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At least 1,333 records · Page 74

All sources NASA NTRS DOE OSTI

DOE OSTI2020

Vertically Aligned Single-Crystalline CoFe 2 O 4 Nanobrush Architectures with High Magnetization and Tailored Magnetic Anisotropy

Micrometer-tall vertically aligned single-crystalline CoFe 2 O 4 nanobrush architectures with extraordinarily large aspect ratio have been achieved by the precise control of a kinetic and thermodynamic non-equilibrium pulsed laser epitaxy process. Direct observations by scanning transmission electron microscopy reveal that the nanobrush crystal is mostly defect-free by nature, and epitaxially connected to the substrate through a continuous 2D interface layer. In contrast, periodic dislocations and lattice defects such as anti-phase boundaries and twin boundaries are frequently observed in the 2D interface layer, suggesting that interface misfit strain relaxation under a non-equilibrium growth condition plays a critical role in the self-assembly of such artificial architectures. Further, magnetic property measurements have found that the nanobrushes exhibit a saturation magnetization value of 6.16 μB/f.u., which is much higher than the bulk value. The discovery not only enables insights into an effective route for fabricating unconventional high-quality nanostructures, but also demonstrates a novel magnetic architecture with potential applications in nanomagnetic devices.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Light-Driven Charge Transport and Optical Sensing in Molecular Junctions

Probing charge and energy transport in molecular junctions (MJs) has not only enabled a fundamental understanding of quantum transport at the atomic and molecular scale, but it also holds significant promise for the development of molecular-scale electronic devices. Recent years have witnessed a rapidly growing interest in understanding light-matter interactions in illuminated MJs. These studies have profoundly deepened our knowledge of the structure–property relations of various molecular materials and paved critical pathways towards utilizing single molecules in future optoelectronics applications. In this article, we survey recent progress in investigating light-driven charge transport in MJs, including junctions composed of a single molecule and self-assembled monolayers (SAMs) of molecules, and new opportunities in optical sensing at the single-molecule level. We focus our attention on describing the experimental design, key phenomena, and the underlying mechanisms. Specifically, topics presented include light-assisted charge transport, photoswitch, and photoemission in MJs. Emerging Raman sensing in MJs is also discussed. Finally, outstanding challenges are explored, and future perspectives in the field are provided.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Effect of Intermediate Semiconducting TiOx Thin Films on Nanoparticle-Mediated Electron Transfer: Electrooxidation of CO

The concept of nanoparticle-mediated electron transfer (eT) across insulating thin films was elucidated theoretically by Allongue and Chazalviel in 2011. In their model, metal nanoparticles (NPs) are immobilized atop passivating, self-assembled monolayers (SAMs). They found that under certain conditions, related to the thickness of the SAM and the size of the NPs, efficient faradaic oxidation and reduction reactions could proceed at the NP surface. In the absence of NPs, however, eT was suppressed by the insulating SAM thin films. Allongue and Chazalviel concluded that, within certain bounds, eT is mediated by fast tunneling between the conductive electrode and the metal NPs, while the kinetics of the redox reaction are controlled by the NPs. This understanding has been confirmed using a variety of experimental models. The theory is based on electron tunneling; therefore, the nature of the intervening medium (the insulator in prior studies) should not affect the eT rate. In the present manuscript, however, we show that the theory breaks down under certain electrochemical conditions when the medium between conductors is an n-type semiconductor. Specifically, we find that in the presence of either Au or Pt NPs immobilized on a thin film of TiOx, CO electrooxidation does not proceed. In contrast, the exact same systems lead to the efficient reduction of oxygen. At present, we are unable to explain this finding within the context of the model of Allongue and Chazalviel.

Galyamova, Aigerim↗

DOE OSTI2021

Induction of Protection in Mice against a Chlamydia muridarum Respiratory Challenge by a Vaccine Formulated with the Major Outer Membrane Protein in Nanolipoprotein Particles

