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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Dynamic Construction, Perception, and Remodeling of Plant Cell Walls

Plant cell walls are dynamic structures that are synthesized by plants to provide durable coverings for the delicate cells they encase. They are made of polysaccharides, proteins, and other biomolecules and have evolved to withstand large amounts of physical force and to resist external attack by herbivores and pathogens but can in many cases expand, contract, and undergo controlled degradation and reconstruction to facilitate developmental transitions and regulate plant physiology and reproduction. Recent advances in genetics, microscopy, biochemistry, structural biology, and physical characterization methods have revealed a diverse set of mechanisms by which plant cells dynamically monitor and regulate the composition and architecture of their cell walls, but much remains to be discovered about how the nanoscale assembly of these remarkable structures underpins the majestic forms and vital ecological functions achieved by plants.

biofuels (including algae and biomass), bio-inspir↗
DOE OSTI2024

Building an ab initio solvated DNA model using Euclidean neural networks

Accurately modeling large biomolecules such as DNA from first principles is fundamentally challenging due to the steep computational scaling of ab initio quantum chemistry methods. This limitation becomes even more prominent when modeling biomolecules in solution due to the need to include large numbers of solvent molecules. We present a machine-learned electron density model based on a Euclidean neural network framework that includes a built-in understanding of equivariance to model explicitly solvated double-stranded DNA. By training the machine learning model using molecular fragments that sample the key DNA and solvent interactions, we show that the model predicts electron densities of arbitrary systems of solvated DNA accurately, resolves polarization effects that are neglected by classical force fields, and captures the physics of the DNA-solvent interaction at the ab initio level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Towards resolving protein structures at the atomic scale using atom probe tomography

In the field of Structural Biology, Atom Probe Tomography (APT) is in the nascent stages of development wherein coarse-grained visuals of proteins have been captured. The characterization of organic samples or biomolecules through the technique is currently limited to the detection of a few dominant signatures. The problem of indecipherable characterization can inherently be traced back to multiple forms of technique-specific responses to organic samples and consequent triggers leading to organic-sample and sample-medium interactions. While it is possible for captured manifestations of protein reconstructions to seemingly appear intact from a basic visual purview, the parameter-protein associative responses throughout the structure as a direct consequence of the inherent workings of the technique (until harmonized with organic sample complexity and behavior) and field evaporation-based factors make non-aberrative atomic associations infeasible. The work focused on identifying and theorizing the (above stated and other) fundamental mechanisms that stronghold the study of intricate atomic to higher order associations in proteins through APT. Attempts at structure elucidation of the cryogenic sample under study, through indirect associations (and methods) based on other imaging techniques, further revealed the distinct and highly distortive nature at the atomic scale deterring structural tunability and thus characterization of APT based cryogenic samples under analysis. As a direct counter to the atomic scale characterization problem, by taking the experiment-specific uncertainties, and probable APT-centric organic sample-based variabilities into account, a basic result is extracted and presented. Through mass-spectrometric and computational analysis, specific individual amino acids (Sulfur-containing protein-bound amino acids) in proteins and aspects of protein structure (probable backbone fragments, partial sequence - partial backbone portions) have been identified and characterized. Under analysis considerations, a few of the simplest known and easily inferable segments that favor structural deteriorations in the reconstructions are stated. Additionally, to overcome technique-specific deterrents to the characterization of biomolecules in cryogenic sample medium, the development of a protein-labeling strategy tailored to APT is suggested.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Missing data in multi-omics integration: Recent advances through artificial intelligence

Biological systems function through complex interactions between various ‘omics (biomolecules), and a more complete understanding of these systems is only possible through an integrated, multi-omic perspective. This has presented the need for the development of integration approaches that are able to capture the complex, often non-linear, interactions that define these biological systems and are adapted to the challenges of combining the heterogenous data across ‘omic views. A principal challenge to multi-omic integration is missing data because all biomolecules are not measured in all samples. Due to either cost, instrument sensitivity, or other experimental factors, data for a biological sample may be missing for one or more ‘omic techologies. Recent methodological developments in artificial intelligence and statistical learning have greatly facilitated the analyses of multi-omics data, however many of these techniques assume access to completely observed data. A subset of these methods incorporate mechanisms for handling partially observed samples, and these methods are the focus of this review. We describe recently developed approaches, noting their primary use cases and highlighting each method's approach to handling missing data. We additionally provide an overview of the more traditional missing data workflows and their limitations; and we discuss potential avenues for further developments as well as how the missing data issue and its current solutions may generalize beyond the multi-omics context.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Using Macro- and Microscale Preservation in Vertebrate Fossils as Predictors for Molecular Preservation in Fluvial Environments

