein, we report the synthesis of UV-plasmonic Cr2N nanoparticles using a solid-state nitridation reaction. The nanoparticles had an average diameter of 9 ± 5 nm and a positively charged surface that yields stable colloidal suspension. The particles were composed of a crystalline nitride core and an amorphous oxide/oxynitride shell whose thickness varied between 1 and 7 nm. Calculations performed using the finite element method predicted the localized surface plasmon resonance (LSPR) for these nanoparticles to be in the UV-C region (100–280 nm). While a distinctive LSPR peak could not be observed using absorbance measurements, low-loss electron energy loss spectroscopy showed the presence of surface plasmons between 80 and 250 nm (or ∼5 to 15 eV) and bulk plasmons centered around 50–62 nm (or ∼20 to 25 eV). Plasmonic coupling was also observed between the nanoparticles, resulting in resonances between 250 and 400 nm (or ∼2.5 to 5 eV).

Chemistry↗
DOE OSTI2022

Quantum water desalination: Water generation through separate pathways for protons and hydroxide ions in membranes

Much of the water desalination strategies has focused on designing pores and membranes that transport water and reject ions and other molecules at a high rate. In this paper, we discuss an approach where protons (H+) and hydroxide (OH−) ions are transported via different mechanisms through a porous membrane, and subsequently, once they have been transported through the membrane, they recombine to generate water. 2D materials such as graphene and MoS2 have generated significant interest for applications such as desalination. Here, we explore the applicability of one such 2D material—a cubic Ti2C MXene membrane—in desalination by creating a OH− ion selective pore, which significantly suppresses protons but allows OH− ions and water to go through. The catalytic properties of MXenes enable the dissociation of water on the surface, and the dissociated protons translocate through the membrane via quantum-dominated phenomena such as hopping from interstitial-to-interstitial. OH− ions translocate through a positively charged pore and recombine with protons on the other side of the membrane to form water. Our results indicate that water molecules generated via quantum processes can significantly enhance the overall transport of water across the membrane.

Physics↗
DOE OSTI2020

DNA origami protection and molecular interfacing through engineered sequence-defined peptoids

DNA nanotechnology has established approaches for designing programmable and precisely controlled nanoscale architectures through specific Watson−Crick base-pairing, molecular plasticity, and intermolecular connectivity. In particular, superior control over DNA origami structures could be beneficial for biomedical applications, including biosensing, in vivo imaging, and drug and gene delivery. However, protecting DNA origami structures in complex biological fluids while preserving their structural characteristics remains a major challenge for enabling these applications. Here, we developed a class of structurally well-defined peptoids to protect DNA origamis in ionic and bioactive conditions and systematically explored the effects of peptoid architecture and sequence dependency on DNA origami stability. The applicability of this approach for drug delivery, bioimaging, and cell targeting was also demonstrated. A series of peptoids (PE1–9) with two types of architectures, termed as “brush” and “block,” were built from positively charged monomers and neutral oligo-ethyleneoxy monomers, where certain designs were found to greatly enhance the stability of DNA origami. Through experimental and molecular dynamics studies, we demonstrated the role of sequence-dependent electrostatic interactions of peptoids with the DNA backbone. We showed that octahedral DNA origamis coated with peptoid (PE2) can be used as carriers for anticancer drug and protein, where the peptoid modulated the rate of drug release and prolonged protein stability against proteolytic hydrolysis. Finally, we synthesized two alkyne-modified peptoids (PE8 and PE9), conjugated with fluorophore and antibody, to make stable DNA origamis with imaging and cell-targeting capabilities. Our results demonstrate an approach toward functional and physiologically stable DNA origami for biomedical applications.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Molecular characterization of a fungal gasdermin-like protein

