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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Colloidal crystal engineering with metal–organic framework nanoparticles and DNA

Abstract Colloidal crystal engineering with nucleic acid-modified nanoparticles is a powerful way for preparing 3D superlattices, which may be useful in many areas, including catalysis, sensing, and photonics. To date, the building blocks studied have been primarily based upon metals, metal oxides, chalcogenide semiconductors, and proteins. Here, we show that metal–organic framework nanoparticles (MOF NPs) densely functionalized with oligonucleotides can be programmed to crystallize into a diverse set of superlattices with well-defined crystal symmetries and compositions. Electron microscopy and small-angle X-ray scattering characterization confirm the formation of single-component MOF superlattices, binary MOF–Au single crystals, and two-dimensional MOF nanorod assemblies. Importantly, DNA-modified porphyrinic MOF nanorods (PCN-222) were assembled into 2D superlattices and found to be catalytically active for the photooxidation of 2-chloroethyl ethyl sulfide (CEES, a chemical warfare simulant of mustard gas). Taken together, these new materials and methods provide access to colloidal crystals that incorporate particles with the well-established designer properties of MOFs and, therefore, increase the scope of possibilities for colloidal crystal engineering with DNA.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
NASA NTRS2013

Galactic Cosmic Ray Event-Based Risk Model (GERM) Code

This software describes the transport and energy deposition of the passage of galactic cosmic rays in astronaut tissues during space travel, or heavy ion beams in patients in cancer therapy. Space radiation risk is a probability distribution, and time-dependent biological events must be accounted for physical description of space radiation transport in tissues and cells. A stochastic model can calculate the probability density directly without unverified assumptions about shape of probability density function. The prior art of transport codes calculates the average flux and dose of particles behind spacecraft and tissue shielding. Because of the signaling times for activation and relaxation in the cell and tissue, transport code must describe temporal and microspatial density of functions to correlate DNA and oxidative damage with non-targeted effects of signals, bystander, etc. These are absolutely ignored or impossible in the prior art. The GERM code provides scientists data interpretation of experiments; modeling of beam line, shielding of target samples, and sample holders; and estimation of basic physical and biological outputs of their experiments. For mono-energetic ion beams, basic physical and biological properties are calculated for a selected ion type, such as kinetic energy, mass, charge number, absorbed dose, or fluence. Evaluated quantities are linear energy transfer (LET), range (R), absorption and fragmentation cross-sections, and the probability of nuclear interactions after 1 or 5 cm of water equivalent material. In addition, a set of biophysical properties is evaluated, such as the Poisson distribution for a specified cellular area, cell survival curves, and DNA damage yields per cell. Also, the GERM code calculates the radiation transport of the beam line for either a fixed number of user-specified depths or at multiple positions along the Bragg curve of the particle in a selected material. The GERM code makes the numerical estimates of basic physical and biophysical quantities of high-energy protons and heavy ions that have been studied at the NASA Space Radiation Laboratory (NSRL) for the purpose of simulating space radiation biological effects. In the first option, properties of monoenergetic beams are treated. In the second option, the transport of beams in different materials is treated. Similar biophysical properties as in the first option are evaluated for the primary ion and its secondary particles. Additional properties related to the nuclear fragmentation of the beam are evaluated. The GERM code is a computationally efficient Monte-Carlo heavy-ion-beam model. It includes accurate models of LET, range, residual energy, and straggling, and the quantum multiple scattering fragmentation (QMSGRG) nuclear database.

