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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Bacterial genome editing by coupling Cre-lox and CRISPR-Cas9 systems

The past decade has been a golden age for microbiology, marked by the discovery of an unprecedented increase in the number of novel bacterial species. Yet gaining biological knowledge of those organisms has not kept pace with sequencing efforts. To unlock this genetic potential there is an urgent need for generic (i.e. non-species specific) genetic toolboxes. Recently, we developed a method, termed chassis-independent recombinase-assisted genome engineering (CRAGE), enabling the integration and expression of large complex gene clusters directly into the chromosomes of diverse bacteria. Here we expand upon this technology by incorporating CRISPR-Cas9 allowing precise genome editing across multiple bacterial species. To do that we have developed a landing pad that carries one wild-type and two mutant lox sites to allow integration of foreign DNA at two locations through Cre-lox recombinase-mediated cassette exchange (RMCE). The first RMCE event is to integrate the Cas9 and the DNA repair protein genes RecET, and the second RMCE event enables the integration of customized sgRNA and a repair template. Following this workflow, we achieved precise genome editing in four different gammaproteobacterial species. We also show that the inserted landing pad and the entire editing machinery can be removed scarlessly after editing. We report here the construction of a single landing pad transposon and demonstrate its functionality across multiple species. The modular design of the landing pad and accessory vectors allows design and assembly of genome editing platforms for other organisms in a similar way. We believe this approach will greatly expand the list of bacteria amenable to genetic manipulation and provides the means to advance our understanding of the microbial world.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling

Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems. The ezAlign v1.1 software package is publicly available for download at github.com/LLNL/ezAlign. Its underlying methodology is based on a simple alignment of an atomistic template molecule, followed by position-restraint energy minimization, which forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule. The molecules are then combined, solvated, minimized, and equilibrated with position restraints. Validation of the process was conducted on a pure POPC membrane and compared with other popular methods to construct atomistic membranes. Additional examples, including surfactant self-assembly, membrane proteins, and more complex bacterial and human plasma membrane models, are also presented. By providing these examples, parameter files, code, and an easy-to-follow recipe to add new molecules, this work will aid future multiscale modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS2004

Biologically Derived Nanoparticle Arrays via a Site-Specific Reconstitution of Ferritin and their Electrochemistry

Nanoparticle arrays biologically derived from an electrochemically-controlled site-specific biomineralization were fabricated on a gold substrate through the immobilization process of biomolecules. The work reported herein includes the immobilization of ferritin with various surface modifications, the electrochemical biomineralization of ferritins with different inorganic cores, the fabrication of self-assembled arrays with the immobilized ferritin, and the electrochemical characterization of various core materials. Protein immobilization on the substrate is achieved by anchoring ferritins with dithiobis-N-succinimidyl propionate (DTSP). A reconstitution process of electrochemical site-specific biomineralization with a protein cage loads ferritins with different core materials such as Pt, Co, Mn, and Ni. The ferritin acts as a nano-scale template, a biocompatible cage, and a separator between the nanoparticles. The nano-sized metalcored ferritins on a gold substrate displayed a good electrochemical activity for the electron transport and storage, which is suitable for bioelectronics applications such as biofuel cell, bionanobattery, biosensors, etc. Keywords: Ferritin, immobilization, site-specific reconstitution, biomineralization, and bioelectronics

Kim, Jae-Woo↗
DOE OSTI2021

Mutations in artificial self-replicating tiles: A step toward Darwinian evolution

Significance In nature, mutation is the first step of evolution, where it provides the genetic variation for the natural selection to act. Here we take a system of artificial self-replicating tiles, DNA origami, that exhibit templated reproduction. We can generate a small fraction of mutations by introducing a mismatch in hybridization between parent and daughter. We can modify the origami functionality to affect the growth rate of the mutated species, giving it less or more evolutionary advantage, and to become dominant in several generations. The introduction of mutations into an artificial self-replicating system provides new directions for research into self-assembly processes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS2018