Programmed cell death (PCD) in filamentous fungi prevents cytoplasmic mixing following fusion between conspecific genetically distinct individuals (allorecognition) and serves as a defense mechanism against mycoparasitism, genome exploitation, and deleterious cytoplasmic elements (i.e., senescence plasmids). Recently, we identified regulator of cell death-1 ( rcd-1 ), a gene controlling PCD in germinated asexual spores in the filamentous fungus Neurospora crassa . rcd-1 alleles are highly polymorphic and fall into two haplogroups in N. crassa populations. Coexpression of alleles from the two haplogroups, rcd-1–1 and rcd-1–2 , is necessary and sufficient to trigger a cell death reaction. Here, we investigated the molecular bases of rcd-1 -dependent cell death. Based on in silico analyses, we found that RCD-1 is a remote homolog of the N-terminal pore-forming domain of gasdermin, the executioner protein of a highly inflammatory cell death reaction termed pyroptosis, which plays a key role in mammalian innate immunity. We show that RCD-1 localizes to the cell periphery and that cellular localization of RCD-1 was correlated with conserved positively charged residues on predicted amphipathic α-helices, as shown for murine gasdermin-D. Similar to gasdermin, RCD-1 binds acidic phospholipids in vitro, notably, cardiolipin and phosphatidylserine, and interacts with liposomes containing such lipids. The RCD-1 incompatibility system was reconstituted in human 293T cells, where coexpression of incompatible rcd-1–1/rcd-1–2 alleles triggered pyroptotic-like cell death. Oligomers of RCD-1 were associated with the cell death reaction, further supporting the evolutionary relationship between gasdermin and rcd-1 . This report documents an ancient transkingdom relationship of cell death execution modules involved in organismal defense.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cryo-EM structure of RNA-induced tau fibrils reveals a small C-terminal core that may nucleate fibril formation

In neurodegenerative diseases including Alzheimer’s and amyotrophic lateral sclerosis, proteins that bind RNA are found in aggregated forms in autopsied brains. Evidence suggests that RNA aids nucleation of these pathological aggregates; however, the mechanism has not been investigated at the level of atomic structure. Here, we present the 3.4-Å resolution structure of fibrils of full-length recombinant tau protein in the presence of RNA, determined by electron cryomicroscopy (cryo-EM). The structure reveals the familiar in-register cross-β amyloid scaffold but with a small fibril core spanning residues Glu391 to Ala426, a region disordered in the fuzzy coat in all previously studied tau polymorphs. RNA is bound on the fibril surface to the positively charged residues Arg406 and His407 and runs parallel to the fibril axis. The fibrils dissolve when RNase is added, showing that RNA is necessary for fibril integrity. While this structure cannot exist simultaneously with the tau fibril structures extracted from patients’ brains, it could conceivably account for the nucleating effects of RNA cofactors followed by remodeling as fibrils mature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Human sperm TMEM95 binds eggs and facilitates membrane fusion

Tmem95 encodes a sperm acrosomal membrane protein, whose knockout has a male-specific sterility phenotype in mice. Tmem95 knockout murine sperm can bind to, but do not fuse with, eggs. How TMEM95 plays a role in membrane fusion of sperm and eggs has remained elusive. Here, we utilize a sperm penetration assay as a model system to investigate the function of human TMEM95. We show that human TMEM95 binds to hamster egg membranes, providing evidence for a TMEM95 receptor on eggs. Using X-ray crystallography, we reveal an evolutionarily conserved, positively charged region of TMEM95 as a putative receptor-binding surface. Amino acid substitutions within this region of TMEM95 ablate egg-binding activity. We identify monoclonal antibodies against TMEM95 that reduce the number of human sperm fused with hamster eggs in sperm penetration assays. Strikingly, these antibodies do not block binding of sperm to eggs. Taken together, these results provide strong evidence for a specific, receptor-mediated interaction of sperm TMEM95 with eggs and suggest that this interaction may have a role in facilitating membrane fusion during fertilization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Strong adsorption of guanidinium cations to the air–water interface

Combining Deep-UV second harmonic generation spectroscopy with molecular simulations, we confirm and quantify the specific adsorption of guanidinium cations to the air–water interface. Using a Langmuir analysis of measurements at multiple concentrations, we extract the Gibbs free energy of adsorption, finding it larger than typical thermal energies. Molecular simulations clarify the role of polarizability in tuning the thermodynamics of adsorption, and establish the preferential parallel alignment of guanidinium at the air–water interface. As a polyatomic cation, guanidinium represents one of the few examples of a positively charged species to exhibit a propensity for the air-water interface. As such, these results expand on the growing body of work on specific ion adsorption.