Exceptionally preserved fossils retain soft tissues and often the biomolecules that were present in an animal during its life. The majority of terrestrial vertebrate fossils are not traditionally considered exceptionally preserved, with fossils falling on a spectrum ranging from very well-preserved to poorly preserved when considering completeness, morphology and the presence of microstructures. Within this variability of anatomical preservation, high-quality macro-scale preservation (e.g., articulated skeletons) may not be reflected in molecular-scale preservation (i.e., biomolecules). Excavation of the Hayden Quarry (HQ; Chinle Formation, Ghost Ranch, NM, USA) has resulted in the recovery of thousands of fossilized vertebrate specimens. This has contributed greatly to our knowledge of early dinosaur evolution and paleoenvironmental conditions during the Late Triassic Period (~212 Ma). The number of specimens, completeness of skeletons and fidelity of osteohistological microstructures preserved in the bone all demonstrate the remarkable quality of the fossils preserved at this locality. Because the Hayden Quarry is an excellent example of good preservation in a fluvial environment, we have tested different fossil types (i.e., bone, tooth, coprolite) to examine the molecular preservation and overall taphonomy of the HQ to determine how different scales of preservation vary within a single locality. We used multiple high-resolution mass spectrometry techniques (TOF-SIMS, GC-MS, FT-ICR MS) to compare the fossils to unaltered bone from extant vertebrates, experimentally matured bone, and younger dinosaurian skeletal material from other fluvial environments. FT-ICR MS provides detailed molecular information about complex mixtures, and TOF-SIMS has high elemental spatial sensitivity. Using these techniques, we did not find convincing evidence of a molecular signal that can be confidently interpreted as endogenous, indicating that very good macro- and microscale preservation are not necessarily good predictors of molecular preservation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Biomolecular patterning of three dimensional tissue scaffolds

The invention provides methods and compositions for making and using collagen-glycosaminoglycan three-dimensional scaffolds immobilized with biomolecules that are spatially and temporally patterned. The method comprises adding benzophenone to a collagen-glycosaminoglycan three dimensional scaffold in the dark; adding one or more biomolecules to one or more areas of the collagen-glycosaminoglycan three-dimensional scaffold (which can be done optionally in the dark or in the light); and exposing the collagen-2glycosaminoglycan three-dimensional scaffold to light at a wavelength of about 350 to about 365 nm.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Integrated sample-handling and mounting system for fixed-target serial synchrotron crystallography

Serial synchrotron crystallography (SSX) is enabling the efficient use of small crystals for structure–function studies of biomolecules and for drug discovery. An integrated SSX system has been developed comprising ultralow background-scatter sample holders suitable for room and cryogenic temperature crystallographic data collection, a sample-loading station and a humid `gloveless' glovebox. The sample holders incorporate thin-film supports with a variety of designs optimized for different crystal-loading challenges. These holders facilitate the dispersion of crystals and the removal of excess liquid, can be cooled at extremely high rates, generate little background scatter, allow data collection over >90° of oscillation without obstruction or the risk of generating saturating Bragg peaks, are compatible with existing infrastructure for high-throughput cryocrystallography and are reusable. The sample-loading station allows sample preparation and loading onto the support film, the application of time-varying suction for optimal removal of excess liquid, crystal repositioning and cryoprotection, and the application of sealing films for room-temperature data collection, all in a controlled-humidity environment. The humid glovebox allows microscope observation of the sample-loading station and crystallization trays while maintaining near-saturating humidities that further minimize the risks of sample dehydration and damage, and maximize working times. This integrated system addresses common problems in obtaining properly dispersed, properly hydrated and isomorphous microcrystals for fixed-orientation and oscillation data collection. Its ease of use, flexibility and optimized performance make it attractive not just for SSX but also for single-crystal and few-crystal data collection. Fundamental concepts that are important in achieving desired crystal distributions on a sample holder via time-varying suction-induced liquid flows are also discussed.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Sol–Gel‐Based Advanced Porous Silica Materials for Biomedical Applications