Chlamydia trachomatis is a sexually transmitted bacterium that infects over 130 million individuals worldwide annually. To implement a vaccine, we developed a cell-free co-translational system to express the Chlamydia muridarum major outer membrane protein (MOMP). This approach uses a nanolipoprotein particles (tNLP) made from ApoA1 protein, amphiphilic telodendrimer and lipids that self-assemble to form 10–25 nm discs. These tNLP provide a protein-encapsulated lipid support to solubilize and fold membrane proteins. The cell-free system co-translated MOMP and ApoA1 in the presence of telodendrimer mixed with lipids. The MOMP-tNLP complex was amenable to CpG and FSL-1 adjuvant addition. To investigate the ability of MOMP-tNLP+CpG+FSL-1 to induce protection against an intranasal (i.n.) C. muridarum challenge, female mice were vaccinated intramuscularly (i.m.) or i.n. and i.m. simultaneously 4 weeks apart. Following vaccination with MOMP-tNLP+CpG+FSL-1, mice mounted significant humoral and cell-mediated immune responses. Following the i.n. challenge, mice vaccinated with MOMP-tNLP+CpG+FSL-1 i.n. + i.m. group were protected as determined by the percentage change in body weight and by the number of C. muridarum inclusion forming units (IFU) recovered from the lungs. To our knowledge, this is the first time a MOMP-based vaccine formulated in tNLP has been shown to protect against C. muridarum.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens

Multivalent presentation of viral glycoproteins can substantially increase the elicitation of antigen-specific antibodies. To enable a new generation of anti-viral vaccines, we designed self-assembling protein nanoparticles with geometries tailored to present the ectodomains of influenza, HIV, and RSV viral glycoprotein trimers. We first de novo designed trimers tailored for antigen fusion, featuring N-terminal helices positioned to match the C termini of the viral glycoproteins. Trimers that experimentally adopted their designed configurations were incorporated as components of tetrahedral, octahedral, and icosahedral nanoparticles, which were characterized by cryo-electron microscopy and assessed for their ability to present viral glycoproteins. Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles presented antigenically intact prefusion HIV-1 Env, influenza hemagglutinin, and RSV F trimers in the predicted geometries. This work demonstrates that antigen-displaying protein nanoparticles can be designed from scratch, and provides a systematic way to investigate the influence of antigen presentation geometry on the immune response to vaccination.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The molecular mechanism of load adaptation by branched actin networks

Branched actin networks are self-assembling molecular motors that move biological membranes and drive many important cellular processes, including phagocytosis, endocytosis, and pseudopod protrusion. When confronted with opposing forces, the growth rate of these networks slows and their density increases, but the stoichiometry of key components does not change. The molecular mechanisms governing this force response are not well understood, so we used single-molecule imaging and AFM cantilever deflection to measure how applied forces affect each step in branched actin network assembly. Although load forces are observed to increase the density of growing filaments, we find that they actually decrease the rate of filament nucleation due to inhibitory interactions between actin filament ends and nucleation promoting factors. The force-induced increase in network density turns out to result from an exponential drop in the rate constant that governs filament capping. The force dependence of filament capping matches that of filament elongation and can be explained by expanding Brownian Ratchet theory to cover both processes. We tested a key prediction of this expanded theory by measuring the force-dependent activity of engineered capping protein variants and found that increasing the size of the capping protein increases its sensitivity to applied forces. In summary, we find that Brownian Ratchets underlie not only the ability of growing actin filaments to generate force but also the ability of branched actin networks to adapt their architecture to changing loads.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes

Identifying virulence-critical genes from pathogens is often limited by functional redundancy. To rapidly interrogate the contributions of combinations of genes to a biological outcome, we have developed a mu ltiplex, r andomized C RISPR i nterference s equencing (MuRCiS) approach. At its center is a new method for the randomized self-assembly of CRISPR arrays from synthetic oligonucleotide pairs. When paired with PacBio long-read sequencing, MuRCiS allowed for near-comprehensive interrogation of all pairwise combinations of a group of 44 Legionella pneumophila virulence genes encoding highly conserved transmembrane proteins for their role in pathogenesis. Both amoeba and human macrophages were challenged with L. pneumophila bearing the pooled CRISPR array libraries, leading to the identification of several new virulence-critical combinations of genes. lpg2888 and lpg3000 were particularly fascinating for their apparent redundant functions during L. pneumophila human macrophage infection, while lpg3000 alone was essential for L. pneumophila virulence in the amoeban host Acanthamoeba castellanii . Thus, MuRCiS provides a method for rapid genetic examination of even large groups of redundant genes, setting the stage for application of this technology to a variety of biological contexts and organisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes

Identifying virulence-critical genes from pathogens is often limited by functional redundancy. To rapidly interrogate the contributions of combinations of genes to a biological outcome, we have developed a multiplex, randomized CRISPR interference sequencing (MuRCiS) approach. At its center is a new method for the randomized self-assembly of CRISPR arrays from synthetic oligonucleotide pairs. When paired with PacBio long-read sequencing, MuRCiS allowed for near-comprehensive interrogation of all pairwise combinations of a group of 44 Legionella pneumophila virulence genes encoding highly conserved transmembrane proteins for their role in pathogenesis. Both amoeba and human macrophages were challenged with L. pneumophila bearing the pooled CRISPR array libraries, leading to the identification of several new virulence-critical combinations of genes. lpg2888 and lpg3000 were particularly fascinating for their apparent redundant functions during L. pneumophila human macrophage infection, while lpg3000 alone was essential for L. pneumophila virulence in the amoeban host Acanthamoeba castellanii. Thus, MuRCiS provides a method for rapid genetic examination of even large groups of redundant genes, setting the stage for application of this technology to a variety of biological contexts and organisms.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes

Ellis, Nicole A. (ORCID:0000000195928415)↗

NASA NTRS1968

A new view of the ''synthesis of life.''

Experimental research concerned with origin of life, studying synthesis of precursor polymers and self assembly into protocells

Fox, S. W.↗

NASA NTRS1970

Can man start an evolution

Proteinoids self assembly into primitive cell from observations of polypeptide generation during amino acid heating

Fox, S. W.↗

NASA NTRS1976

Contributions of experimental protobiogenesis to the theory of evolution

Inferences from experiments in protobiogenesis are examined as a forward extension of the theory of evolutionary biology. A nondiscontinuous, intraconsistent theory of general evolution embracing both protobiology and biology is outlined. This overview emphasizes Darwinian selection in the later stages of evolution, and stereochemical molecular selection in some of its earlier stages. It incorporates the concept of limitation of the scope of evolution by internal constraints on variation, based on the argument that internally limiting constraints observed in experiments with molecules are operative in organisms, if chemical processes occur within biological processes and biological processes are assumed to be exponentializations of chemical processes. Major evolutionary events might have occurred by rapid self-assembly processes analogous to those observed in the formation of phase-separated microspheres from amorphous powder or supersaturated solutions.

Fox, S. W.↗

NASA NTRS1982

Criteria for the emergence and evolution of life in the solar system

It is proposed that there are at least 25 specific conditions or requirements which have to be fulfilled in order for life to appear and evolve in a planetary system such as ours. The criteria are grouped into five major general areas: (1) Planetary criteria relate to the physical properties of the planet as it is formed and as it becomes a cosmic body with the potential to provide an abode for life. (2) Chemical criteria concern the composition, availability of effective energy sources, and chemical constraints of the environment where reactions take place for the prebiological formation of biochemical compounds. (3) Protobiological criteria relate to the prebiologically synthesized oligomeric and polymeric biomolecules, how they interact cooperatively to form protobiological structures and functions, and self-assemble to give rise to a living system. (4) Evolutionary criteria are concerned with the processes responsible for the increase in complexity of organisms by genomic multiplication, symbiotic integration, and cellular differentiation, as well as with the negentropic ability of organisms to continuously recycle all the volatile biogenic elements. (5) Stellar criteria relate to the elemental composition mass, lifetime, and other features of Main Sequence stars which may be surrounded by planetary systems similar to our own.

Oro, J.↗

NASA NTRS1986

Clay energetics in chemical evolution

Clays have been implicated in the origin of terrestrial life since the 1950's. Originally they were considered agents which aid in selecting, concentrating and promoting oligomerization of the organic monomeric substituents of cellular life forms. However, more recently, it has been suggested that minerals, with particular emphasis on clays, may have played a yet more fundamental role. It has been suggested that clays are prototypic life forms in themselves and that they served as a template which directed the self-assembly of cellular life. If the clay-life theory is to have other than conceptual credibility, clays must be shown by experiment to execute the operations of cellular life, not only individually, but also in a sufficiently concerted manner as to produce some semblance of the functional attributes of living cells. Current studies are focussed on the ability of clays to absorb, store and transfer energy under plausible prebiotic conditions and to use this energy to drive chemistry of prebiotic relevance. Conclusions of the work are applicable to the role of clays either as substrates for organic chemistry, or in fueling their own life-mimetic processes.