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

Resurfacing promotes antibacterial activity of a lipid A–binding nanobody

Nanobodies have been pursued as candidates for antimicrobial design due to their small size and versatile binding capacities, but direct antibacterial activity of a nanobody has yet to be described. Here, we employed a bacterial surface display platform to screen a synthetic library of nanobody variants for antimicrobial potential. We identified a candidate that binds the essential lipid A component of gram-negative lipopolysaccharide. Nonetheless, this nanobody required a weakened outer membrane to access its target and elicit its toxic activity. Borrowing from observations of innate immune proteins, we found that resurfacing nanobodies with positively charged residues enabled them to bind and perturb the gram-negative outer membrane, but this alone was not sufficient for toxic activity. However, when we resurface our lipid A-targeting nanobody, it gained the ability to disrupt the outer membrane and enact its antibacterial function against wild-type bacteria. This development of a dual-function nanobody that can reach and bind previously inaccessible gram-negative targets introduces a route for antimicrobial biologic advancement.

antibacterial↗
DOE OSTI2021

Structural analysis of the catalytic domain of Artemis endonuclease/SNM1C reveals distinct structural features

The endonuclease Artemis is responsible for opening DNA hairpins during V(D)J recombination and for processing a subset of pathological DNA double-strand breaks. Artemis is an attractive target for the development of therapeutics to manage various B cell and T cell tumors, because failure to open DNA hairpins and accumulation of chromosomal breaks may reduce the proliferation and viability of pre-T and pre-B cell derivatives. However, structure-based drug discovery of specific Artemis inhibitors has been hampered by a lack of crystal structures. Here, we report the structure of the catalytic domain of recombinant human Artemis. The catalytic domain displayed a polypeptide fold similar overall to those of other members in the DNA cross-link repair gene SNM1 family and in mRNA 3'-end-processing endonuclease CPSF-73, containing metallo-β-lactamase and β-CASP domains and a cluster of conserved histidine and aspartate residues capable of binding two metal atoms in the catalytic site. As in SNM1A, only one zinc ion was located in the Artemis active site. However, Artemis displayed several unique features. Unlike in other members of this enzyme class, a second zinc ion was present in the β-CASP domain that leads to structural reorientation of the putative DNA-binding surface and extends the substrate-binding pocket to a new pocket, pocket III. Moreover, the substrate-binding surface exhibited a dominant and extensive positive charge distribution compared with that in the structures of SNM1A and SNM1B, presumably because of the structurally distinct DNA substrate of Artemis. The structural features identified here may provide opportunities for designing selective Artemis inhibitors.

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

Modelling dust transport in DIII-D with DTOKS-Upgrade

Comprehensive upgrades to the dust transport code Dust in TOKamaks (DTOKS) that extend the plasma-dust interaction model are presented and compared with recent measurements of dust transport in DIII-D. Simulations incorporating variation in physical properties of graphite dust with temperature and size in a stationary plasma background suggest a substantial decrease in lifetimes due principally to thermal expansion. The trajectories of 53 dust grains identified from analysis of visible camera data taken across two similar shots were used to measure the dust particle velocity distributions. Dust tracks terminated mostly at the outer divertor strike point having a mean observation time of 2.1 ± 0.4 ms. Stochastic modelling of 200 graphite dust particles in the DIII-D tokamak performed with DTOKS-U using plasma simulations generated by OEDGE found similar behaviour, with particles ablating rapidly after acquiring a positive charge in the region close to the outer strike point, creating an acute source of neutral carbon atoms. The simulated mean lifetime, 11 ± 2 ms, showed approximate agreement with experimental observation when corrected by accounting for dust visibility and ignoring the longest trajectories 1.5 ± 0.2 ms. Synthetic diagnostic data generated from coupling the results of DTOKS-U with the visualisation software Calcam offers a powerful new tool for validation of simulations and predictive calculations of dust dynamics.