Cucinotta, Francis A.↗
NASA NTRSDate not supplied

Investigation of Prophage Regions of Bacterial Strains Isolated from the International Space Station (ISS)

Space flight agencies are planning missions back to the Moon and to Mars. When sending humans into space, it is impossible to separate them from microorganisms, either in their associated microbiome or in the spacecraft environment, which are modified through the movement of genetic material. Bacteriophages, small viruses that invade and replicate within bacterial cells, play a central role in the genetic composition and evolution of microorganisms. Lysogenic bacteriophages can insert themselves into the DNA of their bacterial hosts, forming prophage regions, which can also transfer genes from previous hosts. Thus, we aimed to identify and classify all prophages from twelve bacterial species cultured from the International Space Station (ISS) from 2017 to 2018. We determined representative bacterial strains for each species, whose genomes were analyzed to identify prophage regions. Complete prophages were identified through database searches and the number of prophage regions were compared to terrestrial analogs. Additionally, prophage region and genome sizes were compared for each species, identifying the percentage of bacteriophage DNA in each genome. We determined that the prophage-susceptible bacterial species isolated from the ISS had a higher number of prophage regions when compared to terrestrial analogs, as well as having a larger percentage of their genomes made up of prophage material. Of the eighteen complete prophages identified, 72.2% were of family Siphoviridae and 27.8% were of family Myoviridae. Only one of the prophages had a BLAST similarity over 80%, suggesting that the remainder of prophages are novel species. These results imply that there is a higher rate of prophage transduction and lysogeny during spaceflight, and that the prophages present are novel.

Phage↗
DOE OSTI2021

Gene editing through microfluidic delivery

Gene editing can be performed by introducing gene-editing components into a cell by mechanical cell disruption. Related apparatus, systems, techniques, and articles are also described. The methods and systems of the invention solve the problem of intracellular delivery of gene editing components and gene editing complexes to target cells. The results described herein indicate that delivery of gene editing components, e.g., protein, ribonucleic acid (RNA), and deoxyribonucleic acid (DNA), by mechanical disruption of cell membranes leads to successful gene editing. Because intracellular delivery of gene editing materials is a current challenge, the methods provide a robust mechanism to engineer target cells without the use of potentially harmful viral vectors or electric fields.

Sharei, Armon R.↗
DOE OSTI2022

Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine

Abstract Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide. Graphical Abstract

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2001

Microbial Contamination of Allende and Murchison Carbonaceous Chondrites; Developing a Protocol for Life Detection in Extraterrestrial Materials Using Biotechnology

The arguments used to refute the McKay et al., (1996) hypothesis of possible Martian life in ALH84001 failed to use contamination of the meteorite as a source. This has worrying implications for our ability to detect terrestrial microbiota in meteorites and therefore any potential extraterrestrial biosignatures in both meteorites and possible returned samples. We report on imaging and microbial culturing of both Allende and Murchison carbonaceous chondrites and on the use of molecular biology techniques on a sample of Allende. Contaminating fungi and bacteria were observed (in the case of Murchison) and cultured from both meteorites. DNA was successfully extracted and subsequent PCR showed the presence of both bacterial and fungal DNA although no Archaea were detected. These results show that it is possible to use molecular biological techniques on very small quantities (300 mg) of extraterrestrial material.

Steele, A.↗
DOE OSTI2022

The impact of G-quadruplex dynamics on inter-tetrad electronic couplings: a hybrid computational study

The G-quadruplex is a fascinating nucleic acid motif with implications in biology, medicine, and nanotechnologies. G-quadruplexes can form in the telomeres at the edges of chromosomes and in other guanine-rich regions of the genome. They can also be engineered for exploitation as biological materials for nanodevices. Their higher stiffness and higher charge transfer rates make them better candidates in nanodevices than duplex DNA. For the development of molecular nanowires, it is important to optimize electron transport along the wire axis. One powerful basis to do so is by manipulating the structure, based on known effects that structural changes have on electron transport. Here, for this work, we investigate such effects, by a combination of classical simulations of the structure and dynamics and quantum calculations of electronic couplings. We find that this structure–function relationship is complex. A single helix shape parameter alone does not embody such complexity, but rather a combination of distances and angles between stacked bases influences charge transfer efficiency. By analyzing linear combinations of shape descriptors for different topologies, we identify the structural features that most affect charge transfer efficiency. We discuss the transferability of the proposed model and the limiting effects of inherent flexibility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Nonequilibrium design strategies for functional colloidal assemblies