Coyne, L. M.↗

NASA NTRS1993

Applicability of PM3 to transphosphorylation reaction path: Toward designing a minimal ribozyme

A growing body of evidence shows that RNA can catalyze many of the reactions necessary both for replication of genetic material and the possible transition into the modern protein-based world. However, contemporary ribozymes are too large to have self-assembled from a prebiotic oligonucleotide pool. Still, it is likely that the major features of the earliest ribozymes have been preserved as molecular fossils in the catalytic RNA of today. Therefore, the search for a minimal ribozyme has been aimed at finding the necessary structural features of a modern ribozyme (Beaudry and Joyce, 1990). Both a three-dimensional model and quantum chemical calculations are required to quantitatively determine the effects of structural features of the ribozyme on the reaction it catalyzes. Using this model, quantum chemical calculations must be performed to determine quantitatively the effects of structural features on catalysis. Previous studies of the reaction path have been conducted at the ab initio level, but these methods are limited to small models due to enormous computational requirements. Semiempirical methods have been applied to large systems in the past; however, the accuracy of these methods depends largely on a simple model of the ribozyme-catalyzed reaction, or hydrolysis of phosphoric acid. We find that the results are qualitatively similar to ab initio results using large basis sets. Therefore, PM3 is suitable for studying the reaction path of the ribozyme-catalyzed reaction.

Manchester, John I.↗

NASA NTRS1997

Microgravity Processing and Photonic Applications of Organic and Polymeric Materials

In recent years, a great deal of interest has been directed toward the use of organic materials in the development of high-efficiency optoelectronic and photonic devices. There is a myriad of possibilities among organics which allow flexibility in the design of unique structures with a variety of functional groups. The use of nonlinear optical (NLO) organic materials such as thin-film waveguides allows full exploitation of their desirable qualities by permitting long interaction lengths and large susceptibilities allowing modest power input. There are several methods in use to prepare thin films, such as Langmuir-Blodgett (LB) and self-assembly techniques, vapor deposition, growth from sheared solution or melt, and melt growth between glass plates. Organics have many features that make them desirable for use in optical devices such as high second- and third-order nonlinearities, flexibility of molecular design, and damage resistance to optical radiation. However, their use in devices has been hindered by processing difficulties for crystals and thin films. In this chapter, we discuss photonic and optoelectronic applications of a few organic materials and the potential role of microgravity on processing these materials. It is of interest to note how materials with second- and third-order nonlinear optical behavior may be improved in a diffusion-limited environment and ways in which convection may be detrimental to these materials.

Frazier, Donald O.↗

NASA NTRS1998

The Effects of Ground and Space Processing on the Properties of Organic, Polymeric, and Colloidal Materials

In recent years, a great deal of interest has been directed toward the use of organic materials in the development of high-efficiency optoelectronic and phototonic devices. There is a myriad of possibilities among organic materials which allow flexibility in the design of unique structures with a variety of functional groups. The use of nonlinear optical (NLO) organic materials as thin film wave-guides allows full exploitation of their desirable qualifies by permitting long interaction lengths and large susceptibilities allowing modest power input. There are several methods in use to prepare thin films such as Langmuir-Blodgett (LB) and self-assembly techniques, vapor deposition, growth from sheared solution or melt, and melt growth between glass plates. Organic-based materials have many features that make them desirable for use in optical devices, such as high second-and third-order nonlinearity, flexibility of molecular design, and damage resistance to optical radiation. However, their use in devices has been hindered by processing difficulties for crystals and thin films. We discuss the potential role of microgravity processing of a few organic and polymeric materials. It is of interest to note how materials with second-and third-order NLO behavior may be improved in a diffusion-limited environment and ways in which convection may be detrimental to these materials. We focus our discussion on third-order materials for all-optical switching, and second-order materials for frequency conversion and electrooptics. The goal of minimizing optical loss obviously depends on processing methods. For solution-based processes, such as solution crystal growth and solution photopolymerization, it is well known that thermal and solutal density gradients can initiate buoyancy-driven convection. Resultant fluid flows can affect transport of material to and from growth interfaces and become manifest in the morphology and homogeneity of the growing film or crystal. Likewise, buoyancy-driven convection can hinder production of defect-free, high-quality crystals or films during crystal and film growth by vapor deposition.

Frazier, Donald O.↗