Physics↗
DOE OSTI2022

Faradaic efficiency in protonic-ceramic electrolysis cells

Abstract Proton-conducting ceramics (e.g. doped barium zirconates or cerates) are typically mixed ionic-electronic conductors (MIECs). The electronic conduction, typically in the form of positively charged small polarons or electron holes, leads to ‘electronic leakage.’ In an ideal steam-electrolysis cell, one gas-phase H 2 molecule is produced from every two electrons delivered from an external power source. In other words, such ideal behavior achieves 100% faradaic efficiency. However, the electronic flux associated with MIEC membranes contributes to reduced faradaic efficiency. The present paper develops a model that predicts the behavior of faradaic efficiency as a function of electrolysis-cell operating conditions. Although the model framework is more general, the paper focuses on the behavior of a cell based upon a BaCe 0.7 Zr 0.1 Y 0.1 Yb 0.1 O 3 − δ (BCZYYb) membrane. The study predicts the effects of operating conditions, including temperature, pressure, and gas compositions.

Zhu, Huayang↗
DOE OSTI2024

A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain

Abstract SARS-CoV-2 nucleocapsid (N) protein is a structural component of the virus with essential roles in the replication and packaging of the viral RNA genome. The N protein is also an important target of COVID-19 antigen tests and a promising vaccine candidate along with the spike protein. Here, we report a compact stem-loop DNA aptamer that binds tightly to the N-terminal RNA-binding domain of SARS-CoV-2 N protein. Crystallographic analysis shows that a hexanucleotide DNA motif (5′-TCGGAT-3′) of the aptamer fits into a positively charged concave surface of N-NTD and engages essential RNA-binding residues including Tyr109, which mediates a sequence-specific interaction in a uracil-binding pocket. Avid binding of the DNA aptamer allows isolation and sensitive detection of full-length N protein from crude cell lysates, demonstrating its selectivity and utility in biochemical applications. We further designed a chemically modified DNA aptamer and used it as a probe to examine the interaction of N-NTD with various RNA motifs, which revealed a strong preference for uridine-rich sequences. Our studies provide a high-affinity chemical probe for the SARS-CoV-2 N protein RNA-binding domain, which may be useful for diagnostic applications and investigating novel antiviral agents.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Phycobilisome protein ApcG interacts with PSII and regulates energy transfer in Synechocystis

Photosynthetic organisms harvest light using pigment–protein complexes. In cyanobacteria, these are water-soluble antennae known as phycobilisomes (PBSs). The light absorbed by PBS is transferred to the photosystems in the thylakoid membrane to drive photosynthesis. The energy transfer between these complexes implies that protein–protein interactions allow the association of PBS with the photosystems. However, the specific proteins involved in the interaction of PBS with the photosystems are not fully characterized. Here, we show in Synechocystis sp. PCC 6803 that the recently discovered PBS linker protein ApcG (sll1873) interacts specifically with PSII through its N-terminal region. Growth of cyanobacteria is impaired in apcG deletion strains under light-limiting conditions. Furthermore, complementation of these strains using a phospho-mimicking version of ApcG causes reduced growth under normal growth conditions. Interestingly, the interaction of ApcG with PSII is affected when a phospho-mimicking version of ApcG is used, targeting the positively charged residues interacting with the thylakoid membrane, suggesting a regulatory role mediated by phosphorylation of ApcG. Low-temperature fluorescence measurements showed decreased PSI fluorescence in apcG deletion and complementation strains. The PSI fluorescence was the lowest in the phospho-mimicking complementation strain, while the pull-down experiment showed no interaction of ApcG with PSI under any tested condition. In conclusion, our results highlight the importance of ApcG for selectively directing energy harvested by the PBS and imply that the phosphorylation status of ApcG plays a role in regulating energy transfer from PSII to PSI.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Search for the production of Higgs-portal scalar bosons in the NuMI beam using the MicroBooNE detector