Here, we use a nonequilibrium variational principle to optimize the steady-state, shear-induced interconversion of self-assembled nanoclusters of DNA-coated colloids. Employing this principle within a stochastic optimization algorithm allows us to identify design strategies for functional materials. We find that far-from-equilibrium shear flow can significantly enhance the flux between specific colloidal states by decoupling trade-offs between stability and reactivity required by systems in equilibrium. For isolated nanoclusters, we find nonequilibrium strategies for amplifying transition rates by coupling a given reaction coordinate to the background shear flow. We also find that shear flow can be made to selectively break detailed balance and maximize probability currents by coupling orientational degrees of freedom to conformational transitions. For a microphase consisting of many nanoclusters, we study the flux of colloids hopping between clusters. We find that a shear flow can amplify the flux without a proportional compromise on the microphase structure. This approach provides a general means of uncovering design principles for nanoscale, autonomous, functional materials driven far from equilibrium.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2011

The Analysis of the Patterns of Radiation-Induced DNA Damage Foci by a Stochastic Monte Carlo Model of DNA Double Strand Breaks Induction by Heavy Ions and Image Segmentation Software

To create a generalized mechanistic model of DNA damage in human cells that will generate analytical and image data corresponding to experimentally observed DNA damage foci and will help to improve the experimental foci yields by simulating spatial foci patterns and resolving problems with quantitative image analysis. Material and Methods: The analysis of patterns of RIFs (radiation-induced foci) produced by low- and high-LET (linear energy transfer) radiation was conducted by using a Monte Carlo model that combines the heavy ion track structure with characteristics of the human genome on the level of chromosomes. The foci patterns were also simulated in the maximum projection plane for flat nuclei. Some data analysis was done with the help of image segmentation software that identifies individual classes of RIFs and colocolized RIFs, which is of importance to some experimental assays that assign DNA damage a dual phosphorescent signal. Results: The model predicts the spatial and genomic distributions of DNA DSBs (double strand breaks) and associated RIFs in a human cell nucleus for a particular dose of either low- or high-LET radiation. We used the model to do analyses for different irradiation scenarios. In the beam-parallel-to-the-disk-of-a-flattened-nucleus scenario we found that the foci appeared to be merged due to their high density, while, in the perpendicular-beam scenario, the foci appeared as one bright spot per hit. The statistics and spatial distribution of regions of densely arranged foci, termed DNA foci chains, were predicted numerically using this model. Another analysis was done to evaluate the number of ion hits per nucleus, which were visible from streaks of closely located foci. In another analysis, our image segmentaiton software determined foci yields directly from images with single-class or colocolized foci. Conclusions: We showed that DSB clustering needs to be taken into account to determine the true DNA damage foci yield, which helps to determine the DSB yield. Using the model analysis, a researcher can refine the DSB yield per nucleus per particle. We showed that purely geometric artifacts, present in the experimental images, can be analytically resolved with the model, and that the quantization of track hits and DSB yields can be provided to the experimentalists who use enumeration of radiation-induced foci in immunofluorescence experiments using proteins that detect DNA damage. An automated image segmentaiton software can prove useful in a faster and more precise object counting for colocolized foci images.