Fuel Cell Model Validation with Power Module Test Data

The AES Modular Power Systems (AMPS) Fuel Cell team at the NASA Glenn Research Center (GRC) has created a Microsoft Excel model of a regenerative fuel cell (RFC) system for potential lunar and Martian applications. Due to some limitations of this model, including the ability to predict transient effects in the thermal and fluidic performance of the system, a system-level transient thermal/fluids model was desired. GT-SUITE is a transient multi-physics simulation tool that is popular in the automotive industry and has a built-in template for proton exchange membrane (PEM) fuel cells. However, terrestrial fuel cells used in the automotive industry vary significantly from aerospace fuel cells. A validation effort was undertaken to compare GT SUITE model results to actual data collected during the 2015 AMPS (Advanced Exploration Systems (AES) Modular Power Systems) Power Module Demonstration in which the AMPS team used a PEM fuel cell system to power a 478 kilogram rover assembly at the Dunes test site located at GRC. The purpose of the model was to evaluate the efficacy of using GT SUITE to model a non-flow through PEM fuel cell system. The validation effort examined electrochemical performance including fuel cell stack voltage and power supplied, the thermal performance of the stack namely stack temperature and heat rejection rates, and the fluidic performance of the system including pressures, reactant consumption, and water production rates.

Model Validation↗
DOE OSTI2021

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Heterotrimetallic Mixed‐Valent Molecular Precursors Containing Periodic Table Neighbors: Assignment of Metal Positions and Oxidation States

Abstract A known trinuclear structure was used to design the heterobimetallic mixed‐valent, mixed‐ligand molecule [Co II (hfac) 3 −Na−Co III (acac) 3 ] ( 1 ). This was used as a template structure to develop heterotrimetallic molecules [Co II (hfac) 3 −Na−Fe III (acac) 3 ] ( 2 ) and [Ni II (hfac) 3 −Na−Co III (acac) 3 ] ( 3 ) via isovalent site‐specific substitution at either of the cobalt positions. Diffraction methods, synchrotron resonant diffraction, and multiple‐wavelength anomalous diffraction were applied beyond simple structural investigation to provide an unambiguous assignment of the positions and oxidation states for the periodic table neighbors in the heterometallic assemblies. Molecules of 2 and 3 are true heterotrimetallic rather than a statistical mixture of two heterobimetallic counterparts. Trinuclear platform 1 exhibits flexibility in accommodating a variety of di‐ and trivalent metals, which can be further utilized in the design of molecular precursors for the NaMM′O 4 functional oxide materials.

Han, Haixiang↗
NASA NTRS2011

Post-Fragmentation Whole Genome Amplification-Based Method

This innovation is derived from a proprietary amplification scheme that is based upon random fragmentation of the genome into a series of short, overlapping templates. The resulting shorter DNA strands (<400 bp) constitute a library of DNA fragments with defined 3 and 5 termini. Specific primers to these termini are then used to isothermally amplify this library into potentially unlimited quantities that can be used immediately for multiple downstream applications including gel eletrophoresis, quantitative polymerase chain reaction (QPCR), comparative genomic hybridization microarray, SNP analysis, and sequencing. The standard reaction can be performed with minimal hands-on time, and can produce amplified DNA in as little as three hours. Post-fragmentation whole genome amplification-based technology provides a robust and accurate method of amplifying femtogram levels of starting material into microgram yields with no detectable allele bias. The amplified DNA also facilitates the preservation of samples (spacecraft samples) by amplifying scarce amounts of template DNA into microgram concentrations in just a few hours. Based on further optimization of this technology, this could be a feasible technology to use in sample preservation for potential future sample return missions. The research and technology development described here can be pivotal in dealing with backward/forward biological contamination from planetary missions. Such efforts rely heavily on an increasing understanding of the burden and diversity of microorganisms present on spacecraft surfaces throughout assembly and testing. The development and implementation of these technologies could significantly improve the comprehensiveness and resolving power of spacecraft-associated microbial population censuses, and are important to the continued evolution and advancement of planetary protection capabilities. Current molecular procedures for assaying spacecraft-associated microbial burden and diversity have inherent sample loss issues at practically every step, particularly nucleic acid extraction. In engineering a molecular means of amplifying nucleic acids directly from single cells in their native state within the sample matrix, this innovation has circumvented entirely the need for DNA extraction regimes in the sample processing scheme.