We present the strongest experimental limits to date on the mixing angle, 𝜃, with which a new scalar particle, 𝑆, mixes with the Higgs field in the mass range 110 MeV < 𝑚 𝑆 <155 MeV. This result uses the MicroBooNE liquid argon time projection chamber to search for decays of these Higgs-portal scalar particles through the 𝑆 → 𝑒 + ⁢𝑒 − channel with the decays of kaons in the NuMI neutrino beam acting as the source of the scalar particles. The analysis uses an exposure of 2.01 × 10 21 protons on target of NuMI beam data including periods when the beam focusing system was configured to focus positively charged hadrons and separate periods when negatively charged hadrons were focused. The analysis searches for scalar particles produced from kaons decaying in flight in the beam’s decay volume and at rest in the target and absorber. At 𝑚 𝑆 =125 MeV (𝑚 𝑆 =150 MeV) we set a limit of 𝜃 < 3.19 ×10 −4 (𝜃 < 2.79 ×10 −4 ) at the 95% confidence level.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Theoretical Analysis of Resonant Tunneling Enhanced Field Emission

In this paper, we develop an exact analytical quantum theory for field emission from surfaces with a nearby quantum well, by solving the one-dimensional time-independent Schrödinger equation. The quantum well, which may be introduced by ions, atoms, nanoparticles, etc., is simplified as a square potential well with depth H, width d, and distance to the surface L. The theory is used to analyze the effects of the quantum well (d, H, and L), the cathode properties (work function W and Fermi energy E F ), and dc field F. It is found that the quantum well can lead to resonant tunneling enhanced field emission up to several orders of magnitude larger than that from bare cathode surfaces. In the meantime, the electron-emission-energy spectrum is significantly narrowed. The strong enhancement region is bounded by the conditions eFL + H ≥ W + C and eFL ≤ W, with e being the elementary charge (positive) and C a constant dependent on dc field F. It is also found that the linear shift of resonance peaks in the electron-emission-energy spectrum with dc field F follows ε p =ε p⁢0 –e⁢FL, with ε p⁢0 being approximately the eigenenergies for electrons confined in a square potential well without a dc field. Finally, the theory provides insights for the design of high-efficiency field emitters, which can produce a high current and highly collimated electron beams.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Search for the chiral magnetic wave using anisotropic flow of identified particles at energies available at the BNL Relativistic Heavy Ion Collider

The chiral magnetic wave (CMW) has been theorized to propagate in the deconfined nuclear medium formed in high-energy heavy-ion collisions, and to cause a difference in elliptic flow (v 2 ) between negatively and positively charged hadrons. Experimental data consistent with the CMW have been reported by the STAR Collaboration at the Relativistic Heavy Ion Collider (RHIC), based on the charge asymmetry dependence of the pion v 2 from Au+Au collisions at $\sqrt{s_{NN}}$ = 27 to 200 GeV. In this comprehensive study, we present the STAR measurements of elliptic flow and triangular flow of charged pions, along with the v 2 of charged kaons and protons, as a function of charge asymmetry in Au+Au collisions at $\sqrt{s_{NN}}$ = 27, 39, 62.4 and 200 GeV. The slope parameters extracted from the linear dependence of the v2 difference on charge asymmetry for different particle species are reported and compared in different centrality intervals. In addition, the slopes of v 2 for charged pions in small systems, i.e., p+Au and d+Au at $\sqrt{s_{NN}}$ = 200 GeV, are also presented and compared with those in large systems, i.e., Au+Au at $\sqrt{s_{NN}}$ = 200 GeV and U+U at 193 GeV. Our results provide new insights for the possible existence of the CMW, and further constrain the background contributions in heavy-ion collisions at RHIC energies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