Ponomarev, Artem↗
DOE OSTI2023

High-strength, lightweight nano-architected silica

Continuous nanolattices are an emerging class of mechanical metamaterials that are highly attractive due to their superior strength-to-weight ratios, which originate from their spatial architectures and nanoscale-sized elements possessing near-theoretical strength. Rational design of frameworks remains challenging below 50 nm because of limited methods to arrange small elements into complex architectures. Here, we fabricate silica frameworks with ~4- to 20-nm-thick elements using self-assembly and silica templating of DNA origami nanolattices and perform in situ micro-compression testing to examine the mechanical properties. We observe strong effects of lattice dimensions on yield strength (σ $\mathcal{y}$ ) and failure mode. Silica nanolattices are found to exhibit yield strengths higher than those of any known engineering materials with similar mass density. The robust coordination of the nanothin and strong silica elements leads to the combination of lightweight and high-strength framework materials offering an effective strategy for the fabrication of nanoarchitected materials with superior mechanical properties.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
NASA NTRS1991

Fiber optic-based biosensor

The NRL fiber optic biosensor is a device which measures the formation of a fluorescent complex at the surface of an optical fiber. Antibodies and DNA binding proteins provide the mechanism for recognizing an analyze and immobilizing a fluorescent complex on the fiber surface. The fiber optic biosensor is fast, sensitive, and permits analysis of hazardous materials remote from the instrumentation. The fiber optic biosensor is described in terms of the device configuration, chemistry for protein immobilization, and assay development. A lab version is being used for assay development and performance characterization while a portable device is under development. Antibodies coated on the fiber are stable for up to two years of storage prior to use. The fiber optic biosensor was used to measure concentration of toxins in the parts per billion (ng/ml) range in under a minute. Immunoassays for small molecules and whole bacteria are under development. Assays using DNA probes as the detection element can also be used with the fiber optic sensor, which is currently being developed to detect biological warfare agents, explosives, pathogens, and toxic materials which pollute the environment.

Ligler, Frances S.↗
DOE OSTI2021

Nanoparticle Superlattices through Template-Encoded DNA Dendrimers

The chemical interactions that lead to the emergence of hierarchical structures are often highly complex and difficult to program. In this paper, the synthesis of a series of superlattices based upon 30 different structurally reconfigurable DNA dendrimers is reported, each of which presents a well-defined number of single-stranded oligonucleotides (i.e., sticky ends) on its surface. Such building blocks assemble with complementary DNA-functionalized gold nanoparticles (AuNPs) to yield five distinct crystal structures, depending upon choice of dendrimer and defined by phase symmetry. These DNA dendrimers can associate to form micelle-dendrimers, whereby the extent of association can be modulated based upon surfactant concentration and dendrimer length to produce a low-symmetry Ti5Ga4-type phase that has yet to be reported in the field of colloidal crystal engineering. Taken together, colloidal crystals that feature three different types of particle bonding interactions.template-dendron, dendrimer-dendrimer, and DNA-modified AuNP-dendrimer.are reported, illustrating how sequence-defined recognition and dynamic association can be combined to yield complex hierarchical materials.

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

Confinement and Processing Can Alter the Morphology and Periodicity of Bottlebrush Block Copolymers in Thin Films

Bottlebrush block copolymers (BBCPs) are intriguing architectural variations on linear BCPs with highly tunable structure. Confinement can have a significant impact on polymer assembly, giving rise to changes in morphology, assembly kinetics, and properties like the glass transition. Given that confinement leads to significant changes in the persistence length of bottlebrush homopolymers, it is reasonable to expect that BBCPs will see significant changes in their structure and periodicity relative to the bulk morphology. Understanding how confinement influences assembly will be important for designing BBCPs for thin film applications including membranes, integrated photonic structures, and potentially BCP lithography. In this work, in order to study the effects of confinement on BBCP conformation and morphology, a blade coating was used to prepare films with continuous variation in film thickness. Unlike thin films of linear BCPs, islands/holes were not observed, and instead mixtures of parallel and perpendicular morphologies emerge after annealing. The lamellar periodicity ($L_0$) of the morphologies is found to be thickness dependent, increasing $L_0$ with decreasing film thickness for blade coated films. Films coated out of tetrahydrofuran (THF) resulted in a single well-defined lamellar periodicity, verified through atomic force microscopy (AFM) and grazing incidence small-angle X-ray scattering (GISAXS), which increases dramatically from the bulk value (30.6 nm) and continues to increase as the film thickness decreases. The largest observed $L_0$ was 65.5 nm, and this closely approaches the estimated upper limit of 67 nm corresponding to a fully extended backbone in a bilayer arrangement. Films coated out of propylene glycol methyl ether acetate (PGMEA) resulted in a mixture of perpendicular lamellae and a smaller, likely cylindrical morphology. The lamellar portion of the film shows the same thickness dependence as the lamellae observed in the THF coated films. The scaling of the lamellar $L_0$ with respect to film thickness follows predictions for confined semiflexible polymers with weak excluded volume interactions and can be related to models for confinement of DNA. Spin coated films shows the same reduction in periodicity, although at very different film thicknesses. This result suggests that the material has shallow free-energy barriers to transitioning between different $L_0$ and morphologies, a property that could be taken advantage of for patterning diverse structures with a single material.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Old Woman Creek Wetland Sediment and Electrochemical Sensor Microbial Community, 2023