Benardini, James↗
DOE OSTI2022

Confined Growth of DNA-Assembled Superlattice Films

Here, we study the assembly of DNA-functionalized nanocubes under lateral confinement in microscale square trenches on a DNA-functionalized substrate. Microfocus small-angle X-ray scattering (SAXS) and scanning electron microscopy (SEM) are used to characterize the superlattices (SLs). The results indicate that nanocubes form simple-cubic SLs with square-prism morphology and a (100) out-of-plane orientation to maximize DNA bonding. In-plane, SLs align with the template, exposing their {100} side facets, and the degree of alignment depends on trench size. Interestingly, the distribution of in-plane orientations determined from SAXS and SEM do not agree, indicating that the internal and external structures of the SLs differ. To understand this discrepancy, X-ray ptychography is employed to image the internal structures of the SLs, revealing that SLs which appear to be single-crystalline in SEM may have subsurface grain boundaries, depending on trench size. SEM reveals that the SLs grow via nucleation and growth of randomly oriented domains, which then coalesce; this mechanism explains the observed dependence of alignment and defect structure on size. Interestingly, crystallization occurs via an unusual growth mode, whereby continuous SL layers grow on top of several misoriented islands. Overall, this work elucidates the effect of lateral confinement on the crystallization of DNA-functionalized nanoparticles and shows how X-ray ptychography can be used to gain insight into nanoparticle crystallization.

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

Anomalous Anisotropic Nanoparticle Aggregation in Cu 2 (OH) 3 Br Gels

Aerogels are of interest for their ability to uniformly incorporate nanoscale features into macroscopic assemblies, which enabled applications that require low density, high surface area, and/or bicontinuous networks. The structure of the nanoporous network is intrinsically linked to the macroscopic properties of aerogels. Hence, control of this structure is of paramount importance. Small-angle X-ray scattering (SAXS) is used here to monitor nanoparticle aggregation in situ in Cu 2 (OH) 3 Br aerogels formed via epoxide-assisted gelation. Anomalous anisotropic aggregation is observed in the absence of templating agents and is attributed to the molecular structure of the inorganic nanoparticles themselves. This is a fundamental departure from the models currently used to describe traditional inorganic sol–gel chemistry where nanoparticles are believed to undergo isotropic diffusion- and/or kinetically limited aggregation. Time-resolved SAXS indicates that Cu 2 (OH) 3 Br nanoparticles nucleate rapidly from solution to form unbranched chain-like aggregates rather than branched mass-fractal aggregates. Sizes of primary particles (~1.5 nm) and the chain-like structure of their aggregates are independent of particle concentration (gel density), while rates of particle aggregation, gelation time, and aggregate size are strongly dependent upon particle concentration, which implies that the chemistry of particle formation and the physics of particle aggregation are independent processes. Because the conditions necessary for creating anisotropic structures are not unique to Cu 2 (OH) 3 Br, these results could provide insight into the structure and gelation mechanisms of other inorganic aerogels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2004

Electrochemical Reconstitution of Biomolecules for Applications as Electrocatalysts for the Bionanofuel Cell