Abstract Porous silica‐based materials have burgeoning applications ranging from fillers and additives, to adsorbents, catalysts, and recently therapeutic agents and vaccines in nanomedicine. The preponderance of these materials is made by sol–gel processing wherein soluble silica precursors are reacted to form amorphous networks composed of siloxane bonds. The facile sol–gel approach allows for an unlimited variety of binary tertiary and more complex chemical compositions including organic ligands and networks resulting in so‐called organic–inorganic hybrid materials. Here, a brief review of the recent progress in sol–gel‐derived silica materials prepared as particles, thin films, biosilica/silica bioreplicas (of molecules, cells and organisms), and their related preparation, properties, and bioapplications is provided. First, it highlights the recent achievements of mesoporous silica nanoparticles in biomedical applications, including therapeutic agent delivery, multimodal imaging and theranostics, and bone tissue engineering and repair. Second, the research in evaporation‐induced self‐assembly (EISA)‐based mesostructured silica thin films and cell‐directed EISA in bio/nano interfaces for various bioapplications, such as bioactive coatings, biosensing, and living cell immobilization, has been reviewed. Third, the pioneering work in biomimetic silicification/immobilization of biomolecules and bio‐organisms and silica bioreplication of complex bio‐organisms is summarized. Finally, it is concluded with personal perspectives on the directions of future work on this field.

Lei, Qi↗
DOE OSTI2025

Elastomeric Nanocomposite with Solvent‐Free, One Step, In Situ Shear Exfoliation of Graphite to Graphene

A graphene nanoflake (GNF)‐enhanced elastomeric nanocomposite (G‐EMC) is fabricated following an innovative, cost‐effective, single‐step, in situ shear exfoliation (ISE) method from low‐cost bulk material, graphite, where uniform mixing happens simultaneously within the elastomer matrix. Electron microscopy, atomic force microscopy, and photo‐induced force microscopy results show good dispersion of GNFs with exfoliation to a few layers and uniform distribution in the elastomer matrix. X‐ray photoelectron spectroscopy analysis shows less than 1% oxygen‐containing functional groups/impurity, enhanced bonding through the formation of edge sites as fracture occurs across the GNF basal plane, and pi‐pi interactions with newly exfoliated planar basal plane surfaces of the GNFs. Raman spectroscopy results confirm the formation of GNFs with only a few layers of graphene formed by the ISE process. Fabricated 10 wt.% G‐EMC nanocomposites show a 400%–500% increase in strength and fracture toughness. And 35 wt.% G‐EMCs provide an electrical conductivity of 25.64 S m −1 and a sensor gauge factor of 45. The resulting intrinsic piezo resistivity of the fabricated nanocomposite has been exploited to fabricate a multi‐functional wired and wireless sensor for detecting different body movements, speech, human vital functions, solvents, and biomolecules.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Permeability-Engineered Compartmentalization Enables In Vitro Reconstitution of Sustained Synthetic Biology Systems

In nature, biological compartments such as cells rely on dynamically controlled permeability for matter exchange and complex cellular activities. Likewise, the ability to engineer compartment permeability is crucial for in vitro systems to gain sustainability, robustness, and complexity. However, rendering in vitro compartments such a capability is challenging. Here, a facile strategy is presented to build permeability-configurable compartments, and marked advantages of such compartmentalization are shown in reconstituting sustained synthetic biology systems in vitro. Through microfluidics, the strategy produces micrometer-sized layered microgels whose shell layer serves as a sieving structure for biomolecules and particles. In this configuration, the transport of DNAs, proteins, and bacteriophages across the compartments can be controlled an guided by a physical model. Through permeability engineering, a compartmentalized cell-free protein synthesis system sustains multicycle protein production; ≈100 000 compartments are repeatedly used in a five-cycle synthesis, featuring a yield of 2.2 mg mL -1 . Further, the engineered bacteria-enclosing compartments possess near-perfect phage resistance and enhanced environmental fitness. In a complex river silt environment, compartmentalized whole-cell biosensors show maintained activity throughout the 32 h pollutant monitoring. It is anticipated that permeability-engineered compartmentalization should pave the way for practical synthetic biology applications such as green bioproduction, environmental sensing, and bacteria-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Self‐Assembly of 0D/3D Perovskite Bi‐Layer from a Micro‐Emulsion Ink