We are developing a technique to monitor microbiological activities referred to as zero resistance ammetry, which entails the deployment of graphite electrodes in sediments. Measurement of current between electrodes of contrasting redox regimes and/or predominant terminal electron accepting processes can be used as an indicator of the extents of microbiological activity. We deployed an electrode array at depths of 2 mm, 4 mm, 76 mm, 78 mm, 152 mm, 154 mm, 227 mm, and 229 mm below the wetland sediment water interface in the Old Woman Creek National Estuarine Research Center, Huron, OH, USA (Lat. = 41.380833, Long. = -82.508889). A core was collected from adjacent sediment and subsamples were collected from depth intervals of 0 – 25 mm, 25 – 127 mm, 127 – 128 mm, and below 178 mm. To determine if the microbial communities attached to the electrodes were reflective of the adjacent sediment-associated microbial community, we conducted a 16S rRNA gene-based (V4 region) survey of these respective materials. This data package contains the results of these surveys, including metadata on the depths from which samples were collected (samples.csv), DNA extraction and sequencing information (OWC_DEPTH_AMPLICON_SEQUENCING_METADATA), sequence processing information (OWC_DEPTH_BIOINFORMATIC_METADATA.csv), an operational taxonomic unit (OTU) table (OWC_DEPTH_97OTUS_TABLE.csv), and nucleotide sequences of OTUs (OWC_DEPTH_97OTUS_SEQS.fasta). All files can be opened using a text-editing application. The fasta file is compatible with bioinformatics applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Programmable Photoluminescence via Intrinsic and DNA-Fluorophore Association in a Mixed Cluster Heterometallic MOF

In this report a rapid and facile design strategy to create a highly complex optical tag with programmable, multimodal photoluminescent properties is described. This was achieved via intrinsic and DNA-fluorophore hidden signatures. As a first covert feature of the tag, an intricate novel heterometallic near-infrared (NIR)-emitting mesoporous metal–organic framework (MOF) was designed and synthesized. The material is constructed from two chemically distinct, homometallic hexanuclear clusters based on Nd and Yb. Uniquely, the Nd-based cluster is observed here for the first time in a MOF and consists of two staggered Nd μ3-oxo trimers. To generate controlled, multimodal, and tailorable emission with difficult to counterfeit features, the NIR-emissive MOF was post-synthetically modified via a fluorescent DNA oligo labeling design strategy. The surface attachment of several distinct fluorophores, including the simultaneous attachment of up to three distinct fluorescently labeled oligos was achieved, with excitation and emission properties across the visible spectrum (480-800 nm). The DNA inclusion as a secondary covert element in the tag was demonstrated via the detection of SYBR Gold dye association. Importantly, the approach implemented here serves as a rapid and tailorable way to encrypt distinct information in a facile and modular fashion and provides an innovative technology in the quest toward complex optical tags.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