Platinum-cored ferritins were synthesized as electrocatalysts by electrochemical biomineralization of immobilized apoferritin with platinum. The platinum cored ferritin was fabricated by exposing the immobilized apoferritin to platinum ions at a reduction potential. On the platinum-cored ferritin, oxygen is reduced to water with four protons and four electrons generated from the anode. The ferritin acts as a nano-scale template, a biocompatible cage, and a separator between the nanoparticles. This results in a smaller catalyst loading of the electrodes for fuel cells or other electrochemical devices. In addition, the catalytic activity of the ferritin-stabilized platinum nanoparticles is enhanced by the large surface area and particle size phenomena. The work presented herein details the immobilization of ferritin with various surface modifications, the electrochemical biomineralization of ferritin with different inorganic cores, and the fabrication of self-assembled 2-D arrays with thiolated ferritin.

Kim, Jae-Woo↗
NASA NTRS1993

Automated system for analyzing the activity of individual neurons

This paper presents a signal processing system that: (1) provides an efficient and reliable instrument for investigating the activity of neuronal assemblies in the brain; and (2) demonstrates the feasibility of generating the command signals of prostheses using the activity of relevant neurons in disabled subjects. The system operates online, in a fully automated manner and can recognize the transient waveforms of several neurons in extracellular neurophysiological recordings. Optimal algorithms for detection, classification, and resolution of overlapping waveforms are developed and evaluated. Full automation is made possible by an algorithm that can set appropriate decision thresholds and an algorithm that can generate templates on-line. The system is implemented with a fast IBM PC compatible processor board that allows on-line operation.

Bankman, Isaac N.↗
DOE OSTI2021

On the Origin of Sinter‐Resistance and Catalyst Accessibility in Raspberry‐Colloid‐Templated Catalyst Design

Abstract Nanoparticle (NP) sintering is a major cause of the deactivation of supported catalysts. Raspberry‐colloid‐templated (RCT) catalysts are an emerging class of materials that show an unprecedented level of sinter‐resistance and exhibit high catalytic activity. Here a comprehensive study of the origin of NP stability and accessibility in RCT catalysts using theoretical modeling, 3D electron microscopy, and epitaxial overgrowth is reported. The approach is showcased for silica‐based RCT catalysts containing dilute Pd‐in‐Au NPs previously used in hydrogenation and oxidation catalysis. Modeling of the contact line of the silica precursor infiltrating into the assembled raspberry colloids suggests that a large part of the particles must be embedded into silica, which is confirmed by quantitative visualization of >200 individual NPs by dual‐axis electron tomography. The RCT catalysts have a unique structure in which all NPs reside at the pore wall but have >50% of their surface embedded in the matrix, giving rise to the strongly enhanced thermal and mechanical stability. Importantly, epitaxial overgrowth of Ag on the supported NPs reveals that not only the NP surface exposed to the pore but the embedded interface as well remained chemically accessible. This mechanistic understanding provides valuable guidance in the design of stable catalytic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1992

Teaching, learning, and planetary exploration

The progress accomplished in the first five months of the three-year grant period of Teaching, Learning, and Planetary Exploration is presented. The objectives of this project are to discover new education products and services based on space science, particularly planetary exploration. An Exploration in Education is the umbrella name for the education projects as they are seen by teachers and the interested public. As described in the proposal, our approach consists of: (1) increasing practical understanding of the potential role and capabilities of the research community to contribute to basic education using new discoveries; (2) developing an intellectual framework for these contributions by supplying criteria and templates for the teacher's stories; (3) attracting astronomers, engineers, and technical staff to the project and helping them form productive education partnerships for the future, (4) exploring relevant technologies and networks for authoring and communicating the teacher's stories; (5) enlisting the participation of potential user's of the teacher's stories in defining the products; (6) actually producing and delivering many educationally useful teacher's stories; and (7) reporting the pilot study results with critical evaluation. Technical progress was made by assembling our electronic publishing stations, designing electronic publications based on space science, and developing distribution approaches for electronic products. Progress was made addressing critical issues by developing policies and procedures for securing intellectual property rights and assembling a focus group of teachers to test our ideas and assure the quality of our products. The following useful materials are being produced: the TOPS report; three electronic 'PictureBooks'; one 'ElectronicArticle'; three 'ElectronicReports'; ten 'PrinterPosters'; and the 'FaxForum' with an initial complement of printed materials. We have coordinated with planetary scientists and astronomers both at the technical and policy level to assure the efficiency and ultimate utility of these efforts to derive educational benefits from the space science and exploration program as a whole.