Abstract 2D/3D bilayer perovskite synthesized using sequential deposition methods has shown effectiveness in enhancing the stability of perovskite solar devices. However, these approaches present several limitations such as uncontrolled chemical processes, disordered interfacial states, and microscale heterogeneities that can chemically, structurally, and electronically compromise the performance of solar modules. Here, this work demonstrates an emulsion‐based self‐assembly approach using natural lipid biomolecules in a nonionic solution system to form a 0D/3D bilayer structure. The new capping layer is composed of 0D‐entity nanoparticles of perovskite encapsulated by a hydrophobic lipid membrane, analogous to a cell structure, formed through a molecular self‐assembly process. This 0D layer provides a strong water repellent characteristics, optimum interface microstructure, and excellent homogeneity that drives significant enhancement in stability. Solar modules with a large active area of 70 cm 2 fabricated using films comprising of 0D/3D bilayer structure are found to show consistent efficiency of >19% for 2800 h of continuous illumination in the air (60% relative humidity). This emulsion‐based self‐assembly approach is expected to have a transformative impact on the design and development of stable perovskite‐based devices.

0D/3D bilayers↗
DOE OSTI2021

Mass Spectrometry Imaging of Bio‐oligomer Polydispersity in Plant Tissues by Laser Desorption Ionization from Silicon Nanopost Arrays

Abstract Mass spectrometry imaging (MSI) enables simultaneous spatial mapping for diverse molecules in biological tissues. Matrix‐assisted laser desorption ionization (MALDI) mass spectrometry (MS) has been a mainstream MSI method for a wide range of biomolecules. However, MALDI‐MSI of biological homopolymers used for energy storage and molecular feedstock is limited by, e.g., preferential ionization for certain molecular classes. Matrix‐free nanophotonic ionization from silicon nanopost arrays (NAPAs) is an emerging laser desorption ionization (LDI) platform with ultra‐trace sensitivity and molecular imaging capabilities. Here, we show complementary analysis and MSI of polyhydroxybutyric acid (PHB), polyglutamic acid (PGA), and polysaccharide oligomers in soybean root nodule sections by NAPA‐LDI and MALDI. For PHB, number and weight average molar mass, polydispersity, and oligomer size distributions across the tissue section and in regions of interest were characterized by NAPA‐LDI‐MSI.

Samarah, Laith Z.↗
DOE OSTI2022

Peptoid-Directed Formation of Five-Fold Twinned Au Nanostars through Particle Attachment and Facet Stabilization

While bio-inspired synthesis offers great potential for controlling nucleation and growth of inorganic particles, precisely tuning biomolecule-particle interactions is a long-standing challenge. Herein, we used variations in peptoid sequence to manipulate peptoid-Au interaction, leading to synthesis of concave five-fold twinned, five-pointed Au nanostars via a process of repeated particle attachment and facet stabilization. Ex situ and liquid-phase TEM observations show that a balance between particle attachment biased to occur near the star points, preferential growth along the [100] direction, and stabilization of (111) facets is critical to forming star-shaped particles. Molecular simulations predict that interaction strengths between peptoids and distinct Au facets differ significantly and thus can alter attachment kinetics and surface energies to form the stars. This work provides new insights into how sequence-defined ligands affect particle growth to regulate crystal morphology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Rapid RASER MRI

Conventional Magnetic Resonance Imaging (MRI) relies on high-power Radio-Frequency (RF) pulses to excite nuclear spins and in turn generate NMR signals. These pulses require large high-power RF-amplifiers and cause heat deposition in the tissue, which must be minimized for safety, presenting a growing problem when moving toward ever-higher field MRI. An alternative to RF-pulse excitation is self-excitation of nuclear spins using Radiofrequency Amplification by Stimulated Emission of Radiation (RASER), where the nuclear spins undergo spontaneous transition, without RF excitation, from an over-populated state to a ground state. Here, the feasibility of recording rapid proton RASER MRI images of pyrazine at low concentration (120 mM) with large matrix (128x128 pixels) in as little as 78 ms is demonstrated at 500 MHz (11.7 T). We also recorded a time-series of images using a single bolus hyperpolarized pyrazine highlighting the feasibility of dynamic tracking. Here, the demonstrated approach allows recording MRI scans without transmit-receive electronics of the MRI scanner, which is highly desirable for portable MRI as well as the emerging field of hyperpolarized MRI using, e.g., HP protons, 129 Xe gas or HP 13 C labeled biomolecules as molecular tracers and imaging agents.