Brown, Robert A.↗
DOE OSTI2021

Nitride-Oxide-Metal Heterostructure with Self-Assembled Core–Shell Nanopillar Arrays: Effect of Ordering on Magneto-Optical Properties

Magneto-optical (MO) coupling incorporates photon-induced change of magnetic polarization that can be adopted in ultrafast switching, optical isolators, mode convertors, and optical data storage components for advanced optical integrated circuits. However, integrating plasmonic, magnetic, and dielectric properties in one single material system poses challenges since one natural material can hardly possess all these functionalities. Here, co-deposition of a three-phase heterostructure composed of a durable conductive nitride matrix with embedded core–shell vertically aligned nanopillars, is demonstrated. Additionally, the unique coupling between ferromagnetic NiO core and atomically sharp plasmonic Au shell enables strong MO activity out-of-plane at room temperature. Further, a template growth process is applied, which significantly enhances the ordering of the nanopillar array. The ordered nanostructure offers two schemes of spin polarization which result in stronger antisymmetry of Kerr rotation. The presented complex hybrid metamaterial platform with strong magnetic and optical anisotropies is promising for tunable and modulated all-optical-based nanodevices.

36 MATERIALS SCIENCE↗
NASA NTRS1990

Circularity measuring system: A shape gauge designed especially for use on large objects

The Circularity Measuring System (CMS) was developed to make an in-situ determination of shape similarity for selected fit large cylinders (RSRM segments). It does this to a repeatable accuracy of 0.10 mm (0.004 inch). This is less that the goal of 0.07 mm (0.003 inch), but was determined adequate because of the addition of an assembly aid that increased the entry chamfer of the clevis side of the joint. The usefulness of the CMS is demonstrated by the application to measurements other than its specified design purpose, such as submarine hull circularity, SRM mid-case circularity, as well as circularity of interfacing SRM tooling, specifically the rounding devices and horizontal disassembly devices. Commercialization of the tool is being pursued, since it is an enhancement of metrology technology for circularity determination. The most accurate in-situ technology it replaces is determined from a template. The CMS is an improvement in accuracy and operation.

Rohrkaste, G. R.↗
DOE OSTI2022

Mesocrystalline Ordering and Phase Transformation of Iron Oxide Biominerals in the Ultrahard Teeth of Cryptochiton stelleri

Biological organisms naturally synthesize complex, hierarchical, multifunctional materials through mineralization processes at ambient conditions and under physiological pH. One such example is the ultrahard and wear-resistant radular teeth found in mollusks, which are used to scape against the rock to feed on algae. Herein, the biologically controlled structural development of the hard, outer magnetite-containing shell of the chitin teeth is revealed. Specifically, the formation of a series of mesocrystalline iron oxide phases, templated by chitin-binding proteins, is identified. The initial domains, consisting of ferrihydrite mesocrystals with a spherulite-like morphology, undergo a solid-state phase transformation to form magnetite while maintaining mesocrystallinity, likely via a shear-induced solid-state reaction, without any noticeable architectural changes. Subsequent growth via Ostwald ripening leads to nearly single-crystalline rod-like elements. In addition, an interpenetrating organic matrix is identified that, at early stages of tooth development, potentially contains iron-binding proteins that guide the self-assembly of the mesocrystalline mineral and influence the preferred orientation of the later-formed magnetite nanorods, which ultimately determines the mechanical behavior of the mature chiton teeth.

36 MATERIALS SCIENCE↗