MRI↗
DOE OSTI2020

Effect of Electrochemical Oxidation on Physicochemical Properties of Fe-Containing Single-Walled Carbon Nanotubes

Metal catalysts are necessary for fabricating carbon nanotubes, but are often considered impurities in the end products, and arduous steps are used to remove catalyst residues from the nanotube structure. However, as metals can be electrocatalytic, instead of removing them we can utilize their role in detection of analgesics. Herein, we study the physicochemical properties of Fe-containing single-walled carbon nanotubes (SWCNTs), and the effect of simple oxidative pretreatment on them. We show that a gentle anodic pretreatment i) increased the amount of oxidized Fe nanoparticles, most likely exhibiting phases Fe3O4 and Fe2O3 and ii) effectively removed disordered carbonaceous material from SWCNT bundles surfaces. Pretreatment had only a marginal effect on sensitivity towards analgesics. However, interestingly, selectivity of Fe-SWCNTs towards paracetamol and morphine could be modified with pretreatment. Through this kind of in-depth investigation, we can, to a certain extent, correlate various material properties of SWCNTs with the observed electrochemical performance. We show this approach allows us to evaluate what factors in SWCNTs truly affect the electrochemical detection of biomolecules.

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

Aromatic Amide Foldamers Show Conformation‐Dependent Electronic Properties

Electron transport in organic molecules and biomolecules is governed by electronic structure and molecular conformations. Despite recent progress, key challenges remain in understanding the role of intramolecular interactions and three-dimensional (3D) conformations on the electron transport behavior of organic molecules. In this work, the electronic properties of aromatic amide foldamers are characterized that organize into distinct 3D structures, including an extended secondary amide that adopts a trans-conformation and a folded N-methylated tertiary amide that adopts a cis-conformation. Results from single-molecule electronic experiments show that the extended secondary amide exhibits a fourfold enhancement in molecular conductance compared to the folded N-methylated tertiary amide, despite a longer contour length. The results show that extended amide molecules are governed by a through-bond electron transport mechanism, whereas folded amide molecules are dominated by through-space transport. Bulk spectroscopic characterization and density functional theory calculations further reveal that extended amides have a smaller HOMO–LUMO gap and larger transmission values compared to folded amides, consistent with single-molecule electronic experiments. Overall, this work shows that 3D molecular conformations significantly influence the electronic properties of single-molecule junctions.

electron transport↗
DOE OSTI2024

A fast and sensitive size-exclusion chromatography method for plasma extracellular vesicle proteomic analysis

Extracellular vesicles (EVs) carry diverse biomolecules derived from their parental cells, making their components excellent biomarker candidates. However, purifying EVs is a major hurdle in biomarker discovery since current methods require large amounts of samples, are time-consuming and typically have poor reproducibility. Here we describe a simple, fast, and sensitive EV fractionation method using size exclusion chromatography (SEC) on a fast protein liquid chromatography (FPLC) system. Our method uses a Superose 6 Increase 5/150, which has a bed volume of 2.9 mL. The FPLC system and small column size enable reproducible separation of only 50 µL of human plasma in 15 min. To demonstrate the utility of our method, we used longitudinal samples from a group of individuals who underwent intense exercise. A total of 838 proteins were identified, of which, 261 were previously characterized as EV proteins, including classical markers, such as cluster of differentiation (CD)9 and CD81. Quantitative analysis showed low technical variability with correlation coefficients greater than 0.9 between replicates. The analysis captured differences in relevant EV proteins involved in response to physical activity. Our method enables fast and sensitive fractionation of plasma EVs with low variability, which will facilitate biomarker studies in large clinical cohorts.

59 BASIC BIOLOGICAL SCIENCES↗